From 3403df62fa8397fcbdd3aae05e8b3175e899f2bc Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:11:44 +0200 Subject: [PATCH 01/25] Implemented the Phylo library --- .directory | 4 + Align2/APPS/Depend | 168 + Align2/Sources/Depend | 5597 ++++++++++++++++++++ Biopool/APPS/Depend | 1008 ++++ Biopool/Sources/Depend | 3622 +++++++++++++ Energy/APPS/Depend | 2197 ++++++++ Energy/Sources/Depend | 700 +++ Energy/Sources/TorsionPotential/Depend | 1562 ++++++ Lobo/APPS/Depend | 1273 +++++ Lobo/Sources/Depend | 1058 ++++ Makefile | 3 +- Makefile.global | 8 +- Phylo/APPS/Makefile | 57 + Phylo/APPS/clustalw.cc | 197 + Phylo/APPS/fengdoolittle.cc | 109 + Phylo/APPS/phyltree.cc | 172 + Phylo/Sources/AminoAcid.cc | 157 + Phylo/Sources/AminoAcid.h | 143 + Phylo/Sources/ClustalW.cc | 565 ++ Phylo/Sources/ClustalW.h | 245 + Phylo/Sources/ClusteringAlgorithm.h | 60 + Phylo/Sources/DistanceMatrix.cc | 225 + Phylo/Sources/DistanceMatrix.h | 220 + Phylo/Sources/DistanceMatrixBuilder.cc | 59 + Phylo/Sources/DistanceMatrixBuilder.h | 69 + Phylo/Sources/FengDoolittle.cc | 195 + Phylo/Sources/FengDoolittle.h | 105 + Phylo/Sources/FengDoolittleDistance.cc | 74 + Phylo/Sources/FengDoolittleDistance.h | 85 + Phylo/Sources/FitchMargoliash.cc | 224 + Phylo/Sources/FitchMargoliash.h | 58 + Phylo/Sources/IdentityPercentage.cc | 64 + Phylo/Sources/IdentityPercentage.h | 87 + Phylo/Sources/LevenshteinDistance.cc | 62 + Phylo/Sources/LevenshteinDistance.h | 53 + Phylo/Sources/Makefile | 68 + Phylo/Sources/MultipleAlignment.cc | 358 ++ Phylo/Sources/MultipleAlignment.h | 225 + Phylo/Sources/MultipleAlignmentAlgorithm.h | 61 + Phylo/Sources/NJ.cc | 115 + Phylo/Sources/NJ.h | 59 + Phylo/Sources/NewickParser.cc | 261 + Phylo/Sources/NewickParser.h | 145 + Phylo/Sources/PhylogeneticAlgorithm.h | 37 + Phylo/Sources/PhylogeneticTree.cc | 51 + Phylo/Sources/PhylogeneticTree.h | 104 + Phylo/Sources/RootedTree.cc | 485 ++ Phylo/Sources/RootedTree.h | 353 ++ Phylo/Sources/Sequence.cc | 112 + Phylo/Sources/Sequence.h | 116 + Phylo/Sources/SubstitutionMatrix.cc | 405 ++ Phylo/Sources/SubstitutionMatrix.h | 274 + Phylo/Sources/UPGMA.cc | 111 + Phylo/Sources/UPGMA.h | 60 + Phylo/Sources/UnrootedTree.cc | 608 +++ Phylo/Sources/UnrootedTree.h | 473 ++ Phylo/Sources/Visitor.h | 63 + Phylo/Sources/phylo.h | 58 + Phylo/Sources/precalculated_matrices.h | 864 +++ Phylo/Tests/Makefile | 59 + Phylo/Tests/TestClustering.h | 142 + Phylo/Tests/TestDistanceMatrix.h | 122 + Phylo/Tests/TestMSA.h | 117 + Phylo/Tests/TestPhylo.cc | 43 + Phylo/Tests/TestPhylo.o | Bin 0 -> 157008 bytes Phylo/Tests/TestTree.h | 109 + 66 files changed, 26538 insertions(+), 5 deletions(-) create mode 100644 .directory create mode 100644 Align2/APPS/Depend create mode 100644 Biopool/APPS/Depend create mode 100644 Phylo/APPS/Makefile create mode 100644 Phylo/APPS/clustalw.cc create mode 100644 Phylo/APPS/fengdoolittle.cc create mode 100644 Phylo/APPS/phyltree.cc create mode 100644 Phylo/Sources/AminoAcid.cc create mode 100644 Phylo/Sources/AminoAcid.h create mode 100644 Phylo/Sources/ClustalW.cc create mode 100644 Phylo/Sources/ClustalW.h create mode 100644 Phylo/Sources/ClusteringAlgorithm.h create mode 100644 Phylo/Sources/DistanceMatrix.cc create mode 100644 Phylo/Sources/DistanceMatrix.h create mode 100644 Phylo/Sources/DistanceMatrixBuilder.cc create mode 100644 Phylo/Sources/DistanceMatrixBuilder.h create mode 100644 Phylo/Sources/FengDoolittle.cc create mode 100644 Phylo/Sources/FengDoolittle.h create mode 100644 Phylo/Sources/FengDoolittleDistance.cc create mode 100644 Phylo/Sources/FengDoolittleDistance.h create mode 100644 Phylo/Sources/FitchMargoliash.cc create mode 100644 Phylo/Sources/FitchMargoliash.h create mode 100644 Phylo/Sources/IdentityPercentage.cc create mode 100644 Phylo/Sources/IdentityPercentage.h create mode 100644 Phylo/Sources/LevenshteinDistance.cc create mode 100644 Phylo/Sources/LevenshteinDistance.h create mode 100644 Phylo/Sources/Makefile create mode 100644 Phylo/Sources/MultipleAlignment.cc create mode 100644 Phylo/Sources/MultipleAlignment.h create mode 100644 Phylo/Sources/MultipleAlignmentAlgorithm.h create mode 100644 Phylo/Sources/NJ.cc create mode 100644 Phylo/Sources/NJ.h create mode 100644 Phylo/Sources/NewickParser.cc create mode 100644 Phylo/Sources/NewickParser.h create mode 100644 Phylo/Sources/PhylogeneticAlgorithm.h create mode 100644 Phylo/Sources/PhylogeneticTree.cc create mode 100644 Phylo/Sources/PhylogeneticTree.h create mode 100644 Phylo/Sources/RootedTree.cc create mode 100644 Phylo/Sources/RootedTree.h create mode 100644 Phylo/Sources/Sequence.cc create mode 100644 Phylo/Sources/Sequence.h create mode 100644 Phylo/Sources/SubstitutionMatrix.cc create mode 100644 Phylo/Sources/SubstitutionMatrix.h create mode 100644 Phylo/Sources/UPGMA.cc create mode 100644 Phylo/Sources/UPGMA.h create mode 100644 Phylo/Sources/UnrootedTree.cc create mode 100644 Phylo/Sources/UnrootedTree.h create mode 100644 Phylo/Sources/Visitor.h create mode 100644 Phylo/Sources/phylo.h create mode 100644 Phylo/Sources/precalculated_matrices.h create mode 100644 Phylo/Tests/Makefile create mode 100644 Phylo/Tests/TestClustering.h create mode 100644 Phylo/Tests/TestDistanceMatrix.h create mode 100644 Phylo/Tests/TestMSA.h create mode 100644 Phylo/Tests/TestPhylo.cc create mode 100644 Phylo/Tests/TestPhylo.o create mode 100644 Phylo/Tests/TestTree.h diff --git a/.directory b/.directory new file mode 100644 index 0000000..875ce20 --- /dev/null +++ b/.directory @@ -0,0 +1,4 @@ +[Dolphin] +Timestamp=2015,7,11,17,31,9 +Version=3 +VisibleRoles=Icons_text diff --git a/Align2/APPS/Depend b/Align2/APPS/Depend new file mode 100644 index 0000000..839cee9 --- /dev/null +++ b/Align2/APPS/Depend @@ -0,0 +1,168 @@ +subali.o: subali.cc /usr/include/stdc-predef.h \ + ../../Align2/Sources/ScoringS2S.h ../../Align2/Sources/ScoringScheme.h \ + ../../Align2/Sources/AlignmentData.h ../../Align2/Sources/Alignment.h \ + ../../Align2/Sources/AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + 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/usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Align2/Sources/Structure.h \ + ../../Align2/Sources/SubMatrix.h ../../Align2/Sources/Substitution.h \ + ../../Align2/Sources/ScoringP2S.h ../../Align2/Sources/Profile.h \ + ../../Biopool/Sources/AminoAcidCode.h ../../Align2/Sources/ScoringP2P.h \ + ../../Align2/Sources/ScoringFunction.h \ + ../../Align2/Sources/HenikoffProfile.h \ + ../../Align2/Sources/PSICProfile.h \ + ../../Align2/Sources/SeqDivergenceProfile.h \ + ../../Align2/Sources/AGPFunction.h ../../Align2/Sources/GapFunction.h \ + ../../Align2/Sources/NWAlign.h ../../Align2/Sources/Align.h \ + ../../Align2/Sources/Traceback.h ../../Align2/Sources/SequenceData.h \ + ../../Align2/Sources/CrossProduct.h ../../Align2/Sources/LogAverage.h \ + ../../Align2/Sources/DotPFreq.h ../../Align2/Sources/DotPOdds.h \ + ../../Align2/Sources/EDistance.h ../../Align2/Sources/Pearson.h \ + ../../Align2/Sources/JensenShannon.h \ + ../../Align2/Sources/AtchleyDistance.h \ + ../../Align2/Sources/AtchleyCorrelation.h ../../Align2/Sources/SWAlign.h \ + ../../Align2/Sources/FSAlign.h ../../Align2/Sources/VGPFunction.h \ + ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + ../../Biopool/Sources/Identity.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Bond.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/SolvExpos.h ../../Align2/Sources/VGPFunction2.h \ + ../../Align2/Sources/Sec.h ../../Align2/Sources/Ss2.h \ + ../../Align2/Sources/Ss2Input.h ../../Align2/Sources/Prof.h \ + ../../Align2/Sources/ProfInput.h ../../Align2/Sources/stringtools.h \ + ../../Align2/Sources/SecSequenceData.h ../../tools/GetArg.h \ + /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/ctime diff --git a/Align2/Sources/Depend b/Align2/Sources/Depend index e69de29..265882f 100644 --- a/Align2/Sources/Depend +++ b/Align2/Sources/Depend @@ -0,0 +1,5597 @@ +Alignment.o: Alignment.cc /usr/include/stdc-predef.h Alignment.h \ + AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + 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/usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \ + Structure.h SubMatrix.h Substitution.h Traceback.h +NWAlign.o: NWAlign.cc /usr/include/stdc-predef.h NWAlign.h Align.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + 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/usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + 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/usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \ + Structure.h SubMatrix.h Substitution.h Traceback.h +SWAlign.o: SWAlign.cc /usr/include/stdc-predef.h SWAlign.h Align.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + 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/usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \ + Structure.h SubMatrix.h Substitution.h Traceback.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h +FSAlign.o: FSAlign.cc /usr/include/stdc-predef.h FSAlign.h Align.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \ + Structure.h SubMatrix.h Substitution.h Traceback.h +NWAlignNoTermGaps.o: NWAlignNoTermGaps.cc /usr/include/stdc-predef.h \ + NWAlignNoTermGaps.h Align.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \ + Structure.h SubMatrix.h Substitution.h Traceback.h +AlignmentData.o: AlignmentData.cc /usr/include/stdc-predef.h \ + AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h +SequenceData.o: SequenceData.cc /usr/include/stdc-predef.h SequenceData.h \ + AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h +SecSequenceData.o: SecSequenceData.cc /usr/include/stdc-predef.h \ + SecSequenceData.h AlignmentData.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h +VGPFunction.o: VGPFunction.cc /usr/include/stdc-predef.h VGPFunction.h \ + GapFunction.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/SolvExpos.h +VGPFunction2.o: VGPFunction2.cc /usr/include/stdc-predef.h VGPFunction2.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc GapFunction.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h +Substitution.o: Substitution.cc /usr/include/stdc-predef.h Substitution.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + 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/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc +SubMatrix.o: SubMatrix.cc /usr/include/stdc-predef.h SubMatrix.h \ + Substitution.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc +StructuralAlignment.o: StructuralAlignment.cc /usr/include/stdc-predef.h \ + StructuralAlignment.h /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc AlignmentBase.h \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h +ScoringScheme.o: ScoringScheme.cc /usr/include/stdc-predef.h \ + ScoringScheme.h AlignmentData.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \ + Substitution.h +ScoringS2S.o: ScoringS2S.cc /usr/include/stdc-predef.h ScoringS2S.h \ + ScoringScheme.h AlignmentData.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \ + Substitution.h +ScoringP2S.o: ScoringP2S.cc /usr/include/stdc-predef.h ScoringP2S.h \ + Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringScheme.h AlignmentData.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \ + Substitution.h +ScoringP2P.o: ScoringP2P.cc /usr/include/stdc-predef.h ScoringP2P.h \ + Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h ScoringScheme.h \ + AlignmentData.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Structure.h SubMatrix.h \ + Substitution.h +PssmInput.o: PssmInput.cc /usr/include/stdc-predef.h PssmInput.h \ + Substitution.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc +Profile.o: Profile.cc /usr/include/stdc-predef.h Profile.h Alignment.h \ + AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + 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/usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath +SeqDivergenceProfile.o: SeqDivergenceProfile.cc \ + /usr/include/stdc-predef.h SeqDivergenceProfile.h AGPFunction.h \ + GapFunction.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc NWAlign.h Align.h Alignment.h \ + AlignmentBase.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ScoringScheme.h Structure.h \ + SubMatrix.h Substitution.h Traceback.h Profile.h \ + ../../Biopool/Sources/AminoAcidCode.h ScoringS2S.h SequenceData.h +LogAverage.o: LogAverage.cc /usr/include/stdc-predef.h LogAverage.h \ + Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h SubMatrix.h Substitution.h +CrossProduct.o: CrossProduct.cc /usr/include/stdc-predef.h CrossProduct.h \ + Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h SubMatrix.h Substitution.h +DotPFreq.o: DotPFreq.cc /usr/include/stdc-predef.h DotPFreq.h Profile.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +DotPOdds.o: DotPOdds.cc /usr/include/stdc-predef.h DotPOdds.h Profile.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +Pearson.o: Pearson.cc /usr/include/stdc-predef.h Pearson.h Profile.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +JensenShannon.o: JensenShannon.cc /usr/include/stdc-predef.h \ + JensenShannon.h Profile.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + 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../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +EDistance.o: EDistance.cc /usr/include/stdc-predef.h EDistance.h \ + Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + 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\ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +AtchleyDistance.o: AtchleyDistance.cc /usr/include/stdc-predef.h \ + AtchleyDistance.h Profile.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +AtchleyCorrelation.o: AtchleyCorrelation.cc /usr/include/stdc-predef.h \ + AtchleyCorrelation.h Profile.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath ScoringFunction.h +Panchenko.o: Panchenko.cc /usr/include/stdc-predef.h Panchenko.h \ + Profile.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath PssmInput.h Substitution.h ScoringFunction.h +Zhou.o: Zhou.cc /usr/include/stdc-predef.h Zhou.h Profile.h Alignment.h \ + AlignmentBase.h ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc \ + ../../Biopool/Sources/AminoAcidCode.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath PssmInput.h Substitution.h ScoringFunction.h +ThreadingInput.o: ThreadingInput.cc /usr/include/stdc-predef.h \ + ThreadingInput.h Substitution.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc +Ss2Input.o: Ss2Input.cc /usr/include/stdc-predef.h Ss2Input.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iostream \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ios_base.h \ + 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/usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath Substitution.h +ProfInput.o: ProfInput.cc /usr/include/stdc-predef.h ProfInput.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iostream \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + 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/usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath stringtools.h Substitution.h +Sec.o: Sec.cc /usr/include/stdc-predef.h Sec.h AlignmentData.h \ + Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + 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/usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility 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/usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath stringtools.h Substitution.h Structure.h \ + SubMatrix.h +ThreadingSs2.o: ThreadingSs2.cc /usr/include/stdc-predef.h ThreadingSs2.h \ + AlignmentData.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + 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/usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Ss2Input.h Substitution.h \ + Structure.h SubMatrix.h ThreadingInput.h +ThreadingProf.o: ThreadingProf.cc /usr/include/stdc-predef.h \ + ThreadingProf.h AlignmentData.h Alignment.h AlignmentBase.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ProfInput.h stringtools.h \ + Substitution.h Structure.h SubMatrix.h ThreadingInput.h +ReverseScore.o: ReverseScore.cc /usr/include/stdc-predef.h ReverseScore.h \ + Align.h Alignment.h AlignmentBase.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc AlignmentData.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h GapFunction.h ScoringScheme.h \ + Structure.h SubMatrix.h Substitution.h Traceback.h \ + ../../tools/StatTools.h +stringtools.o: stringtools.cc /usr/include/stdc-predef.h stringtools.h \ + /usr/include/c++/4.9/iostream \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h diff --git a/Biopool/APPS/Depend b/Biopool/APPS/Depend new file mode 100644 index 0000000..1af4e12 --- /dev/null +++ b/Biopool/APPS/Depend @@ -0,0 +1,1008 @@ +PdbCorrector.o: PdbCorrector.cc /usr/include/stdc-predef.h \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h ../../Biopool/Sources/XyzSaver.h \ + ../../Biopool/Sources/SeqSaver.h ../../Biopool/Sources/IntSaver.h +PdbSecondary.o: PdbSecondary.cc /usr/include/stdc-predef.h \ + ../../Biopool/Sources/Protein.h ../../Biopool/Sources/Component.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../Biopool/Sources/Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/PdbSaver.h ../../Biopool/Sources/XyzSaver.h \ + ../../Biopool/Sources/SeqSaver.h ../../Biopool/Sources/IntSaver.h \ + ../../tools/GetArg.h /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \ + ../../tools/String2Number.h +PdbEditor.o: PdbEditor.cc /usr/include/stdc-predef.h \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h +Pdb2Seq.o: Pdb2Seq.cc /usr/include/stdc-predef.h \ + ../../Biopool/Sources/Protein.h ../../Biopool/Sources/Component.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../Biopool/Sources/Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/SeqSaver.h ../../tools/GetArg.h \ + /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \ + ../../tools/String2Number.h +pdb2secondary.o: pdb2secondary.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + ../../tools/matrix3.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h +pdbshifter.o: pdbshifter.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h +pdbMover.o: pdbMover.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h diff --git a/Biopool/Sources/Depend b/Biopool/Sources/Depend index e69de29..f221352 100644 --- a/Biopool/Sources/Depend +++ b/Biopool/Sources/Depend @@ -0,0 +1,3622 @@ +Identity.o: Identity.cc /usr/include/stdc-predef.h Identity.h \ + /usr/include/c++/4.9/iostream \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc +SimpleBond.o: SimpleBond.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h SimpleBond.h \ + /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc +Bond.o: Bond.cc /usr/include/stdc-predef.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h Bond.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h +Component.o: Component.cc /usr/include/stdc-predef.h Component.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h SimpleBond.h Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Loader.h Saver.h Visitor.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +Monomer.o: Monomer.cc /usr/include/stdc-predef.h Monomer.h Component.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h SimpleBond.h Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Loader.h Saver.h Visitor.h +Polymer.o: Polymer.cc /usr/include/stdc-predef.h Polymer.h Component.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h SimpleBond.h Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Loader.h Saver.h Visitor.h AminoAcid.h Group.h Monomer.h SideChain.h \ + AminoAcidCode.h IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath +Atom.o: Atom.cc /usr/include/stdc-predef.h Atom.h AtomCode.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc Identity.h Group.h Monomer.h \ + Component.h Bond.h Loader.h Saver.h Visitor.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath +Group.o: Group.cc /usr/include/stdc-predef.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +SideChain.o: SideChain.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc SideChain.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h +AminoAcid.o: AminoAcid.cc /usr/include/stdc-predef.h AminoAcid.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + 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/usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \ + IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +Spacer.o: Spacer.cc /usr/include/stdc-predef.h Spacer.h Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + 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/usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \ + Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h 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\ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h 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/usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + 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/usr/include/c++/4.9/bits/stl_multiset.h +IntLoader.o: IntLoader.cc /usr/include/stdc-predef.h IntLoader.h Spacer.h \ + Bond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + 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/usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \ + Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h LigandSet.h Ligand.h \ + NucleotideCode.h +SeqSaver.o: SeqSaver.cc /usr/include/stdc-predef.h SeqSaver.h SideChain.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h Ligand.h NucleotideCode.h +PdbLoader.o: PdbLoader.cc /usr/include/stdc-predef.h PdbLoader.h \ + /usr/include/string.h /usr/include/features.h \ + /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h Loader.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc AminoAcid.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Saver.h Visitor.h SideChain.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath Spacer.h Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h LigandSet.h Ligand.h \ + NucleotideCode.h Protein.h Nucleotide.h AminoAcidHydrogen.h \ + /usr/include/c++/4.9/list /usr/include/c++/4.9/bits/stl_list.h \ + /usr/include/c++/4.9/bits/list.tcc +PdbSaver.o: PdbSaver.cc /usr/include/stdc-predef.h PdbSaver.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \ + IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h LigandSet.h Ligand.h \ + NucleotideCode.h Protein.h +SeqLoader.o: SeqLoader.cc /usr/include/stdc-predef.h SeqLoader.h \ + SideChain.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h RelLoader.h Spacer.h Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h +IntCoordConverter.o: IntCoordConverter.cc /usr/include/stdc-predef.h \ + IntCoordConverter.h /usr/include/c++/4.9/iostream \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc Atom.h AtomCode.h \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc Identity.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath AminoAcid.h \ + Group.h Monomer.h Component.h Bond.h Loader.h Saver.h Visitor.h \ + SideChain.h AminoAcidCode.h +SeqConstructor.o: SeqConstructor.cc /usr/include/stdc-predef.h \ + SeqConstructor.h Spacer.h Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \ + Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h RelLoader.h +Ligand.o: Ligand.cc /usr/include/stdc-predef.h Ligand.h Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Polymer.h Component.h Loader.h Saver.h Visitor.h Group.h Monomer.h \ + AminoAcidCode.h NucleotideCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +LigandSet.o: LigandSet.cc /usr/include/stdc-predef.h LigandSet.h Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Polymer.h Component.h Loader.h Saver.h Visitor.h Ligand.h Group.h \ + Monomer.h AminoAcidCode.h NucleotideCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +SolvExpos.o: SolvExpos.cc /usr/include/stdc-predef.h SolvExpos.h Spacer.h \ + Bond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc Identity.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc Atom.h AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + Polymer.h Component.h Loader.h Saver.h Visitor.h AminoAcid.h Group.h \ + Monomer.h SideChain.h AminoAcidCode.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h +AminoAcidHydrogen.o: AminoAcidHydrogen.cc /usr/include/stdc-predef.h \ + AminoAcidHydrogen.h AminoAcid.h Group.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \ + IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/list \ + /usr/include/c++/4.9/bits/stl_list.h /usr/include/c++/4.9/bits/list.tcc +Nucleotide.o: Nucleotide.cc /usr/include/stdc-predef.h Nucleotide.h \ + Group.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h IntCoordConverter.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath NucleotideCode.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +RelLoader.o: RelLoader.cc /usr/include/stdc-predef.h RelLoader.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \ + IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h +XyzSaver.o: XyzSaver.cc /usr/include/stdc-predef.h XyzSaver.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \ + IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h Ligand.h NucleotideCode.h +RelSaver.o: RelSaver.cc /usr/include/stdc-predef.h RelSaver.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Group.h Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h SideChain.h AminoAcidCode.h \ + IntCoordConverter.h ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath AminoAcid.h Spacer.h Polymer.h \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h +XyzLoader.o: XyzLoader.cc /usr/include/stdc-predef.h XyzLoader.h Group.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Atom.h AtomCode.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + SimpleBond.h /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h Identity.h Monomer.h Component.h \ + Bond.h Loader.h Saver.h Visitor.h Ligand.h Polymer.h AminoAcidCode.h \ + NucleotideCode.h SideChain.h IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath AminoAcid.h \ + Spacer.h /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h diff --git a/Energy/APPS/Depend b/Energy/APPS/Depend index e69de29..de1fa8e 100644 --- a/Energy/APPS/Depend +++ b/Energy/APPS/Depend @@ -0,0 +1,2197 @@ +frst.o: frst.cc /usr/include/stdc-predef.h /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h \ + ../../Energy/Sources/EffectiveSolvationPotential.h \ + ../../Energy/Sources/RapdfPotential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h +correlation.o: correlation.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h ../../tools/matrix3.h ../../tools/StatTools.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h +energy2zscore.o: energy2zscore.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../tools/StatTools.h +frstZscore.o: frstZscore.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h \ + ../../Energy/Sources/EffectiveSolvationPotential.h \ + ../../Energy/Sources/RapdfPotential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h \ + /usr/include/c++/4.9/numeric /usr/include/c++/4.9/bits/stl_numeric.h +mutationGenerator.o: mutationGenerator.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + ../../tools/matrix3.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h +pdb2tor.o: pdb2tor.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h +tap2plot.o: tap2plot.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h \ + ../../Energy/Sources/EffectiveSolvationPotential.h \ + ../../Energy/Sources/RapdfPotential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h +pdb2solv.o: pdb2solv.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h \ + ../../Energy/Sources/PolarSolvationPotential.h +solv2energy.o: solv2energy.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h +pdb2contact.o: pdb2contact.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h +tapRef.o: tapRef.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiOmega.h \ + ../Sources/TorsionPotential/PhiPsiPreAngle.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h +pdb2energy.o: pdb2energy.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h \ + ../../Energy/Sources/PolarSolvationPotential.h \ + ../../Energy/Sources/RapdfPotential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h \ + ../../tools/StatTools.h +taptable.o: taptable.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../tools/StatTools.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../Sources/TorsionPotential/PhiPsi.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/SimpleBond.h \ + ../../Biopool/Sources/Identity.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../../Energy/Sources/Potential.h +pdb2tap.o: pdb2tap.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h ../../Energy/Sources/Potential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiOmega.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h \ + ../../tools/StatTools.h +pdb2torenergy.o: pdb2torenergy.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/PdbLoader.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Polymer.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h ../../Energy/Sources/Potential.h \ + ../Sources/TorsionPotential/TorsionPotential.h \ + ../Sources/TorsionPotential/PhiPsi.h \ + ../Sources/TorsionPotential/PhiPsiPreAngle.h \ + ../Sources/TorsionPotential/PhiPsiOmega.h \ + ../Sources/TorsionPotential/PhiPsiOmegaPreAngle.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1PreAngle.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h \ + ../Sources/TorsionPotential/PhiPsiOmegaChi1Chi2PreAngle.h \ + ../Sources/TorsionPotential/Omega.h \ + ../Sources/TorsionPotential/Chi1Chi2.h diff --git a/Energy/Sources/Depend b/Energy/Sources/Depend index e69de29..8445bc3 100644 --- a/Energy/Sources/Depend +++ b/Energy/Sources/Depend @@ -0,0 +1,700 @@ +PolarSolvationPotential.o: PolarSolvationPotential.cc \ + /usr/include/stdc-predef.h PolarSolvationPotential.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h Potential.h +SolvationPotential.o: SolvationPotential.cc /usr/include/stdc-predef.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h SolvationPotential.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h Potential.h +RapdfPotential.o: RapdfPotential.cc /usr/include/stdc-predef.h \ + RapdfPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc Potential.h \ + ../../Biopool/Sources/Spacer.h ../../Biopool/Sources/Bond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h /usr/include/c++/4.9/cstring \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h +EnergyFeatures.o: EnergyFeatures.cc /usr/include/stdc-predef.h \ + EnergyFeatures.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h RapdfPotential.h Potential.h \ + SolvationPotential.h TorsionPotential/PhiPsi.h \ + TorsionPotential/TorsionPotential.h \ + TorsionPotential/PhiPsiOmegaChi1Chi2.h +EffectiveSolvationPotential.o: EffectiveSolvationPotential.cc \ + /usr/include/stdc-predef.h EffectiveSolvationPotential.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h Potential.h diff --git a/Energy/Sources/TorsionPotential/Depend b/Energy/Sources/TorsionPotential/Depend index e69de29..c29ca23 100644 --- a/Energy/Sources/TorsionPotential/Depend +++ b/Energy/Sources/TorsionPotential/Depend @@ -0,0 +1,1562 @@ +PhiPsi.o: PhiPsi.cc /usr/include/stdc-predef.h PhiPsi.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h TorsionPotential.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmegaChi1.o: PhiPsiOmegaChi1.cc /usr/include/stdc-predef.h \ + PhiPsiOmegaChi1.h TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmegaChi1Chi2PreAngle.o: PhiPsiOmegaChi1Chi2PreAngle.cc \ + /usr/include/stdc-predef.h PhiPsiOmegaChi1Chi2PreAngle.h \ + TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiPreAngle.o: PhiPsiPreAngle.cc /usr/include/stdc-predef.h \ + PhiPsiPreAngle.h TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmegaPreAngle.o: PhiPsiOmegaPreAngle.cc /usr/include/stdc-predef.h \ + PhiPsiOmegaPreAngle.h TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmegaChi1Chi2.o: PhiPsiOmegaChi1Chi2.cc /usr/include/stdc-predef.h \ + PhiPsiOmegaChi1Chi2.h TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmega.o: PhiPsiOmega.cc /usr/include/stdc-predef.h PhiPsiOmega.h \ + TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/float.h +Chi1Chi2.o: Chi1Chi2.cc /usr/include/stdc-predef.h Chi1Chi2.h \ + TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmegaPreAngle.o: PhiPsiOmegaPreAngle.cc /usr/include/stdc-predef.h \ + PhiPsiOmegaPreAngle.h TorsionPotential.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +PhiPsiOmegaChi1PreAngle.o: PhiPsiOmegaChi1PreAngle.cc \ + /usr/include/stdc-predef.h PhiPsiOmegaChi1PreAngle.h TorsionPotential.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h +Omega.o: Omega.cc /usr/include/stdc-predef.h Omega.h TorsionPotential.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../../Biopool/Sources/Spacer.h \ + ../../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../../Biopool/Sources/Atom.h \ + ../../../Biopool/Sources/AtomCode.h ../../../tools/vector3.h \ + ../../../tools/vglStd.h ../../../tools/vglEndian.h \ + ../../../tools/vglCompilers.h ../../../tools/vglMath.h \ + ../../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h \ + ../../../tools/matrix3.h ../../../Biopool/Sources/Polymer.h \ + ../../../Biopool/Sources/Component.h ../../../Biopool/Sources/Loader.h \ + ../../../Biopool/Sources/Saver.h ../../../Biopool/Sources/Visitor.h \ + ../../../Biopool/Sources/AminoAcid.h ../../../Biopool/Sources/Group.h \ + ../../../Biopool/Sources/Monomer.h ../../../Biopool/Sources/SideChain.h \ + ../../../Biopool/Sources/AminoAcidCode.h \ + ../../../Biopool/Sources/IntCoordConverter.h ../../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../../Energy/Sources/Potential.h diff --git a/Lobo/APPS/Depend b/Lobo/APPS/Depend index e69de29..fcbab73 100644 --- a/Lobo/APPS/Depend +++ b/Lobo/APPS/Depend @@ -0,0 +1,1273 @@ +loboLUT.o: loboLUT.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Lobo/Sources/LoopTable.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + ../../tools/matrix3.h ../../Lobo/Sources/RamachandranData.h \ + ../../Lobo/Sources/LoopTableEntry.h \ + ../../Lobo/Sources/VectorTransformation.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \ + /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h +LoopTablePlot.o: LoopTablePlot.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc \ + ../../Lobo/Sources/RamachandranData.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Lobo/Sources/LoopTableEntry.h \ + ../../Lobo/Sources/VectorTransformation.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/queue \ + /usr/include/c++/4.9/deque /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h ../../tools/GetArg.h \ + /usr/include/c++/4.9/cstdarg ../../tools/FileName.h \ + ../../tools/String2Number.h +ClusterLoopTable.o: ClusterLoopTable.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Lobo/Sources/LoopTable.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + ../../tools/matrix3.h ../../Lobo/Sources/RamachandranData.h \ + ../../Lobo/Sources/LoopTableEntry.h \ + ../../Lobo/Sources/VectorTransformation.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \ + /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h +ClusterRama.o: ClusterRama.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Lobo/Sources/RamachandranData.h +lobo.o: lobo.cc /usr/include/stdc-predef.h /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Lobo/Sources/LoopModel.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Lobo/Sources/RamachandranData.h \ + ../../Lobo/Sources/LoopTableEntry.h \ + ../../Lobo/Sources/VectorTransformation.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \ + /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/SeqConstructor.h \ + ../../Lobo/Sources/ranking_helper.h ../../Lobo/Sources/ranking_helper2.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \ + ../../Energy/Sources/TorsionPotential/PhiPsi.h \ + ../../Energy/Sources/TorsionPotential/TorsionPotential.h \ + ../../Biopool/Sources/PdbLoader.h ../../Biopool/Sources/LigandSet.h \ + ../../Biopool/Sources/Ligand.h ../../Biopool/Sources/NucleotideCode.h \ + ../../Biopool/Sources/Protein.h ../../Biopool/Sources/PdbSaver.h \ + ../../Lobo/Sources/LoboTools.h +loop2torsion.o: loop2torsion.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Lobo/Sources/LoopModel.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Lobo/Sources/RamachandranData.h \ + ../../Lobo/Sources/LoopTableEntry.h \ + ../../Lobo/Sources/VectorTransformation.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \ + /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/SeqConstructor.h \ + ../../Lobo/Sources/ranking_helper.h ../../Lobo/Sources/ranking_helper2.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \ + ../../Energy/Sources/TorsionPotential/PhiPsi.h \ + ../../Energy/Sources/TorsionPotential/TorsionPotential.h \ + ../../Biopool/Sources/PdbLoader.h ../../Biopool/Sources/LigandSet.h \ + ../../Biopool/Sources/Ligand.h ../../Biopool/Sources/NucleotideCode.h \ + ../../Biopool/Sources/Protein.h ../../Biopool/Sources/PdbSaver.h \ + ../../Biopool/Sources/XyzSaver.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/limits.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include-fixed/syslimits.h \ + /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \ + /usr/include/x86_64-linux-gnu/bits/local_lim.h \ + /usr/include/linux/limits.h \ + /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \ + /usr/include/x86_64-linux-gnu/bits/xopen_lim.h +scatEdit.o: scatEdit.cc /usr/include/stdc-predef.h \ + ../../Lobo/Sources/RankAnalyzer.h /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h ../../tools/matrix3.h +backboneAnalyzer.o: backboneAnalyzer.cc /usr/include/stdc-predef.h \ + ../../tools/GetArg.h /usr/include/c++/4.9/iostream \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/iosfwd /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + ../../Biopool/Sources/SimpleBond.h ../../Biopool/Sources/Identity.h \ + ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + ../../tools/matrix3.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/PdbLoader.h /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Biopool/Sources/LigandSet.h ../../Biopool/Sources/Ligand.h \ + ../../Biopool/Sources/NucleotideCode.h ../../Biopool/Sources/Protein.h \ + ../../Biopool/Sources/PdbSaver.h ../../Biopool/Sources/IntSaver.h \ + ../../tools/StatTools.h +loboFull.o: loboFull.cc /usr/include/stdc-predef.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/GetArg.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/cstdarg \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/FileName.h \ + ../../tools/String2Number.h ../../Lobo/Sources/LoopModel.h \ + /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \ + ../../Lobo/Sources/LoopTable.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h ../../tools/matrix3.h \ + ../../Lobo/Sources/RamachandranData.h \ + ../../Lobo/Sources/LoopTableEntry.h \ + ../../Lobo/Sources/VectorTransformation.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + /usr/include/c++/4.9/queue /usr/include/c++/4.9/deque \ + /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/SeqConstructor.h \ + ../../Lobo/Sources/ranking_helper.h ../../Lobo/Sources/ranking_helper2.h \ + ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \ + ../../Energy/Sources/TorsionPotential/PhiPsi.h \ + ../../Energy/Sources/TorsionPotential/TorsionPotential.h \ + ../../Biopool/Sources/PdbLoader.h ../../Biopool/Sources/LigandSet.h \ + ../../Biopool/Sources/Ligand.h ../../Biopool/Sources/NucleotideCode.h \ + ../../Biopool/Sources/Protein.h ../../Biopool/Sources/PdbSaver.h \ + ../../tools/StatTools.h ../../Lobo/Sources/LoboTools.h diff --git a/Lobo/Sources/Depend b/Lobo/Sources/Depend index e69de29..ec7fdca 100644 --- a/Lobo/Sources/Depend +++ b/Lobo/Sources/Depend @@ -0,0 +1,1058 @@ +RamachandranData.o: RamachandranData.cc /usr/include/stdc-predef.h \ + RamachandranData.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/vector3.h ../../tools/vglStd.h \ + ../../tools/vglEndian.h ../../tools/vglCompilers.h ../../tools/vglMath.h \ + ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath +VectorTransformation.o: VectorTransformation.cc \ + /usr/include/stdc-predef.h VectorTransformation.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath +LoopTableEntry.o: LoopTableEntry.cc /usr/include/stdc-predef.h \ + LoopTableEntry.h VectorTransformation.h ../../tools/Debug.h \ + /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/algorithm /usr/include/c++/4.9/utility \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath +LoopTable.o: LoopTable.cc /usr/include/stdc-predef.h LoopTable.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/Debug.h /usr/include/stdlib.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc RamachandranData.h \ + /usr/include/c++/4.9/vector /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc LoopTableEntry.h \ + VectorTransformation.h ../../Biopool/Sources/IntCoordConverter.h \ + ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/queue \ + /usr/include/c++/4.9/deque /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h +LoopModel.o: LoopModel.cc /usr/include/stdc-predef.h LoopModel.h \ + ../../tools/Debug.h /usr/include/c++/4.9/exception \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/cctype \ + /usr/include/ctype.h /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/locale_classes.h /usr/include/c++/4.9/string \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/fstream \ + /usr/include/c++/4.9/bits/codecvt.h /usr/include/c++/4.9/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc /usr/include/string.h \ + /usr/include/x86_64-linux-gnu/bits/string3.h LoopTable.h \ + ../../tools/vector3.h ../../tools/vglStd.h ../../tools/vglEndian.h \ + ../../tools/vglCompilers.h ../../tools/vglMath.h ../../tools/std.h \ + /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + RamachandranData.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc LoopTableEntry.h \ + VectorTransformation.h ../../Biopool/Sources/IntCoordConverter.h \ + ../../Biopool/Sources/Atom.h ../../Biopool/Sources/AtomCode.h \ + ../../Biopool/Sources/SimpleBond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h ../../Biopool/Sources/Identity.h \ + ../../tools/IoTools.h /usr/include/c++/4.9/iomanip \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath /usr/include/c++/4.9/queue \ + /usr/include/c++/4.9/deque /usr/include/c++/4.9/bits/stl_deque.h \ + /usr/include/c++/4.9/bits/deque.tcc \ + /usr/include/c++/4.9/bits/stl_queue.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h ../../Biopool/Sources/Polymer.h \ + ../../Biopool/Sources/Component.h ../../Biopool/Sources/Loader.h \ + ../../Biopool/Sources/Saver.h ../../Biopool/Sources/Visitor.h \ + ../../Biopool/Sources/AminoAcid.h ../../Biopool/Sources/Group.h \ + ../../Biopool/Sources/Monomer.h ../../Biopool/Sources/SideChain.h \ + ../../Biopool/Sources/AminoAcidCode.h /usr/include/c++/4.9/map \ + /usr/include/c++/4.9/bits/stl_tree.h /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h \ + ../../Biopool/Sources/SeqConstructor.h ranking_helper.h \ + ranking_helper2.h ../../Energy/Sources/SolvationPotential.h \ + ../../Energy/Sources/Potential.h ../../Energy/Sources/RapdfPotential.h \ + ../../Energy/Sources/TorsionPotential/PhiPsi.h \ + ../../Energy/Sources/TorsionPotential/TorsionPotential.h +LoopExtractor.o: LoopExtractor.cc /usr/include/stdc-predef.h \ + LoopExtractor.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h ranking_helper.h \ + ranking_helper2.h +ranking_helper.o: ranking_helper.cc /usr/include/stdc-predef.h \ + ranking_helper.h +ranking_helper2.o: ranking_helper2.cc /usr/include/stdc-predef.h \ + ranking_helper2.h +globalStatistic.o: globalStatistic.cc /usr/include/stdc-predef.h \ + globalStatistic.h LoopExtractor.h ../../Biopool/Sources/Spacer.h \ + ../../Biopool/Sources/Bond.h /usr/include/c++/4.9/algorithm \ + /usr/include/c++/4.9/utility \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stl_relops.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/stl_algo.h /usr/include/c++/4.9/cstdlib \ + /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h /usr/include/xlocale.h \ + /usr/include/x86_64-linux-gnu/sys/types.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h \ + /usr/include/c++/4.9/bits/algorithmfwd.h \ + /usr/include/c++/4.9/bits/stl_heap.h \ + /usr/include/c++/4.9/bits/stl_tempbuf.h \ + /usr/include/c++/4.9/bits/stl_construct.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h \ + /usr/include/c++/4.9/bits/memoryfwd.h /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../Biopool/Sources/SimpleBond.h \ + /usr/include/c++/4.9/string /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc \ + ../../Biopool/Sources/Identity.h /usr/include/c++/4.9/iostream \ + /usr/include/c++/4.9/ostream /usr/include/c++/4.9/ios \ + /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc ../../tools/Debug.h \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../Biopool/Sources/Atom.h \ + ../../Biopool/Sources/AtomCode.h ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../Biopool/Sources/Polymer.h ../../Biopool/Sources/Component.h \ + ../../Biopool/Sources/Loader.h ../../Biopool/Sources/Saver.h \ + ../../Biopool/Sources/Visitor.h ../../Biopool/Sources/AminoAcid.h \ + ../../Biopool/Sources/Group.h ../../Biopool/Sources/Monomer.h \ + ../../Biopool/Sources/SideChain.h ../../Biopool/Sources/AminoAcidCode.h \ + ../../Biopool/Sources/IntCoordConverter.h ../../tools/IoTools.h \ + /usr/include/c++/4.9/iomanip ../../tools/String2Number.h \ + /usr/include/c++/4.9/sstream /usr/include/c++/4.9/bits/sstream.tcc \ + /usr/include/c++/4.9/limits /usr/include/c++/4.9/cmath \ + /usr/include/c++/4.9/map /usr/include/c++/4.9/bits/stl_tree.h \ + /usr/include/c++/4.9/bits/stl_map.h \ + /usr/include/c++/4.9/bits/stl_multimap.h /usr/include/c++/4.9/set \ + /usr/include/c++/4.9/bits/stl_set.h \ + /usr/include/c++/4.9/bits/stl_multiset.h ranking_helper.h \ + ranking_helper2.h ranking_helper2.h +RankAnalyzer.o: RankAnalyzer.cc /usr/include/stdc-predef.h RankAnalyzer.h \ + /usr/include/c++/4.9/string \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/os_defines.h \ + /usr/include/features.h /usr/include/x86_64-linux-gnu/sys/cdefs.h \ + /usr/include/x86_64-linux-gnu/bits/wordsize.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs.h \ + /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/cpu_defines.h \ + /usr/include/c++/4.9/bits/stringfwd.h \ + /usr/include/c++/4.9/bits/memoryfwd.h \ + /usr/include/c++/4.9/bits/char_traits.h \ + /usr/include/c++/4.9/bits/stl_algobase.h \ + /usr/include/c++/4.9/bits/functexcept.h \ + /usr/include/c++/4.9/bits/exception_defines.h \ + /usr/include/c++/4.9/bits/cpp_type_traits.h \ + /usr/include/c++/4.9/ext/type_traits.h \ + /usr/include/c++/4.9/ext/numeric_traits.h \ + /usr/include/c++/4.9/bits/stl_pair.h /usr/include/c++/4.9/bits/move.h \ + /usr/include/c++/4.9/bits/concept_check.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.9/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.9/debug/debug.h \ + /usr/include/c++/4.9/bits/stl_iterator.h \ + /usr/include/c++/4.9/bits/ptr_traits.h \ + /usr/include/c++/4.9/bits/predefined_ops.h \ + /usr/include/c++/4.9/bits/postypes.h /usr/include/c++/4.9/cwchar \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h \ + /usr/include/x86_64-linux-gnu/bits/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h \ + /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \ + /usr/include/c++/4.9/bits/allocator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++allocator.h \ + /usr/include/c++/4.9/ext/new_allocator.h /usr/include/c++/4.9/new \ + /usr/include/c++/4.9/exception \ + /usr/include/c++/4.9/bits/atomic_lockfree_defines.h \ + /usr/include/c++/4.9/bits/localefwd.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++locale.h \ + /usr/include/c++/4.9/clocale /usr/include/locale.h \ + /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.9/iosfwd \ + /usr/include/c++/4.9/cctype /usr/include/ctype.h \ + /usr/include/x86_64-linux-gnu/bits/types.h \ + /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \ + /usr/include/x86_64-linux-gnu/bits/endian.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap.h \ + /usr/include/x86_64-linux-gnu/bits/byteswap-16.h \ + /usr/include/c++/4.9/bits/ostream_insert.h \ + /usr/include/c++/4.9/bits/cxxabi_forced.h \ + /usr/include/c++/4.9/bits/stl_function.h \ + /usr/include/c++/4.9/backward/binders.h \ + /usr/include/c++/4.9/bits/range_access.h \ + /usr/include/c++/4.9/bits/basic_string.h \ + /usr/include/c++/4.9/ext/atomicity.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/x86_64-linux-gnu/bits/sched.h \ + /usr/include/x86_64-linux-gnu/bits/time.h \ + /usr/include/x86_64-linux-gnu/bits/timex.h \ + /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \ + /usr/include/x86_64-linux-gnu/bits/setjmp.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h \ + /usr/include/c++/4.9/bits/basic_string.tcc /usr/include/c++/4.9/vector \ + /usr/include/c++/4.9/bits/stl_construct.h \ + /usr/include/c++/4.9/ext/alloc_traits.h \ + /usr/include/c++/4.9/bits/stl_uninitialized.h \ + /usr/include/c++/4.9/bits/stl_vector.h \ + /usr/include/c++/4.9/bits/stl_bvector.h \ + /usr/include/c++/4.9/bits/vector.tcc ../../tools/IoTools.h \ + /usr/include/c++/4.9/iostream /usr/include/c++/4.9/ostream \ + /usr/include/c++/4.9/ios /usr/include/c++/4.9/bits/ios_base.h \ + /usr/include/c++/4.9/bits/locale_classes.h \ + /usr/include/c++/4.9/bits/locale_classes.tcc \ + /usr/include/c++/4.9/streambuf /usr/include/c++/4.9/bits/streambuf.tcc \ + /usr/include/c++/4.9/bits/basic_ios.h \ + /usr/include/c++/4.9/bits/locale_facets.h /usr/include/c++/4.9/cwctype \ + /usr/include/wctype.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_base.h \ + /usr/include/c++/4.9/bits/streambuf_iterator.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/ctype_inline.h \ + /usr/include/c++/4.9/bits/locale_facets.tcc \ + /usr/include/c++/4.9/bits/basic_ios.tcc \ + /usr/include/c++/4.9/bits/ostream.tcc /usr/include/c++/4.9/istream \ + /usr/include/c++/4.9/bits/istream.tcc /usr/include/c++/4.9/iomanip \ + /usr/include/c++/4.9/fstream /usr/include/c++/4.9/bits/codecvt.h \ + /usr/include/c++/4.9/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \ + /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \ + /usr/include/x86_64-linux-gnu/bits/stdio.h \ + /usr/include/x86_64-linux-gnu/bits/stdio2.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h \ + /usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h \ + /usr/include/c++/4.9/bits/fstream.tcc ../../tools/vector3.h \ + ../../tools/vglStd.h ../../tools/vglEndian.h ../../tools/vglCompilers.h \ + ../../tools/vglMath.h ../../tools/std.h /usr/include/math.h \ + /usr/include/x86_64-linux-gnu/bits/huge_val.h \ + /usr/include/x86_64-linux-gnu/bits/huge_valf.h \ + /usr/include/x86_64-linux-gnu/bits/huge_vall.h \ + /usr/include/x86_64-linux-gnu/bits/inf.h \ + /usr/include/x86_64-linux-gnu/bits/nan.h \ + /usr/include/x86_64-linux-gnu/bits/mathdef.h \ + /usr/include/x86_64-linux-gnu/bits/mathcalls.h \ + /usr/include/x86_64-linux-gnu/bits/mathinline.h \ + /usr/include/x86_64-linux-gnu/bits/math-finite.h ../../tools/matrix3.h \ + ../../tools/String2Number.h /usr/include/c++/4.9/sstream \ + /usr/include/c++/4.9/bits/sstream.tcc ../../tools/Debug.h \ + /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \ + /usr/include/x86_64-linux-gnu/bits/waitstatus.h \ + /usr/include/x86_64-linux-gnu/sys/types.h \ + /usr/include/x86_64-linux-gnu/sys/select.h \ + /usr/include/x86_64-linux-gnu/bits/select.h \ + /usr/include/x86_64-linux-gnu/bits/sigset.h \ + /usr/include/x86_64-linux-gnu/bits/select2.h \ + /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib-float.h \ + /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/c++/4.9/limits \ + /usr/include/c++/4.9/cmath diff --git a/Makefile b/Makefile index c0f7aa4..0ef7082 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,8 @@ # Path to project directory. UPDIR = . # Path to subdirectories. -SUBDIRS = tools Energy/Sources Biopool/Sources Align2/Sources Energy/Sources/TorsionPotential Lobo/Sources Lobo/APPS Energy/APPS Biopool/APPS Align2/APPS +SUBDIRS = tools Energy/Sources Biopool/Sources Align2/Sources Energy/Sources/TorsionPotential Lobo/Sources Lobo/APPS Energy/APPS Biopool/APPS Align2/APPS \ + Phylo/Sources Phylo/APPS # # Libraries and paths (which are not defined globally). diff --git a/Makefile.global b/Makefile.global index 1f78a89..c9dfc08 100644 --- a/Makefile.global +++ b/Makefile.global @@ -106,11 +106,11 @@ SUBDIRS += _dummy_ LIB_PATH += -L$(UPDIR)/lib -INC_PATH += -I$(UPDIR)/tools -I$(UPDIR)/Energy/Sources -I$(UPDIR)/Biopool/Sources -I$(UPDIR)/Energy/Sources/TorsionPotential -I$(UPDIR)/Lobo/Sources -I$(UPDIR)/Align2/Sources -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS -I$(UPDIR)/Lobo/APPS +INC_PATH += -I$(UPDIR)/tools -I$(UPDIR)/Energy/Sources -I$(UPDIR)/Biopool/Sources -I$(UPDIR)/Energy/Sources/TorsionPotential -I$(UPDIR)/Lobo/Sources -I$(UPDIR)/Align2/Sources -I$(UPDIR)/Phylo/Sources -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS -I$(UPDIR)/Lobo/APPS -I$(UPDIR)/Phylo/APPS ifdef test - INC_PATH += -I$(UPDIR)/Biopool/Tests -I$(UPDIR)/Energy/Tests -I$(UPDIR)/Align2/Tests -I$(UPDIR)/Lobo/Tests - SUBDIRS = Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests + INC_PATH += -I$(UPDIR)/Biopool/Tests -I$(UPDIR)/Energy/Tests -I$(UPDIR)/Align2/Tests -I$(UPDIR)/Lobo/Tests -I$(UPDIR)/Phylo/Tests + SUBDIRS = Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests Phylo/Tests endif ####### Implicit rules @@ -196,4 +196,4 @@ subinstall: # # Include dependencies # - \ No newline at end of file + diff --git a/Phylo/APPS/Makefile b/Phylo/APPS/Makefile new file mode 100644 index 0000000..6bc40aa --- /dev/null +++ b/Phylo/APPS/Makefile @@ -0,0 +1,57 @@ +#--*-makefile-*----------------------------------------------------------------- +# +# Standard makefile - Phylo/APPS +# +#------------------------------------------------------------------------------- + +# Path to project directory +PROJECT_ROOT = ../.. +BINPATH = $(PROJECT_ROOT)/bin/ +LIBPATH = $(PROJECT_ROOT)/lib/ +UPDIR = $(PROJECT_ROOT) +SUBDIR = + + + +# +# Libraries and paths (which are not defined globally) +# + +LIBS = -lPhylo -lAlign2 -ltools +INC_PATH = -I. -I $(PROJECT_ROOT)/Phylo/Sources +LIB_PATH = -L. + + + +# +# Objects and headers +# + +SOURCES = phyltree.cc clustalw.cc fengdoolittle.cc +OBJECTS = phyltree.o clustalw.o fengdoolittle.o +TARGETS = phyltree clustalw fengdoolittle +EXECS = phyltree clustalw fengdoolittle +LIBRARY = APPSlibPhylo.a + + + +# +# Install rule +# + +compile: all + +all: install +install: $(LIBRARY) $(TARGETS) + mv $(LIBRARY) $(LIBPATH) + mv $(EXECS) $(BINPATH) + + + +# +# Call global Makefile to do the job +# +include ../../Makefile.global + +# Overriding to use C++11 +STANDARDFLAGS = -Wall -Wextra -pedantic -std=c++0x -DNEXCEPTIONS -DLINUX -c \ No newline at end of file diff --git a/Phylo/APPS/clustalw.cc b/Phylo/APPS/clustalw.cc new file mode 100644 index 0000000..2a59c13 --- /dev/null +++ b/Phylo/APPS/clustalw.cc @@ -0,0 +1,197 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . + */ + +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor::Phylo; +using namespace Victor; + + + +/** @brief Shows a helper. */ +static void show_help() { + cout << "CLUSTALW - MULTIPLE SEQUENCE ALIGNMENT TOOL\n" + << "This program calculates a multiple sequence alignment.\n" + << "Options:\n" + << "--in \t Path to input FASTA file\n" + << "[--out ] \t Path to output ClustalW file (default: to screen)\n" + << "[-m ] \t Path to substitution matrix file (default: blosum62.dat)\n" + << "[-o ] \t Open gap penalty (default: 10.0)\n" + << "[-e ] \t Extension gap penalty (default: 0.1)\n" + << "[-d <0|1|2>] \t Distance matrix builder criterion (default: 0)\n" + << " \t -d 0: Distance as 1 - percentage of identity\n" + << " \t -d 1: Use Levenshtein distance\n" + << " \t -d 2: Use Feng-Doolittle distance\n" + << "[-c <0|1|2>] \t Clustering algorithm (default:2)\n" + << " \t -c 0: UPGMA\n" + << " \t -c 1: Fitch-Margoliash\n" + << " \t -c 2: Neighbor Joining\n" + << "[-n <0|1>] \t Substitution matrix family for multiple alignment (default: 1)\n" + << " \t -w 0: PAM series\n" + << " \t -w 1: BLOSUM series\n" + << "[-wo ] \t Initial open gap penalty for ClustalW (default: 10.0)\n" + << "[-we ] \t Initial extension gap penalty for ClustalW (default: 0.2)\n" + << "[-v] \t Verbose (default: no)\n" + << "\n" << endl; +} + + + +/** ClustalW multiple sequence alignment program. + * @param[in] argc ARGument Counter + * @param[in] argv ARGument Vector + * @return 0 in case of success + * @author Marco Zanella + */ +int main(int argc, char *argv[]) { + string input_filename, output_filename, matrix_filename; + unsigned int distance_criterion, clustering, matrix_family; + double gap_open, gap_extension, clustalw_gop, clustalw_gep; + bool verbose; + + + //////////////////////////////////////////////////////////////////// + // Reads options + if (getArg("h", argc, argv)) { + show_help(); + return 0; + } + + getArg("-in", input_filename, argc, argv, "!"); + getArg("-out", output_filename, argc, argv, "!"); + getArg("m", matrix_filename, argc, argv, "blosum62.dat"); + getArg("o", gap_open, argc, argv, 10.0); + getArg("e", gap_extension, argc, argv, 0.1); + getArg("d", distance_criterion, argc, argv, 0); + getArg("c", clustering, argc, argv, 2); + getArg("n", matrix_family, argc, argv, 1); + getArg("wo", clustalw_gop, argc, argv, 10.0); + getArg("we", clustalw_gep, argc, argv, 0.2); + verbose = getArg("v", argc, argv); + + + //////////////////////////////////////////////////////////////////// + // Loads and prepares data + // Alignment + if (verbose) cout << "Loading alignment data..." << endl; + Alignment alignment; + if (input_filename != "!") { + ifstream fasta_file(input_filename); + if (!fasta_file) { + ERROR("Error opening input FASTA file.", exception); + } + + alignment.loadFasta(fasta_file); + if (alignment.size() < 1) { + ERROR("Input FASTA file must contain two sequences.", exception); + } + } else { + ERROR("Missing input FASTA file.", exception); + } + + // Substitution matrix + if (verbose) cout << "Loading substitution matrix..." << endl; + SubMatrix substitution_matrix; + if (matrix_filename != "!") { + ifstream matrix_file(matrix_filename); + if (!matrix_file) { + ERROR("Error opening substitution matrix file.", exception); + } + + substitution_matrix = SubMatrix(matrix_file); + } else { + ERROR("Missing substitution matrix file.", exception); + } + + // Gap function + AGPFunction gap_function(gap_open, gap_extension); + + // Distance builder + DistanceMatrixBuilder *build_matrix; + switch (distance_criterion) { + case 0: + build_matrix = new IdentityPercentage(substitution_matrix, gap_function); + break; + case 1: + build_matrix = new LevenshteinDistance(); + break; + case 2: + build_matrix = new FengDoolittleDistance(substitution_matrix, gap_function); + break; + default: + ERROR("Invalid distance criterion", exception); + exit(-1); + } + + // Clustering algorithm + ClusteringAlgorithm *build_tree; + switch (clustering) { + case 0: + build_tree = new UPGMA(); + break; + case 1: + build_tree = new FitchMargoliash(); + break; + case 2: + build_tree = new NJ(); + break; + default: + ERROR("Invalid clustering algorithm", exception); + exit(-1); + } + + // Substitution matrix family + ClustalW::WeightMatrix weight_family; + switch (matrix_family) { + case 0: + weight_family = ClustalW::PAM; + break; + case 1: + weight_family = ClustalW::BLOSUM; + break; + default: + ERROR("Invalid matrix family", exception); + exit(-1); + } + + + //////////////////////////////////////////////////////////////////// + // Creates ClustalW object + if (verbose) cout << "Configuring ClustalW..." << endl; + ClustalW clustalw(*build_matrix, *build_tree, weight_family, clustalw_gop, clustalw_gep); + if (verbose) cout << "Generating multiple sequence alignment..." << endl; + MultipleAlignment MSA = clustalw(alignment); + + + //////////////////////////////////////////////////////////////////// + // Saves output + if (verbose) cout << "Saving multiple sequence alignment..." << endl; + if (output_filename != "!") { + ofstream clustalw_file(output_filename); + MSA.saveClustalW(clustalw_file); + } else { + MSA.saveClustalW(cout); + } + if (verbose) cout << "done." << endl; + + return 0; +} \ No newline at end of file diff --git a/Phylo/APPS/fengdoolittle.cc b/Phylo/APPS/fengdoolittle.cc new file mode 100644 index 0000000..e95d971 --- /dev/null +++ b/Phylo/APPS/fengdoolittle.cc @@ -0,0 +1,109 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . + */ + +#include +#include +#include +#include + +using namespace Victor::Phylo; +using namespace Victor; + + + +/** @brief Shows a helper. */ +static void show_help() { + cout << "FENG DOOLITTLE - MULTIPLE SEQUENCE ALIGNMENT TOOL\n" + << "TThis program calculates a multiple sequence alignment.\n" + << "Options:\n" + << "--in \t Name of input FASTA file\n" + << "[--out ] \t Name of output alignment file (default: to screen)\n" + << "[-o ] \t Open gap penalty (default: 10.0)\n" + << "[-e ] \t Extension gap penalty (default: 0.1)\n" + << "[-v] \t Verbose (default: no)\n" + << "\n" << endl; +} + + + +/** @brief Feng-Doolittle multiple sequence alignment program. + * @param[in] argc ARGument Counter + * @param[in] argv ARGument Vector + * @author Marco Zanella + * @return 0 in case of success + */ +int main(int argc, char *argv[]) { + string input_filename, output_filename; + double gap_open, gap_extension; + bool verbose; + + + //////////////////////////////////////////////////////////////////// + // Reads options + if (getArg("h", argc, argv)) { + show_help(); + return 0; + } + + getArg("-in", input_filename, argc, argv, "!"); + getArg("-out", output_filename, argc, argv, "!"); + getArg("o", gap_open, argc, argv, 10.0); + getArg("e", gap_extension, argc, argv, 0.1); + verbose = getArg("v", argc, argv); + + + //////////////////////////////////////////////////////////////////// + // Loads and prepares data + // Alignment + if (verbose) cout << "Loading alignment data..." << endl; + Alignment alignment; + if (input_filename != "!") { + ifstream fasta_file(input_filename); + if (!fasta_file) { + ERROR("Error opening input FASTA file.", exception); + } + + alignment.loadFasta(fasta_file); + if (alignment.size() < 1) { + ERROR("Input FASTA file must contain two sequences.", exception); + } + } else { + ERROR("Missing input FASTA file.", exception); + } + + + //////////////////////////////////////////////////////////////////// + // Creates FengDoolittle object + if (verbose) cout << "Configuring Feng-Doolittle algorithm..." << endl; + FengDoolittle feng_doolittle(gap_open, gap_extension); + if (verbose) cout << "Generating multiple sequence alignment..." << endl; + MultipleAlignment MSA = feng_doolittle(alignment); + + + //////////////////////////////////////////////////////////////////// + // Saves output + if (verbose) cout << "Saving multiple sequence alignment..." << endl; + if (output_filename != "!") { + ofstream clustalw_file(output_filename); + MSA.saveClustalW(clustalw_file); + } else { + MSA.saveClustalW(cout); + } + if (verbose) cout << "done." << endl; + + + return 0; +} \ No newline at end of file diff --git a/Phylo/APPS/phyltree.cc b/Phylo/APPS/phyltree.cc new file mode 100644 index 0000000..4a82526 --- /dev/null +++ b/Phylo/APPS/phyltree.cc @@ -0,0 +1,172 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . + */ + +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor::Phylo; +using namespace Victor; + + + +/** @brief Shows an helper. */ +static void show_help() { + cout << "PHYLOGENETIC TREE GENERATOR\n" + << "This program calculates a phylogenetic tree for a given alignment.\n" + << "Options:\n" + << "--in \t Path to input FASTA file\n" + << "[--out ] \t Path to output Newick file (default: to screen\n" + << "[-m ] \t Path to substitution matrix file (default: blosum62.dat)\n" + << "[-o ] \t Open gap penalty (default: 10.0)\n" + << "[-e ] \t Extension gap penalty (default: 0.1)\n" + << "[-d <0|1|2>] \t Distance matrix builder criterion (default: 0)\n" + << " \t -d 0: Distance as 1 - percentage of identity\n" + << " \t -d 1: Use Levenshtein distance\n" + << " \t -d 2: Use Feng-Doolittle distance\n" + << "[-c <0|1|2>] \t Clustering algorithm (default:2)\n" + << " \t -c 0: UPGMA\n" + << " \t -c 1: Fitch-Margoliash\n" + << " \t -c 2: Neighbor Joining\n" + << "[-v] \t Verbose (default: no)\n" + << "\n" << endl; +} + + + +/** @brief Builds a phylogenetic tree. + * @param[in] argc ARGument Counter + * @param[in] argv ARGument Vector + * @return 0 in case of success + * @author Marco Zanella + */ +int main(int argc, char *argv[]) { + string input_filename, output_filename, matrix_filename; + unsigned int distance_criterion, clustering; + double gap_open, gap_extension; + bool verbose; + + + //////////////////////////////////////////////////////////////////// + // Reads options + if (getArg("h", argc, argv)) { + show_help(); + return 0; + } + + getArg("-in", input_filename, argc, argv, "!"); + getArg("-out", output_filename, argc, argv, "!"); + getArg("m", matrix_filename, argc, argv, "blosum62.dat"); + getArg("o", gap_open, argc, argv, 10.0); + getArg("e", gap_extension, argc, argv, 0.1); + getArg("d", distance_criterion, argc, argv, 0); + getArg("c", clustering, argc, argv, 1); + verbose = getArg("v", argc, argv); + + + //////////////////////////////////////////////////////////////////// + // Loads and prepares data + // Alignment + if (verbose) cout << "Loading alignment data..." << endl; + Alignment alignment; + if (input_filename != "!") { + ifstream fasta_file(input_filename); + if (!fasta_file) { + ERROR("Error opening input FASTA file.", exception); + } + + alignment.loadFasta(fasta_file); + if (alignment.size() < 1) { + ERROR("Input FASTA file must contain two sequences.", exception); + } + } else { + ERROR("Missing input FASTA file.", exception); + } + + // Substitution matrix + if (verbose) cout << "Loading substitution matrix..." << endl; + SubMatrix substitution_matrix; + if (matrix_filename != "!") { + ifstream matrix_file(matrix_filename); + if (!matrix_file) { + ERROR("Error opening substitution matrix file.", exception); + } + + substitution_matrix = SubMatrix(matrix_file); + } else { + ERROR("Missing substitution matrix file.", exception); + } + + // Gap function + AGPFunction gap_function(gap_open, gap_extension); + + // Distance builder + DistanceMatrixBuilder *build_matrix; + switch (distance_criterion) { + case 0: + build_matrix = new IdentityPercentage(substitution_matrix, gap_function); + break; + case 1: + build_matrix = new LevenshteinDistance(); + break; + case 2: + build_matrix = new FengDoolittleDistance(substitution_matrix, gap_function); + break; + default: + ERROR("Invalid distance criterion", exception); + exit(-1); + } + + // Clustering algorithm + ClusteringAlgorithm *build_tree; + switch (clustering) { + case 0: + build_tree = new UPGMA(); + break; + case 1: + build_tree = new NJ(); + break; + default: + ERROR("Invalid clustering algorithm", exception); + exit(-1); + } + + + //////////////////////////////////////////////////////////////////// + // Computes phylogenetic tree + if (verbose) cout << "Generating distance matrix..." << endl; + DistanceMatrix distance_matrix = (*build_matrix)(alignment); + if (verbose) cout << "Generating phylogenetic tree..." << endl; + RootedTree tree = (*build_tree)(distance_matrix).asRootedTree(); + + + //////////////////////////////////////////////////////////////////// + // Saves output + if (verbose) cout << "Saving tree..." << endl; + if (output_filename != "!") { + ofstream newick_file(output_filename); + tree.saveNewick(newick_file); + } else { + tree.saveNewick(cout); + } + if (verbose) cout << "done." << endl; + + return 0; +} \ No newline at end of file diff --git a/Phylo/Sources/AminoAcid.cc b/Phylo/Sources/AminoAcid.cc new file mode 100644 index 0000000..bebb028 --- /dev/null +++ b/Phylo/Sources/AminoAcid.cc @@ -0,0 +1,157 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include + +namespace Victor { +namespace Phylo { + typedef AminoAcid::Code Code; + + const char AminoAcid::letter1s[] = { + 'A', 'R', 'N', 'D', 'C', 'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M', + 'F', 'P', 'S', 'T', 'W', 'Y', 'V', + 'U', 'O', + 'B', 'Z', 'J', 'X' + }; + const string AminoAcid::letter3s[] = { + "ALA", "ARG", "ASN", "ASP", "CYS", "GLU", "GLN", "GLY", "HIS", + "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", + "TYR", "VAL", + "SEC", "PYL", + "ASX", "GLX", "XLE", "XAA" + }; + const string AminoAcid::names[] = { + "Alanine", "Arginine", "Asparagine", "Aspartic acid", "Cysteine", + "Glutamic acid", "Glutamine", "Glycine", "Histeine", "Isoleucine", + "Leucine", "Lysine", "Methionine", "Phenylalanine", "Proline", + "Serine", "Threonine", "Tryptophan", "Tyrosine", "Valine", + "Selenocysteine", "Pyrrolisine", + "Asparagine / Aspartic acid", "Glutamine / Glutamic acid", + "Leucine / Isoleucine", "Unspecified / Unknown" + }; + + + + Code + AminoAcid::letter1ToCode(const char code) { + switch (code) { + case 'A': return A; + case 'R': return R; + case 'N': return N; + case 'D': return D; + case 'C': return C; + case 'E': return E; + case 'Q': return Q; + case 'G': return G; + case 'H': return H; + case 'I': return I; + case 'L': return L; + case 'K': return K; + case 'M': return M; + case 'F': return F; + case 'P': return P; + case 'S': return S; + case 'T': return T; + case 'W': return W; + case 'Y': return Y; + case 'V': return V; + + case 'U': return U; + case 'O': return O; + + case 'B': return B; + case 'Z': return Z; + case 'J': return J; + default: return X; + } + } + + + + Code + AminoAcid::letter3ToCode(const string &code) { + size_t index = 0; + bool found = false; + + while (!found && index < X) { + found = code == letter3s[index]; + if (!found) { + index++; + } + } + + return (Code) index; + } + + + + AminoAcid::AminoAcid(const Code code) + : code(code) { + } + + + + AminoAcid::AminoAcid(const char code) + : code(letter1ToCode(code)) { + } + + + + AminoAcid::AminoAcid(const string &code) + : code(letter3ToCode(code)) { + } + + + + AminoAcid::AminoAcid(const AminoAcid &origin) + : AminoAcid(origin.code) { + } + + + + AminoAcid::~AminoAcid() { + } + + + + Code + AminoAcid::getCode() const { + return code; + } + + + + char + AminoAcid::getSingleLetter() const { + return letter1s[code]; + } + + + + string + AminoAcid::getThreeLetter() const { + return letter3s[code]; + } + + + + string + AminoAcid::getFullName() const { + return names[code]; + } + +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/AminoAcid.h b/Phylo/Sources/AminoAcid.h new file mode 100644 index 0000000..30acb27 --- /dev/null +++ b/Phylo/Sources/AminoAcid.h @@ -0,0 +1,143 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_AMINOACID_H_ +#define _VICTOR_PHYLO_AMINOACID_H_ + +/** Number of amino acids. */ +#define _AMINOACID_SIZE 26 +#include + +using std::string; + +namespace Victor{ +namespace Phylo { + +/** @brief Implements an amino acid. + * + * @author Marco Zanella + */ +class AminoAcid { + public: + /** Hashed values for known amino acids. */ + typedef enum { + A, ///< Alanine + R, ///< Arginine + N, ///< Asparagine + D, ///< Aspartic acid + C, ///< Cysteine + E, ///< Glutamic acid + Q, ///< Glutamine + G, ///< Glycine + H, ///< Histidine + I, ///< Isoleucine + L, ///< Leucine + K, ///< Lysine + M, ///< Methionine + F, ///< Phenylalanine + P, ///< Proline + S, ///< Serine + T, ///< Threonine + W, ///< Tryptophan + Y, ///< Tyrosine + V, ///< Valine + + U, ///< Selenocysteine + O, ///< Pyrrolisine + + B, ///< Asparagine or aspartic acid + Z, ///< Glutamine or glutamic acid + J, ///< Leucine or isoleucine + X ///< Unspecified or unknown + } Code; + + + + /** @brief Returns code of given amino acid. + * @param[in] code Single letter code + * @return Hash value + */ + static Code letter1ToCode(const char code); + + + + /** @brief Returns code of given amino acid. + * @param[in] code Three letter code + * @return Hash value + */ + static Code letter3ToCode(const string &code); + + + + /** @brief Builds an amino acid of given code. + * @param[in] code Code of the amino acid + */ + explicit AminoAcid(const Code code); + + /** @brief Builds an amino acid of given code. + * @param[in] code Single letter code + */ + explicit AminoAcid(const char code); + + /** @brief Builds an amino acid of given code. + * @param[in] code Three letter code + */ + explicit AminoAcid(const string &code); + + /** @brief Copy constructor. + * @param[in] origin Original object + */ + explicit AminoAcid(const AminoAcid &origin); + + /** @brief Destructor. */ + virtual ~AminoAcid(); + + + + /** @brief Returns code of this amino acid. + * @return Code of this amino acid + */ + Code getCode() const; + + /** @brief Returns single letter code of this amino acid. + * @return Single letter code + */ + char getSingleLetter() const; + + /** @brief Returns thre letters code of this amino acid. + * @return Three letters code + */ + string getThreeLetter() const; + + /** @brief Returns fullname of this amino acid. + * @return Full name of this amino acid + */ + string getFullName() const; + + + + private: + static const char letter1s[_AMINOACID_SIZE]; ///< 1-letter codes of amino acids + static const string letter3s[_AMINOACID_SIZE]; ///< 3-letters code of amino acids + static const string names[_AMINOACID_SIZE]; ///< Full names of amino acids + + const Code code; ///< Code of this amino acid +}; + +} +} + +#endif // _VICTOR_PHYLO_AMINOACID_H_ \ No newline at end of file diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc new file mode 100644 index 0000000..14c6638 --- /dev/null +++ b/Phylo/Sources/ClustalW.cc @@ -0,0 +1,565 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +/** Maximum distance to search gaps (position-specific GOP). */ +#define GAP_SEARCH_DISTANCE 8 +#include + +using namespace std; +using namespace Victor::Phylo; + +/** Direction for a traceback. */ +typedef enum { + NONE, ///< No direction + UP, ///< Up + LEFT, ///< Left + DIAG ///< Diagonal +} Direction; + +/** @brief Pascarella and Argos residue specific gap modification factors. + * @return Map from residues to factors. + */ +static map PascarellaArgos(); + +/** @brief Selects best direction. + * @param[in] diagonal Score from the diagonal + * @param[in] up Score from top + * @param[in] left Score from bottom + * @return Best direction + */ +static inline Direction select_direction( + const double diagonal, + const double up, + const double left); + +/** @brief Performs the traceback operation. + * @param[in] A First MSA + * @param[in] B Second MSA + * @param[in] direction Traceback matrix + * @return Vector of residues + */ +static vector traceback( + const MultipleAlignment &A, + const MultipleAlignment &B, + vector> &direction); + +/** @brief Builds a vector of sequences. + * + * Joins sequences from two MSAs and a vector of residues. + * @param[in] A First MSA + * @param[in] B Second MSA + * @param[in] residues Vector of residues + * @return Vector of sequences + */ +static vector join( + const MultipleAlignment &A, + const MultipleAlignment &B, + vector &residues); + + + + + +namespace Victor { +namespace Phylo { + typedef map Weights; + typedef vector Sequences; + + map ClustalW::gap_modifiers = PascarellaArgos(); + + ClustalW::ClustalW( + const DistanceMatrixBuilder &distance_matrix_builder, + const ClusteringAlgorithm &clustering_algorithm, + const WeightMatrix weight_matrix, + const double gap_open, + const double gap_extension) + : build_matrix(distance_matrix_builder), + build_tree(clustering_algorithm), + weight_matrix(weight_matrix), + gap_open(gap_open), + gap_extension(gap_extension) { + } + + + + ClustalW::ClustalW(const ClustalW &origin) + : ClustalW( + origin.build_matrix, + origin.build_tree, + origin.weight_matrix, + origin.gap_open, + origin.gap_extension + ) { + } + + + + ClustalW::~ClustalW() { + } + + + + MultipleAlignment & + ClustalW::apply(const AlignmentBase &alignment) const { + // Reads sequences + Sequences sequences = Sequence::toMap(alignment); + + // Computes distance matrix (pairwise alignments) + DistanceMatrix d = build_matrix(alignment); + + // Computes guide tree and weights + RootedTree guide_tree = build_tree(d).asRootedTree(); + Weights weights = getWeights(guide_tree); + + // Progressive alignments + return align(sequences, guide_tree, weights); + } + + + + Weights + ClustalW::getWeights(const RootedTree &guide_tree) const { + map weights; + + // Computes weighs for every sequence + double max_weight = 0.0; + for (auto &leaf : guide_tree.getLeaves()) { + RootedTree node = *leaf; + double weight = node.getDistance(); + const string id = node.getLabel(); + + while (!node.isRoot()) { + weight += node.getDistance() / node.getLeavesNumber(); + node = node.getParent(); + } + + weights[id] = weight; + max_weight = max(weight, max_weight); + } + + // Normalizes weights + for (auto &entry : weights) { + weights[entry.first] = entry.second / max_weight; + } + + return weights; + } + + + + MultipleAlignment & + ClustalW::align( + Sequences &sequences, + const RootedTree &node, + Weights &weights) const { + + //////////////////////////////////////////////////////////////// + // Single sequence: just returns it + if (node.isLeaf()) { + const string identifier = node.getLabel(); + const string residues = sequences[identifier]; + return *(new MultipleAlignment(Sequence(identifier, residues))); + } + + + //////////////////////////////////////////////////////////////// + // Single inheritance: straightforward + if (node.getChildrenNumber() == 1) { + return align(sequences, node[0], weights); + } + + + //////////////////////////////////////////////////////////////// + // Two sequences: performs alignment + const MultipleAlignment A = align(sequences, node[0], weights), + B = align(sequences, node[1], weights); + const SubstitutionMatrix ss(getSubstitutionMatrix(node)); + const size_t M = A.getLength(), + N = B.getLength(); + + +#if VERBOSE==1 + cout << "Now aligning:" << endl; + for (size_t i = 0; i < A.getSize(); i++) { + cout << A.getSequence(i).getIdentifier() << endl; + } + cout << "---------- against ----------" << endl; + for (size_t j = 0; j < B.getSize(); j++) { + cout << B.getSequence(j).getIdentifier() << endl; + } + cout << endl << endl; +#endif + + + // Allocates score and traceback matrices + vector> score(N + 1); + vector> direction(N + 1); + for (size_t i = 0; i <= N; i++) { + score[i] = vector(M + 1); + direction[i] = vector(M + 1); + } + + + // Initializes first row + score[0][0] = 0; + direction[0][0] = NONE; + for (size_t j = 1; j <= M; j++) { + const double GOP = getPositionSpecificGOP(A, B, ss, 0); + const double GEP = getPositionSpecificGEP(A, B, j - 1); + score[0][j] = -(GOP + GEP * (j - 1)); + direction[0][j] = LEFT; + } + + + // Initializes first column + for (size_t i = 1; i <= N; i++) { + const double GOP = getPositionSpecificGOP(B, A, ss, 0), + GEP = getPositionSpecificGEP(B, A, i - 1); + score[i][0] = -(GOP + GEP * (i - 1)); + direction[i][0] = UP; + } + + + // Calculates score matrix + size_t hgaps = 1, vgaps = 1; + for (size_t i = 1; i <= N; i++) { + for (size_t j = 1; j <= M; j++) { + double vgap = 0.9; + double hgap = 0.9; + + hgap = getPositionSpecificGOP(A, B, ss, j - 1) + + hgaps * getPositionSpecificGEP(A, B, j - 1); + + vgap = getPositionSpecificGOP(B, A, ss, i - 1) + + vgaps * getPositionSpecificGEP(B, A, i - 1); + +hgap = (direction[i][j - 1] != LEFT) + ? getPositionSpecificGOP(A, B, ss, j - 1) + : getPositionSpecificGEP(A, B, j - 1); +vgap = (direction[i - 1][j] != UP) + ? getPositionSpecificGOP(B, A, ss, i - 1) + : getPositionSpecificGEP(B, A, i - 1); + + const double d = score[i-1][j-1] + S(A, B, i, j, ss, weights), + u = score[i - 1][j] - vgap, + l = score[i][j - 1] - hgap; + + Direction dir = select_direction(d, u, l); + score[i][j] = max(d, max(u, l)); + direction[i][j] = dir; + + // Written in a LP-fashion way for performance reasons + vgaps = (dir == UP) * (vgaps + 1); + hgaps = (dir == LEFT) * (hgaps + 1); + } + } + + + // Traceback + vector residues = traceback(A, B, direction); + + + // Builds sequences + vector joint = join(A, B, residues); + + + // Returns multiple alignment + return *(new MultipleAlignment(joint)); + } + + + + double + ClustalW::getInitialGOP( + const MultipleAlignment &A, + const MultipleAlignment &B, + const SubstitutionMatrix &matrix) const { + const double M = A.getLength(), + N = B.getLength(), + avg = matrix.getAvgMismatchScore(), + identity = A.getPercentIdentity(); + return gap_open + log(min(M, N)) * avg * identity; + } + + + + double + ClustalW::getInitialGEP( + const MultipleAlignment &A, + const MultipleAlignment &B) const { + const double N = A.getLength(), + M = B.getLength(); + return gap_extension * (1.0 + abs(log(N / M))); + } + + + + double + ClustalW::getPositionSpecificGOP( + const MultipleAlignment &A, + const MultipleAlignment &B, + const SubstitutionMatrix &matrix, + const size_t position) const { + double GOP = getInitialGOP(A, B, matrix); + + // If there are sequences with gaps, ignore other rules + if (A.getGapNumber(position) > 0) { + return GOP * 0.3 * (1.0 - A.getGapNumber(position) / A.getSize()); + } + + + // Checks for gaps within 8 spaces + size_t distance = 0; + bool gaps_nearby = false; + while (!gaps_nearby && distance <= GAP_SEARCH_DISTANCE) { + distance++; + const size_t gaps_before = A.getGapNumber(position - distance), + gaps_after = A.getGapNumber(position + distance); + gaps_nearby = (gaps_before + gaps_after) > 0; + } + if (gaps_nearby) { + GOP = GOP * (4.0 - distance / 4.0); + } + + + // Checks for hydrophilic stretches + if (A.hasHydrophilicStretch(position)) { + GOP = GOP * 2.0 / 3.0; + } + + + // Uses Pascarella-Argos table, if no hydropilic stretches + else { + const string &residues = A.getResidues(position); + double average = 0.0; + + for (char residue : residues) { + average += gap_modifiers[residue]; + } + average /= A.getSize(); + + GOP = GOP * average; + } + + return GOP; + } + + + + double + ClustalW::getPositionSpecificGEP( + const MultipleAlignment &A, + const MultipleAlignment &B, + const size_t position) const { + const double GEP = getInitialGEP(A, B); + + return (A.getGapNumber(position) > 0) ? GEP * 0.5 : GEP; + } + + + + SubstitutionMatrix & + ClustalW::getSubstitutionMatrix(const RootedTree &guide_tree) const { + const double max_distance = guide_tree.getRoot().getMaxDistance(); + const double raw_distance = guide_tree[0].getDistance(guide_tree[1]); + const double distance = raw_distance / max_distance; + SubstitutionMatrix::Identifier identifier; + + // PAM family + if (weight_matrix == PAM && distance >= 0.8) + identifier = SubstitutionMatrix::PAM20; + else if (weight_matrix == PAM && distance >= 0.6) + identifier = SubstitutionMatrix::PAM60; + else if (weight_matrix == PAM && distance >= 0.4) + identifier = SubstitutionMatrix::PAM120; + else if (weight_matrix == PAM) + identifier = SubstitutionMatrix::PAM350; + + // BLOSUM family + else if (weight_matrix == BLOSUM && distance >= 0.8) + identifier = SubstitutionMatrix::BLOSUM80; + else if (weight_matrix == BLOSUM && distance >= 0.6) + identifier = SubstitutionMatrix::BLOSUM62; + else if (weight_matrix == BLOSUM && distance >= 0.3) + identifier = SubstitutionMatrix::BLOSUM45; + else if (weight_matrix == BLOSUM) + identifier = SubstitutionMatrix::BLOSUM30; + + // Default + else + identifier = SubstitutionMatrix::BLOSUM62; + + + SubstitutionMatrix matrix(identifier); + + // Shifts matrix so that minimum value is 0 + return matrix - matrix.getMinScore(); + } + + + + double + ClustalW::S( + const MultipleAlignment &A, + const MultipleAlignment &B, + const size_t i, + const size_t j, + const SubstitutionMatrix &matrix, + Weights &weights) { + const size_t M = A.getSize(), + N = B.getSize(); + double score = 0.0; + + // Full version + for (size_t a = 0; a < M; a++) { + const Sequence seqA = A.getSequence(a); + const char rA = seqA.getResidues()[j - 1]; + const double wA = weights[seqA.getIdentifier()]; + for (size_t b = 0; b < N; b++) { + const Sequence seqB = B.getSequence(b); + const char rB = seqB.getResidues()[i - 1]; + const double wB = weights[seqB.getIdentifier()]; + + score += (1 - (rA == '-' || rB == '-')) * matrix(rA, rB) * wA * wB; + } + } + score /= (M * N); + + // Consensus only version + /* + const char a = A.getConsensus(i), + b = B.getConsensus(j); + score = (1 - (a == '-' || b == '-')) * matrix(a, b); + */ + + return score; + } +} // namespace Phylo +} // namespace Victor + + + + + +//////////////////////////////////////////////////////////////////////// +// Support (local) functions. +static map PascarellaArgos() { + map modifiers; + + modifiers['A'] = 1.13; + modifiers['C'] = 1.13; + modifiers['D'] = 0.96; + modifiers['E'] = 1.31; + modifiers['F'] = 1.20; + modifiers['G'] = 0.61; + modifiers['H'] = 1.00; + modifiers['I'] = 1.32; + modifiers['K'] = 0.96; + modifiers['L'] = 1.21; + modifiers['M'] = 1.29; + modifiers['N'] = 0.63; + modifiers['P'] = 0.74; + modifiers['Q'] = 1.07; + modifiers['R'] = 0.72; + modifiers['S'] = 0.76; + modifiers['T'] = 0.89; + modifiers['V'] = 1.25; + modifiers['Y'] = 1.00; + modifiers['W'] = 1.23; + + return modifiers; +} + + + +static inline Direction select_direction( + const double diagonal, + const double up, + const double left) { + return (diagonal > up && diagonal > left) + ? DIAG + : ((up > left) ? UP : LEFT); +} + + + +static vector traceback( + const MultipleAlignment &A, + const MultipleAlignment &B, + vector> &direction) { + const size_t M = A.getSize(), + N = B.getSize(); + size_t i = B.getLength(), + j = A.getLength(); + vector residues(M + N); + Direction next = direction[i][j]; + + while (next != NONE) { + if (next == DIAG) { + i--; j--; + for (size_t k = 0; k < M; k++) + residues[k] = A.getResidues(j)[k] + residues[k]; + + for (size_t k = 0; k < N; k++) + residues[M + k] = B.getResidues(i)[k] + residues[M + k]; + } else if (next == UP) { + i--; + for (size_t k = 0; k < M; k++) + residues[k] = "-" + residues[k]; + + for (size_t k = 0; k < N; k++) + residues[M + k] = B.getResidues(i)[k] + residues[M + k]; + } else { + j--; + for (size_t k = 0; k < M; k++) + residues[k] = A.getResidues(j)[k] + residues[k]; + + for (size_t k = 0; k < N; k++) + residues[M + k] = "-" + residues[M + k]; + } + + next = direction[i][j]; + } + + return residues; +} + + + +static vector join( + const MultipleAlignment &A, + const MultipleAlignment &B, + vector &residues) { + const size_t M = A.getSize(), + N = B.getSize(); + vector sequences; + + for (size_t i = 0; i < M; i++) { + sequences.push_back(Sequence( + A.getSequence(i).getIdentifier(), + residues[i] + )); + } + + for (size_t j = 0; j < N; j++) { + sequences.push_back(Sequence( + B.getSequence(j).getIdentifier(), + residues[M + j] + )); + } + + return sequences; +} \ No newline at end of file diff --git a/Phylo/Sources/ClustalW.h b/Phylo/Sources/ClustalW.h new file mode 100644 index 0000000..59990cc --- /dev/null +++ b/Phylo/Sources/ClustalW.h @@ -0,0 +1,245 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_CLUSTALW_H_ +#define _VICTOR_PHYLO_CLUSTALW_H_ + +#define _GLIBCXX_IOMANIP +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor::Align2; + +namespace Victor { +namespace Phylo { + +/** @brief Implements the ClustalW algorithm. + * + * Implements ClustalW as a functor. + * ClustalW is a progressive multiple sequence alignment program. It is + * an improved version of the original Clustal which uses sequence + * weighting, position-specific gap penalties and weight matrix choice. + * + * For more information see: + * - CLUSTAL W: improving the sensitivity of progressive multiple sequence + * alignment through sequence weighting, position-specific gap penalties + * and weight matrix choice + * + * This class follows the Strategy and Facade Design Patterns. + * + * Please note that neither the original paper nor other available + * resources provide a good/serious description of the (many) implementation + * details. Moreover, the freely available source code of Clustal W is + * far too complex and too poorly documented. For these reason, this + * work (had to) follow a reverse-engeneering approach. + * + * @author Marco Zanella + */ +class ClustalW: public MultipleAlignmentAlgorithm { + public: + /** Available weight matrix families. */ + typedef enum { + PAM, ///< PAM series + BLOSUM ///< BLOSUM series + } WeightMatrix; + + + + /** @brief Builds a ClustalW aligner configured with given paramters. + * @param[in] distance_matrix_builder Distance matrix builder + * @param[in] clustering_algorithm Clustering algorithm + * @param[in] weight_matrix Weight matrix family (progressive alignment) + * @param[in] gap_open Gap open penalty (progressive alignment) + * @param[in] gap_extension Gap extension penalty (progressive alignment) + */ + explicit ClustalW( + const DistanceMatrixBuilder &distance_matrix_builder, + const ClusteringAlgorithm &clustering_algorithm, + const WeightMatrix weight_matrix, + const double gap_open = 10.0, + const double gap_extension = 0.1); + + /** @brief Copy constructor. + * @param[in] origin Original object + */ + explicit ClustalW(const ClustalW &origin); + + /** @brief Destructor. */ + virtual ~ClustalW(); + + + + /** @brief Builds an MSA from an alignment. + * @param[in] alignment The alignment + * @return Multiple sequence alignment + */ + virtual MultipleAlignment &apply(const AlignmentBase &alignment) const; + + + + private: + typedef map Weights; ///< Weight map + typedef map Sequences; ///< Set of sequences + + /** Residue-specific gap modification factors (Pascarella and Argos). */ + static map gap_modifiers; + + const DistanceMatrixBuilder &build_matrix; ///< Distance matrix builder + const ClusteringAlgorithm &build_tree; ///< Phylogenetic tree builder + const WeightMatrix weight_matrix; ///< Weight matrix family + const double gap_open; ///< Gap open penalty + const double gap_extension; ///< Gap extension penalty + + + /** @brief Returns weights. + * + * Weights are normalized. + * @param[in] guide_tree Guide tree of the alignment + * @return Weights of the sequences + */ + Weights getWeights(const RootedTree &guide_tree) const; + + + + /** @brief Performs multiple sequence alignment. + * + * Order of alignments is determined by topology of guide tree. + * @param[in] sequences Sequences to align + * @param[in] node Node on the guide tree + * @param[in] weights Weights + * @return Multiple sequence alignment + */ + MultipleAlignment &align( + Sequences &sequences, + const RootedTree &node, + Weights &weights) const; + + + + /** @brief Returns initial gap opening penalty. + * + * Initial gap opening penalty is computed considering dependence on + * the weight matrix, dependence on the similarity of the sequences + * and dependences on the length of the sequences: + * GOP = GOP + log(min(N, M)) * (average mismatch score) * (percentage + * of identity) + * where M, N are the length of the sequences. + * @param[in] A First (group of) sequence + * @param[in] B Second (group of) sequence + * @param[in] matrix Substitution matrix + * @return Initial gap opening penalty + */ + double getInitialGOP( + const MultipleAlignment &A, + const MultipleAlignment &B, + const SubstitutionMatrix &matrix) const; + + /** @brief Returns initial gap extension penalty. + * + * Initial gap extension penalty is computed considering dependence + * on the difference in the lengths of the sequences: + * GEP = GEP * (1.0 + |log(N/M)|) + * where M, N are the length of the sequences. + * @param[in] A First (group of) sequence + * @param[in] B Second (group of) sequence + * @return Initial gap extension penalty + */ + double getInitialGEP( + const MultipleAlignment &A, + const MultipleAlignment &B) const; + + /** @brief Returns position-specific gap open penalty. + * + * Position-specific gap open penalty is computed considering + * presence of gaps, nearby gaps and hydrophilic stretches. + * @param[in] A First (group of) sequence + * @param[in] B Second (group of) sequence + * @param[in] matrix Substitution matrix + * @param[in] position Current position + * @return Position-specific gap open penalty + */ + double getPositionSpecificGOP( + const MultipleAlignment &A, + const MultipleAlignment &B, + const SubstitutionMatrix &matrix, + const size_t position) const; + + /** @brief Returns position-specific gap extension penalty. + * + * Position specific gap extension penalty is computed considering + * presence of gaps: if there is a gap, GEP is halved. + * @param[in] A First (group of) sequence + * @param[in] B Second (group of) sequence + * @param[in] position Current positon + * @return Position-specific gap extension penalty + */ + double getPositionSpecificGEP( + const MultipleAlignment &A, + const MultipleAlignment &B, + const size_t position) const; + + /** @brief Returns a substitution matrix. + * + * Returns substitution matrix depending on the distance of the + * (groups of) sequences to align. Substitution matrix is shifted so + * that its minimum value is 0. + * @param[in] guide_tree Guide tree + * @return Substitution matrix + */ + SubstitutionMatrix &getSubstitutionMatrix(const RootedTree &guide_tree) const; + + + + /** @brief Returns match score. + * + * Computes match score between given MSAs, at given positions, using + * given substitutioin matrix and given weights for the sequences. + * @param[in] A First MSA + * @param[in] B Second MSA + * @param[in] i Row + * @param[in] j Column + * @param[in] matrix Substitution matrix + * @param[in] weights Weights of the sequences + * @return Score of the alignment. + */ + static double S( + const MultipleAlignment &A, + const MultipleAlignment &B, + const size_t i, + const size_t j, + const SubstitutionMatrix &matrix, + Weights &weights); +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_CLUSTALW_H_ \ No newline at end of file diff --git a/Phylo/Sources/ClusteringAlgorithm.h b/Phylo/Sources/ClusteringAlgorithm.h new file mode 100644 index 0000000..b58ebf5 --- /dev/null +++ b/Phylo/Sources/ClusteringAlgorithm.h @@ -0,0 +1,60 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_CLUSTERINGALGORITHM_H_ +#define _VICTOR_PHYLO_CLUSTERINGALGORITHM_H_ + +#include +#include +#include + +namespace Victor { +namespace Phylo { + +/** @brief A clustering algorithm. + * + * Clustering algorithms are phylogenetic algorithms which produce + * phylogenetic trees by using information about distances among + * alignments. + * + * Clustering algorithms are implemented as functors from a distance matrix to + * a phylogenetic tree. + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class ClusteringAlgorithm: public PhylogeneticAlgorithm { + public: + /** @brief Builds a phylogenetic tree from given distance matrix. + * @param[in] matrix Distance matrix + * @return Phylogenetic tree + */ + inline PhylogeneticTree &operator()(const DistanceMatrix &matrix) const { + return apply(matrix); + } + + /** @brief Builds a phylogenetic tree from given distance matrix. + * @param[in] matrix Distance matrix + * @return Phylogenetic tree + */ + virtual PhylogeneticTree &apply(const DistanceMatrix &matrix) const = 0; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_CLUSTERINGALGORITHM_ \ No newline at end of file diff --git a/Phylo/Sources/DistanceMatrix.cc b/Phylo/Sources/DistanceMatrix.cc new file mode 100644 index 0000000..5125d29 --- /dev/null +++ b/Phylo/Sources/DistanceMatrix.cc @@ -0,0 +1,225 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include + +namespace Victor { +namespace Phylo { + typedef DistanceMatrix::key key; + + const double DistanceMatrix::min_distance = 0.0; + const double DistanceMatrix::max_distance = std::numeric_limits::max(); + + + DistanceMatrix::~DistanceMatrix() { + } + + + + double + DistanceMatrix::operator()(const string &a, const string &b) const { + return getElement(a, b); + } + + + DistanceMatrix & + DistanceMatrix::operator()(const string &a, const string &b, const double distance) { + return setDistance(a, b, distance); + } + + + + bool + DistanceMatrix::isEmpty() const { + return getSize() <= 1; + } + + + + bool + DistanceMatrix::isSet(const string &a, const string &b) const { + return isSetDirectional(a, b) || isSetDirectional(b, a); + } + + + + bool + DistanceMatrix::hasOTU(const string &OTU) const { + for (auto &label : OTUs) { + if (label == OTU) { + return true; + } + } + return false; + } + + + + double + DistanceMatrix::getElement(const string &a, const string &b) const { + if (a == b) { + return min_distance; + } else if (isSetDirectional(a, b)) { + return find(make_pair(a, b))->second; + } else if (isSetDirectional(b, a)) { + return find(make_pair(b, a))->second; + } else { + return max_distance; + } + } + + + + set + DistanceMatrix::getOTUs() const { + return OTUs; + } + + + + size_t + DistanceMatrix::getSize() const { + return OTUs.size(); + } + + + + double + DistanceMatrix::getMinimum() const { + double min = max_distance; + + for (auto &entry : *this) { + if (entry.second <= min) { + min = entry.second; + } + } + + return min; + } + + + + key + DistanceMatrix::getMinimumPosition() const { + double min = max_distance; + key pos; + for (auto &entry : *this) { + if (entry.second <= min) { + min = entry.second; + pos = entry.first; + } + } + + return pos; + } + + + + double + DistanceMatrix::getMaximum() const { + double max = min_distance; + + for (auto &entry : *this) { + if (entry.second >= max) { + max = entry.second; + } + } + + return max; + } + + + + key + DistanceMatrix::getMaximumPosition() const { + double max = min_distance; + key pos; + + for (auto &entry : *this) { + if (entry.second >= max) { + max = entry.second; + pos = entry.first; + } + } + + return pos; + } + + + + DistanceMatrix & + DistanceMatrix::setDistance(const string &a, const string &b, const double distance) { + key pos = (isSetDirectional(a, b)) ? make_pair(a, b) : make_pair(b, a); + (*this)[pos] = distance; + return *this; + } + + + + DistanceMatrix & + DistanceMatrix::unsetDistance(const string &a, const string &b) { + if (isSetDirectional(a, b)) + this->erase(find(make_pair(a, b))); + if (isSetDirectional(b, a)) + this->erase(find(make_pair(b, a))); + return *this; + } + + + + DistanceMatrix & + DistanceMatrix::unsetDistance(const string &OTU) { + for (auto &other : getOTUs()) { + unsetDistance(OTU, other); + } + return *this; + } + + + + DistanceMatrix & + DistanceMatrix::addOTU(const string &OTU) { + if (!hasOTU(OTU)) { + OTUs.insert(OTU); + } + return *this; + } + + + DistanceMatrix & + DistanceMatrix::removeOTU(const string &OTU) { + // Removes OTU from list + OTUs.erase(OTU); + + // Removes OTU from distances + for (auto &i : OTUs) { + erase(make_pair(i, OTU)); + erase(make_pair(OTU, i)); + } + + return *this; + } + + + + bool + DistanceMatrix::isSetDirectional(const string &a, const string &b) const { + return find(make_pair(a, b)) != end(); + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/DistanceMatrix.h b/Phylo/Sources/DistanceMatrix.h new file mode 100644 index 0000000..9b3b981 --- /dev/null +++ b/Phylo/Sources/DistanceMatrix.h @@ -0,0 +1,220 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_DISTANCEMATRIX_H_ +#define _VICTOR_PHYLO_DISTANCEMATRIX_H_ + +#include +#include +#include +#include + +using std::string; +using std::pair; +using std::vector; +using std::set; +using std::map; + +namespace Victor { +namespace Phylo { + +/** @brief Implements a distance matrix. + * + * A distance matrix holds distances among OTUs. + * This class uses Method Cascading (through Method Chaining). + * + * @author Marco Zanella + */ +class DistanceMatrix: public map, double> { + public: + /** Key to access an entry in the matrix. */ + typedef pair key; + + + /** @brief Destructor. */ + virtual ~DistanceMatrix(); + + + + /** @brief Returns distance between given OTUs. + * + * If there is no recorded distance between given OTUs, returns + * maximum representable distance. + * Distance matrices are symmetric, hence order of indeces does not + * matter. + * @param[in] a First OTU + * @param[in] b Second OTU + * @return Distance between given OTUs + */ + double operator()(const string &a, const string &b) const; + + /** @brief Sets distance between given OTUs. + * + * If a distance was previously recorder for given OTUs, it is + * overwritten. + * @param[in] a First OTU + * @param[in] b Second OTU + * @param[in] distance Distance between a and b + * @return This matrix itself + */ + DistanceMatrix &operator()(const string &a, const string &b, const double distance); + + + + /** @brief Tells whether this matrix is empty. + * + * A distance matrix is empty when it contains 1 or less OTUs. + * @retval true This distance matrix is empty + * @retval false This distance matrix is not empty + */ + bool isEmpty() const; + + /** @brief Tells whether there is a distance recorder between given OTUs. + * + * Distance matrices are symmetric, hence order of indeces does not + * matter. + * @param[in] a First OTU + * @param[in] b Second OTU + * @retval true There is a record for given OTUs + * @retval false There is no record for given OTUs + */ + bool isSet(const string &a, const string &b) const; + + /** @brief Tells whether given OTU exists in this matrix. + * @param[in] OTU Given OTU + * @retval true Given OTU exists in this matrix + * @retval false Given OTU does not exist in this matrix + */ + bool hasOTU(const string &OTU) const; + + + + /** @brief Returns distance between given OTUs. + * + * If there is no recorded distance between given OTUs, returns + * maximum representable distance. + * Distance matrices are symmetric, hence order of indeces does not + * matter. + * @param[in] a First OTU + * @param[in] b Second OTU + * @return Distance between given OTUs + */ + double getElement(const string &a, const string &b) const; + + /** @brief Returns OTUs in this matrix. + * @return OTUs as vector + */ + set getOTUs() const; + + /** @brief Returns number of OTUs in this matrix. + * @return Number of OTUs in this matrix + */ + size_t getSize() const; + + /** @brief Returns minimum distance in this matrix. + * @return Minimum distance in this matrix + */ + double getMinimum() const; + + /** @brief Returns position of minimum distance in this matrix. + * + * Returns position as a pair, where strings are + * the OTUs. + * @return Position of minimum distance + */ + key getMinimumPosition() const; + + /** @brief Returns maximum distance in this matrix. + * @return Maximum distance in this matrix + */ + double getMaximum() const; + + /** @brief Returns position of maximum distance in this matrix. + * + * Returns position as a pair, where strings are + * the OTUs. + * @return Position of maximum distance + */ + key getMaximumPosition() const; + + + + /** @brief Sets distance between given OTUs. + * + * If a distance was previously recorder for given OTUs, it is + * overridden. + * @param[in] a First OTU + * @param[in] b Second OTU + * @param[in] distance Distance between a and b + * @return This matrix itself + */ + DistanceMatrix &setDistance(const string &a, const string &b, const double distance); + + /** @brief Unsets the distance between given OTUs. + * + * If no distance was set, nothing happens. + * @param[in] a First OTU + * @param[in] b Second OTU + * @return This matrix itself + */ + DistanceMatrix &unsetDistance(const string &a, const string &b); + + /** @brief Unsets every distance involving given OTU. + * @param[in] OTU OTU + * @return This matrix itself + */ + DistanceMatrix &unsetDistance(const string &OTU); + + /** @brief Adds a new OTU to this matrix. + * + * If given OTU already exists in this matrix, nothing happens. + * @param[in] OTU Given OTU + * @return This matrix itself + */ + DistanceMatrix &addOTU(const string &OTU); + + /** @brief Removes an OTU from this matrix. + * + * Data about given OTU (i.e. distances) is not removed. + * @param[in] OTU Given OTU + * @return This matrix itself + */ + DistanceMatrix &removeOTU(const string &OTU); + + + + private: + static const double min_distance; ///< Minimum representable distance + static const double max_distance; ///< Maximum representable distance + + set OTUs; ///< OTUs in this matrix + + + /** @brief Tells whether there is a distance recorder between given OTUs. + * + * Order of OTUs matters. + * @param[in] a First OTU + * @param[in] b Second OTU + * @retval true There is a record for given OTUs + * @retval false There is no record for given OTUs + */ + bool isSetDirectional(const string &a, const string &b) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_DISTANCEMATRIX_ \ No newline at end of file diff --git a/Phylo/Sources/DistanceMatrixBuilder.cc b/Phylo/Sources/DistanceMatrixBuilder.cc new file mode 100644 index 0000000..30b6cc5 --- /dev/null +++ b/Phylo/Sources/DistanceMatrixBuilder.cc @@ -0,0 +1,59 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include + +namespace Victor { +namespace Phylo { + DistanceMatrixBuilder::~DistanceMatrixBuilder() { + } + + + + DistanceMatrix & + DistanceMatrixBuilder::operator()(const AlignmentBase &alignment) const { + return apply(alignment); + } + + + + DistanceMatrix & + DistanceMatrixBuilder::apply(const AlignmentBase &alignment) const { + const size_t n = alignment.size() + 1; + const vector sequences = Sequence::toSequences(alignment); + DistanceMatrix * const d = new DistanceMatrix(); + + // Adds OTUs to the matrix + for (auto &sequence : sequences) { + d->addOTU(sequence.getIdentifier()); + } + + // Computes distance matrix + for (size_t i = 0; i < n; i++) { + for (size_t j = i + 1; j < n; j++) { + (*d)( + sequences[i].getIdentifier(), + sequences[j].getIdentifier(), + computeDistance(sequences[i].getResidues(), sequences[j].getResidues()) + ); + } + } + + return *d; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/DistanceMatrixBuilder.h b/Phylo/Sources/DistanceMatrixBuilder.h new file mode 100644 index 0000000..5a80465 --- /dev/null +++ b/Phylo/Sources/DistanceMatrixBuilder.h @@ -0,0 +1,69 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_DISTANCEMATRIXBUILDER_H_ +#define _VICTOR_PHYLO_DISTANCEMATRIXBUILDER_H_ + +#define _GLIBCXX_IOMANIP +#include +#include + +using namespace Victor::Align2; + +namespace Victor { +namespace Phylo { + +/** @brief Implements an algorithm for building a distance matrix. + * + * Builds a distance matrix from an alignment. + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class DistanceMatrixBuilder { + public: + /** @brief Destructor. */ + virtual ~DistanceMatrixBuilder(); + + + + /** @brief Builds a distance matrix from given alignment. + * @param[in] alignment Alignment + * @return Distance matrix + */ + DistanceMatrix &operator()(const AlignmentBase &alignment) const; + + /** @brief Builds a distance matrix from given alignment. + * @param[in] alignment Alignment + * @return Distance matrix + */ + DistanceMatrix &apply(const AlignmentBase &alignment) const; + + + + private: + /** @brief Returns distance between two sequences. + * @param[in] seq1 First sequence + * @param[in] seq2 Second sequence + * @return Distance between seq1 and seq2 + */ + virtual double computeDistance(const string &seq1, const string &seq2) const = 0; +}; + +} // namespace Phylo +} // namespace Victor +#endif // _VICTOR_PHYLO_DISTANCEMATRIXBUILDER_H_ \ No newline at end of file diff --git a/Phylo/Sources/FengDoolittle.cc b/Phylo/Sources/FengDoolittle.cc new file mode 100644 index 0000000..2324bd9 --- /dev/null +++ b/Phylo/Sources/FengDoolittle.cc @@ -0,0 +1,195 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include + +using namespace std; +using namespace Victor::Phylo; + +/** @brief Replaces gaps in a sequence. + * @param[in] sequence Sequence + * @return Sequence where gaps have been replaced + */ +static string &replace_gaps(const string &sequence); + +/** @brief Returns the PAM 250 substitution matrix. + * @return PAM 250 matrix + */ +static SubMatrix &init_matrix(); + + + +namespace Victor { +namespace Phylo { + typedef map Sequences; + + // For some unknown reasons, matrix cannot be initialized statically (althought + // it is a static member). A good place is the constructor. + SubMatrix FengDoolittle::matrix; + const FitchMargoliash FengDoolittle::build_tree; + + + FengDoolittle::FengDoolittle(const double gap_open, const double gap_extension) + : gap_function(*new AGPFunction(gap_open, gap_extension)) { + matrix = init_matrix(); + } + + + + FengDoolittle::FengDoolittle(const FengDoolittle &origin) + : gap_function(origin.gap_function) { + } + + + + FengDoolittle::~FengDoolittle() { + } + + + + MultipleAlignment & + FengDoolittle::apply(const AlignmentBase &alignment) const { + // Reads sequences + Sequences sequences = Sequence::toMap(alignment); + + // Computes distance matrix (pairwise alignment) + FengDoolittleDistance build_matrix(matrix, gap_function); + DistanceMatrix d = build_matrix(alignment); + + // Computes guide tree + RootedTree guide_tree = build_tree(d).asRootedTree(); + + // Progressive alignments + return align(sequences, guide_tree); + } + + + + MultipleAlignment & + FengDoolittle::align( + Sequences &sequences, + const RootedTree &node) const { + //////////////////////////////////////////////////////////////// + // Single sequence: trivially aligned + if (node.isLeaf()) { + const string identifier = node.getLabel(), + residues = sequences[identifier]; + return *(new MultipleAlignment(Sequence(identifier, residues))); + } + + + //////////////////////////////////////////////////////////////// + // Single inheritance: straightforward + if (node.getChildrenNumber() == 1) { + return align(sequences, node[0]); + } + + + //////////////////////////////////////////////////////////////// + // Two MSAs: performs alignment + const MultipleAlignment A = align(sequences, node[0]), + B = align(sequences, node[1]); + double max_score = -999999.0; + string horizontal, vertical; + + +#if VERBOSE==1 + cout << "Now aligning:" << endl; + for (size_t i = 0; i < A.getSize(); i++) { + cout << A.getSequence(i).getIdentifier() << endl; + } + cout << "---------- against ----------" << endl; + for (size_t j = 0; j < B.getSize(); j++) { + cout << B.getSequence(j).getIdentifier() << endl; + } + cout << endl << endl; +#endif + + + // Finds best alignment + for (size_t i = 0; i < A.getSize(); i++) { + const string seqA = replace_gaps(A.getSequence(i).getResidues()); + for (size_t j = 0; j < B.getSize(); j++) { + const string seqB = replace_gaps(B.getSequence(j).getResidues()); + + AlignmentData *data = new SequenceData(2, seqA, seqB, "", ""); + ScoringS2S scoring_scheme(&matrix, data, nullptr, 1.0); + NWAlign nw_align(data, &gap_function, &scoring_scheme); + const double score = nw_align.getScore(); + + if (score > max_score) { + max_score = score; + horizontal = nw_align.getMatch()[0]; + vertical = nw_align.getMatch()[1]; + } + } + } + + + // Builds a new MSA using best alignment + vector new_sequences; + for (size_t i = 0; i < A.getSize(); i++) { + const string identifier = A.getSequence(i).getIdentifier(), + sequence = A.getSequence(i).getResidues(); + size_t cursor = 0; + string residues = ""; + for (char residue : horizontal) { + residues += (residue != '-') ? sequence[cursor++] : '-'; + } + new_sequences.push_back(Sequence(identifier, residues)); + } + + for (size_t i = 0; i < B.getSize(); i++) { + const string identifier = B.getSequence(i).getIdentifier(), + sequence = B.getSequence(i).getResidues(); + size_t cursor = 0; + string residues = ""; + for (char residue : vertical) { + residues += (residue != '-') ? sequence[cursor++] : '-'; + } + new_sequences.push_back(Sequence(identifier, residues)); + } + + + // Returns multiple alignmnet + return *(new MultipleAlignment(new_sequences)); + } + +} // namespace Phylo +} // namespace Victor + + + +//////////////////////////////////////////////////////////////////////// +// Support functions +static string &replace_gaps(const string &sequence) { + string *new_sequence = new string(); + + for (char residue : sequence) { + (*new_sequence) += (residue != '-') ? residue : 'X'; + } + + return *new_sequence; +} + + + +static SubMatrix &init_matrix() { + SubstitutionMatrix m(SubstitutionMatrix::PAM250); + return (m - m.getMinScore()).asSubMatrix(); +} \ No newline at end of file diff --git a/Phylo/Sources/FengDoolittle.h b/Phylo/Sources/FengDoolittle.h new file mode 100644 index 0000000..41cb499 --- /dev/null +++ b/Phylo/Sources/FengDoolittle.h @@ -0,0 +1,105 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_FENGDOOLITTLE_H_ +#define _VICTOR_PHYLO_FENGDOOLITTLE_H_ + +#define _GLIBCXX_IOMANIP +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor::Align2; + +namespace Victor { +namespace Phylo { + +/** @brief Implements the Feng and Doolittle multiple sequence + * alignment algorithm. + * + * Implements Feng-Doolittle as a functor. + * Feng-Doolittle is a progressive multiple sequence alignment program. + * For more information see: + * - Progressive Sequence Alignment as a Prerequisite to Correct + * Phylogenetic Trees + * + * This class follows the Strategy and the Facade Design Patterns. + * + * @author Marco Zanella + */ +class FengDoolittle: public MultipleAlignmentAlgorithm { + public: + /** @brief Builds a Feng-Doolittle aligner with given configuration. + * @param[in] gap_open Gap opening penalty (default: 10.0) + * @param[in] gap_extension Gap extension penalty (default: 0.1) + */ + explicit FengDoolittle( + const double gap_open = 10.0, + const double gap_extension = 0.1); + + /** @brief Copy constructor. + * @param[in] origin Original Feng-Doolittle aligner + */ + explicit FengDoolittle(const FengDoolittle &origin); + + /** @brief Destructor. */ + ~FengDoolittle(); + + + + /** @brief Builds an MSA from a set of sequences. + * @param[in] alignment Set of sequences + * @return Multiple sequence alignment + */ + virtual MultipleAlignment &apply(const AlignmentBase &alignment) const; + + + + private: + typedef map Sequences; ///< Set of sequences + + static SubMatrix matrix; ///< Substitution matix + static const FitchMargoliash build_tree; ///< Clustering algorithm + + AGPFunction &gap_function; ///< Gap function + + + /** @brief Aligns next nodes in the guide tree. + * @param[in] sequences Sequences to align + * @param[in] node Next node of the guide tree + * @return Multiple sequence alignment + */ + MultipleAlignment &align( + Sequences &sequences, + const RootedTree &node) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_FENGDOOLITTLE_H_ \ No newline at end of file diff --git a/Phylo/Sources/FengDoolittleDistance.cc b/Phylo/Sources/FengDoolittleDistance.cc new file mode 100644 index 0000000..b7dc632 --- /dev/null +++ b/Phylo/Sources/FengDoolittleDistance.cc @@ -0,0 +1,74 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include +#include + +namespace Victor { +namespace Phylo { + FengDoolittleDistance::FengDoolittleDistance( + SubMatrix &matrix, + GapFunction &gap) + : substitution_matrix(matrix), gap_function(gap) { + } + + + + FengDoolittleDistance::FengDoolittleDistance(const FengDoolittleDistance &origin) + : FengDoolittleDistance(origin.substitution_matrix, origin.gap_function) { + } + + + + FengDoolittleDistance::~FengDoolittleDistance() { + } + + + + double + FengDoolittleDistance::computeDistance(const string &seq1, const string &seq2) const { + string r1 = seq1, r2 = seq2; + + std::random_shuffle(r1.begin(), r1.end()); + std::random_shuffle(r2.begin(), r2.end()); + + const double S_x = computeScore(seq1, seq1), + S_y = computeScore(seq2, seq2), + S_xy = computeScore(seq1, seq2), + S_r = computeScore(r1, r2), + d = 2.0 * (S_xy - S_r) / (S_x + S_y + 2.0 * S_r); + + return -log((d > 0.0) ? d : 1.0); + } + + + + double + FengDoolittleDistance::computeScore(const string &seq1, const string &seq2) const { + AlignmentData *alignment_data = new SequenceData(2, seq1, seq2, "", ""); + Structure *structure = nullptr; + const double cSeq = 1.0; + ScoringS2S scoring_scheme(&substitution_matrix, alignment_data, structure, cSeq); + NWAlign align(alignment_data, &gap_function, &scoring_scheme); + + return align.getScore(); + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/FengDoolittleDistance.h b/Phylo/Sources/FengDoolittleDistance.h new file mode 100644 index 0000000..3d9d3da --- /dev/null +++ b/Phylo/Sources/FengDoolittleDistance.h @@ -0,0 +1,85 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_FENGDoolittleDISTANCE_H_ +#define _VICTOR_PHYLO_FENGDoolittleDISTANCE_H_ + +#define _GLIBCXX_IOMANIP +#include +#include +#include + +namespace Victor { +namespace Phylo { + +/** @brief Builds a distance matrix using the Feng-Doolittle algorithm. + * + * Compute pairwise alignment for every pair of sequences, then creates + * the distance matrix using the formula proposed by Feng and Doolittle: + * D(x, y) = -log( ((S(x, y) - Srand) / (S(x, x)/2 + S(y, y)/2 - Srand) ). + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class FengDoolittleDistance: public DistanceMatrixBuilder { + public: + /** @brief Builds a Feng-Doolittle distance metrics with given paramters. + * + * Stores information about wich subsitution matrix to use (example: + * PAM260, BLOSUM50...) and which gap function to use. + * @param[in] matrix Substitution matrix to use + * @param[in] gap Gap function to use + */ + explicit FengDoolittleDistance(SubMatrix &matrix, GapFunction &gap); + + /** @brief Copy constructor. + * @param[in] origin Original Feng-Doolittle object + */ + explicit FengDoolittleDistance(const FengDoolittleDistance &origin); + + /** @brief Destructor. */ + ~FengDoolittleDistance(); + + + + private: + SubMatrix &substitution_matrix; ///< Substitution matrix + GapFunction &gap_function; ///< Gap function + + + /** @brief Returns distance between two sequences. + * @param[in] seq1 First sequence + * @param[in] seq2 Second sequence + * @return Distance between seq1 and seq2 + * @todo S_r is not computed due to complete lack of documentation + */ + virtual double computeDistance(const string &seq1, const string &seq2) const; + + + + /** @brief Performs alignment and returns score. + * @param[in] seq1 First sequence + * @param[in] seq2 Second sequence + * @return Score of the alignment + */ + double computeScore(const string &seq1, const string &seq2) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_FENGDoolittleDISTANCE_H_ \ No newline at end of file diff --git a/Phylo/Sources/FitchMargoliash.cc b/Phylo/Sources/FitchMargoliash.cc new file mode 100644 index 0000000..b84c993 --- /dev/null +++ b/Phylo/Sources/FitchMargoliash.cc @@ -0,0 +1,224 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include + +using Victor::Phylo::DistanceMatrix; + +/** @brief Returns distance between two clusters of nodes. + * @param[in] in_X Set of (names of) nodes in X + * @param[in] in_O Set of (names of) nodes in O + * @param[in] d Reference distance matrix + */ +static double d_XO( + const set &in_X, + const set &in_O, + const DistanceMatrix &d); + +/** @brief Returns union of sets. + * @param[in] A First set + * @param[in] B Second set + * @return Set union between A and B: A U B + */ +template +set set_union(const set &A, const set &B); + +/** @brief Returns difference of sets. + * + * This is a more comfortable inteface to the std set difference function + * which, unfortunately, does not seems a set difference function at all. + * @param[in] A First set + * @param[in] B Second set + * @return Set difference between A and B: A - B + */ +template +set set_difference(const set &A, const set &B); + + + +namespace Victor { +namespace Phylo { + typedef UnrootedTree::Node Node; + + + FitchMargoliash::~FitchMargoliash() { + } + + + + UnrootedTree & + FitchMargoliash::apply(const DistanceMatrix &matrix) const { + UnrootedTree *tree = new UnrootedTree(); + DistanceMatrix d = matrix; + set OTUs = matrix.getOTUs(); + map node_pool; + map size_pool; + map> sets_pool; + + + // Initializes leaves + for (auto &OTU : OTUs) { + Node *leaf = new Node(OTU); + node_pool[OTU] = leaf; + size_pool[OTU] = 1; + sets_pool[OTU].insert(OTU); + tree->addNode(*leaf); + } + + + // Repeats until only three nodes are left + while (d.getSize() > 3) { + OTUs = d.getOTUs(); + set others; + + // Finds closest pair A and B, then join them into a new + // node R + const pair min_pos = d.getMinimumPosition(); + const string A = min_pos.first, + B = min_pos.second, + R = A + "+" + B; + Node *r = new Node(); + node_pool[R] = r; + size_pool[R] = size_pool[A] + size_pool[B]; + sets_pool[R] = set_union(sets_pool[A], sets_pool[B]); + others = set_difference(matrix.getOTUs(), sets_pool[R]); + tree->addNode(*r); + + + // Calculates distances among A, B and the other nodes (O) + const double d_AB = d(A, B), + d_AO = d_XO(sets_pool[A], others, matrix), + d_BO = d_XO(sets_pool[B], others, matrix); + + + // Calculates distances betwen R and A (a), R and B (b), R + // and the other nodes (c) + const double a = std::max(0.5 * (d_AO + d_AB - d_BO), 0.0), + b = std::max(0.5 * (d_BO + d_AB - d_AO), 0.0); + //c = abs(0.5 * (d_AO + d_BO - d_AB)); + + + // Set distances among A, B, R + r->addNeighbor(*node_pool[A], a); + r->addNeighbor(*node_pool[B], b); + + + // Updates distance matrix + for (auto &K : OTUs) { + if (K == A || K == B) continue; + const double d_RK = 0.5 * (d(A, K) + d(B, K)); + d(R, K, d_RK); + } + + + // Removes "consumed" OTUs and adds newly generated one + d.unsetDistance(A) + .unsetDistance(B) + .removeOTU(A) + .removeOTU(B) + .addOTU(R); + } + + + // If there are only three nodes left, the operation is trivial + if (d.getSize() == 3) { + vector OTUs; + for (auto &OTU : d.getOTUs()) { + OTUs.push_back(OTU); + } + + const string A = OTUs[0], + B = OTUs[1], + C = OTUs[2]; + const double a = std::max(0.5 * (d(A, B) + d(A, C) - d(B, C)), 0.0), + b = std::max(0.5 * (d(A, B) + d(B, C) - d(A, C)), 0.0), + c = std::max(0.5 * (d(A, C) + d(B, C) - d(A, B)), 0.0); + + Node *r = new Node(); + tree->addNode(*r); + r->addNeighbor(*node_pool[A], a); + r->addNeighbor(*node_pool[B], b); + r->addNeighbor(*node_pool[C], c); + } + + // If there were only two nodes in the matrix, operation is trivial + if (d.getSize() == 2) { + vector OTUs; + for (auto &OTU : d.getOTUs()) { + OTUs.push_back(OTU); + } + + const string A = OTUs[0], + B = OTUs[1]; + + Node *r = new Node(); + tree->addNode(*r); + r->addNeighbor(*node_pool[A], d(A, B) / 2.0); + r->addNeighbor(*node_pool[B], d(A, B) / 2.0); + } + + return *tree; + } + +} // namespace Phylo +} // namespace Victor + + + +//////////////////////////////////////////////////////////////////////// +// Support (local) functions +static double d_XO( + const set &in_X, + const set &in_O, + const DistanceMatrix &d) { + const size_t N_X = in_X.size(), + N_O = in_O.size(); + double d_xo = 0.0; + + for (auto &x : in_X) { + for (auto &o : in_O) { + d_xo += d(x, o); + } + } + d_xo /= (N_X * N_O); + + return d_xo; +} + + + +template +set set_union(const set &A, const set &B) { + set C = A; + C.insert(B.begin(), B.end()); + return C; +} + + + +template +set set_difference(const set &A, const set &B) { + set result; + + std::set_difference( + A.begin(), A.end(), B.begin(), B.end(), + std::inserter(result, result.end()) + ); + + return result; +} \ No newline at end of file diff --git a/Phylo/Sources/FitchMargoliash.h b/Phylo/Sources/FitchMargoliash.h new file mode 100644 index 0000000..dd06da8 --- /dev/null +++ b/Phylo/Sources/FitchMargoliash.h @@ -0,0 +1,58 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_FITCHMARGOLIASH_H_ +#define _VICTOR_PHYLO_FITCHMARGOLIASH_H_ + +#include +#include + +namespace Victor { +namespace Phylo { + +/** @brief Implements the Fitch-Margoliash clustering algorithm. + * + * Implements Fitch-Margoliash as a functor. + * Fitch-Margoliash algorithm is a bottom-up agglomerative method for + * the creation of phylogenetic trees. This algorithm requires knowledge + * about the distance between each pair of taxa (e.g. species or + * sequences) in order to build the tree. + * + * For more information see: + * - Contruction of Phylogenetic Trees (Fitch and Margoliash) + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class FitchMargoliash: public ClusteringAlgorithm { + public: + /** @brief Destructor. */ + ~FitchMargoliash(); + + + + /** @brief Builds a phylogenetic tree from given distance matrix. + * @param[in] matrix Distance matrix + * @return Phylogenetic tree + */ + virtual UnrootedTree &apply(const DistanceMatrix &matrix) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_FITCHMARGOLIASH_H_ \ No newline at end of file diff --git a/Phylo/Sources/IdentityPercentage.cc b/Phylo/Sources/IdentityPercentage.cc new file mode 100644 index 0000000..5c9ac3d --- /dev/null +++ b/Phylo/Sources/IdentityPercentage.cc @@ -0,0 +1,64 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include + +namespace Victor { +namespace Phylo { + IdentityPercentage::IdentityPercentage( + SubMatrix &matrix, + GapFunction &gap) + : substitution_matrix(matrix), gap_function(gap) { + } + + + + IdentityPercentage::IdentityPercentage(const IdentityPercentage &origin) + : IdentityPercentage(origin.substitution_matrix, origin.gap_function) { + } + + + + IdentityPercentage::~IdentityPercentage() { + } + + + + double + IdentityPercentage::computeDistance(const string &seq1, const string &seq2) const { + return 1.0 - identityPercentage(seq1, seq2); + } + + + + double + IdentityPercentage::identityPercentage(const string &seq1, const string &seq2) const { + AlignmentData *alignment_data = new SequenceData(2, seq1, seq2, "", ""); + ScoringS2S scoring_scheme(&substitution_matrix, alignment_data, nullptr, 1.0); + AlignmentBase alignment; + + NWAlign align(alignment_data, &gap_function, &scoring_scheme); + + vector result = align.getMatch(); + + return alignment.calculatePairwiseIdentity(result[0], result[1]); + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/IdentityPercentage.h b/Phylo/Sources/IdentityPercentage.h new file mode 100644 index 0000000..6192aba --- /dev/null +++ b/Phylo/Sources/IdentityPercentage.h @@ -0,0 +1,87 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_IDENTITYPERCENTAGE_H_ +#define _VICTOR_PHYLO_IDENTITYPERCENTAGE_H_ + +#define _GLIBCXX_IOMANIP +#include +#include +#include + +namespace Victor { +namespace Phylo { + +/** @brief Builds a distance matrix by considering percentage of identity. + * + * Compute pairwise alignment for every pair of sequences, then creates + * the distance matrix using percentage of identity. The distance is + * estimated as 1 - % of identity. + * Percentage of identity is defined as the number of identical residues + * (not considering gaps) divided by the length of the longest sequence + * (not considering gaps). + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class IdentityPercentage: public DistanceMatrixBuilder { + public: + /** @brief Builds an identity percentage metrics with given configuration. + * + * Stores information about wich subsitution matrix to use (example: + * PAM260, BLOSUM50...) and which gap function to use. + * @param[in] matrix Substitution matrix to use + * @param[in] gap Gap function to use + */ + explicit IdentityPercentage(SubMatrix &matrix, GapFunction &gap); + + /** @brief Copy constructor. + * @param[in] origin Original object + */ + explicit IdentityPercentage(const IdentityPercentage &origin); + + /** @brief Destructor. */ + virtual ~IdentityPercentage(); + + + + private: + SubMatrix &substitution_matrix; ///< Substitution matrix + GapFunction &gap_function; ///< Gap function + + + /** @brief Returns distance between two sequences. + * @param[in] seq1 First sequence + * @param[in] seq2 Second sequence + * @return Distance between seq1 and seq2 + */ + virtual double computeDistance(const string &seq1, const string &seq2) const; + + /** @brief Returns percentage of identity between two sequences. + * + * Percentage of identity is returned as a number in [0; 1]. + * @param[in] seq1 First sequence + * @param[in] seq2 Second sequence + * @return Percentage of identity between seq1 and seq2 + */ + double identityPercentage(const string &seq1, const string &seq2) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_IDENTITYPERCENTAGE_H_ \ No newline at end of file diff --git a/Phylo/Sources/LevenshteinDistance.cc b/Phylo/Sources/LevenshteinDistance.cc new file mode 100644 index 0000000..d3b141f --- /dev/null +++ b/Phylo/Sources/LevenshteinDistance.cc @@ -0,0 +1,62 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include + +namespace Victor { +namespace Phylo { + LevenshteinDistance::~LevenshteinDistance() { + } + + + + double + LevenshteinDistance::computeDistance(const string &seq1, const string &seq2) const { + const size_t m = seq1.size(); + const size_t n = seq2.size(); + + if (m == 0) return n; + if (n == 0) return m; + + size_t *costs = new size_t[n + 1]; + + // Initializes cost vector + for (size_t k = 0; k <= n; k++) + costs[k] = k; + + // Computes distances + for (size_t i = 0; i < m; i++) { + size_t corner = i; + costs[0] = i + 1; + + for (size_t j = 0; j < n; j++) { + size_t upper = costs[j + 1]; + + costs[j + 1] = (seq1[i] == seq2[j]) + ? corner + : min(costs[j], min(upper, corner)) + 1; + + corner = upper; + } + } + + double distance = (double) costs[n]; + delete [] costs; + + return distance; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/LevenshteinDistance.h b/Phylo/Sources/LevenshteinDistance.h new file mode 100644 index 0000000..cf310a1 --- /dev/null +++ b/Phylo/Sources/LevenshteinDistance.h @@ -0,0 +1,53 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_LEVENSHTEINDISTANCE_H_ +#define _VICTOR_PHYLO_LEVENSHTEINDISTANCE_H_ + +#include + +namespace Victor { +namespace Phylo { + +/** @brief Builds a distance matrix by considering Levenshtein distance. + * + * Compute pairwise alignment for every pair of sequences, then creates + * the distance matrix using Levenshtein distance. + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class LevenshteinDistance: public DistanceMatrixBuilder { + public: + /** @brief Destructor. */ + virtual ~LevenshteinDistance(); + + + + private: + /** @brief Returns distance between two sequences. + * @param[in] seq1 First sequence + * @param[in] seq2 Second sequence + * @return Distance between seq1 and seq2 + */ + virtual double computeDistance(const string &seq1, const string &seq2) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_LEVENSHTEINDISTANCE_H_ \ No newline at end of file diff --git a/Phylo/Sources/Makefile b/Phylo/Sources/Makefile new file mode 100644 index 0000000..4a75531 --- /dev/null +++ b/Phylo/Sources/Makefile @@ -0,0 +1,68 @@ +#--*-makefile-*----------------------------------------------------------------- +# +# Standard makefile - Phylo +# +#------------------------------------------------------------------------------- + +# Path to project directory +PROJECT_ROOT = ../.. +BINPATH = $(PROJECT_ROOT)/bin/ +LIBPATH = $(PROJECT_ROOT)/lib/ +UPDIR = $(PROJECT_ROOT) +SUBDIR = + + + +# +# Libraries and paths (which are not defined globally) +# + +LIBS = +INC_PATH = -I. +LIB_PATH = -L. + + + +# +# Objects and headers +# + +SOURCES = PhylogeneticTree.cc RootedTree.cc UnrootedTree.cc NewickParser.cc \ + Sequence.cc AminoAcid.cc SubstitutionMatrix.cc \ + DistanceMatrix.cc DistanceMatrixBuilder.cc \ + IdentityPercentage.cc LevenshteinDistance.cc FengDoolittleDistance.cc \ + FitchMargoliash.cc UPGMA.cc NJ.cc \ + MultipleAlignment.cc \ + FengDoolittle.cc ClustalW.cc +OBJECTS = PhylogeneticTree.o RootedTree.o UnrootedTree.o NewickParser.o \ + Sequence.o AminoAcid.o SubstitutionMatrix.o \ + DistanceMatrix.o DistanceMatrixBuilder.o \ + IdentityPercentage.o LevenshteinDistance.o FengDoolittleDistance.o \ + FitchMargoliash.o UPGMA.o NJ.o \ + MultipleAlignment.o \ + FengDoolittle.o ClustalW.o +TARGETS = +EXECS = +LIBRARY = libPhylo.a + + + +# +# Install rule +# + +compile: all + +all: install +install: $(LIBRARY) $(TARGETS) + mv $(LIBRARY) $(LIBPATH) + + + +# +# Call global Makefile to do the job +# +include ../../Makefile.global + +# Overriding to use C++11 +STANDARDFLAGS = -Wall -Wextra -pedantic -std=c++0x -DNEXCEPTIONS -DLINUX -c diff --git a/Phylo/Sources/MultipleAlignment.cc b/Phylo/Sources/MultipleAlignment.cc new file mode 100644 index 0000000..ba2e358 --- /dev/null +++ b/Phylo/Sources/MultipleAlignment.cc @@ -0,0 +1,358 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#define HYDROPHILIC_RANGE 5 +#define HYDROPHILIC_RESIDUES "DEGKNQPRS" +#include +#include + +/** @brief Tells whether a residue is a hydrophiic residue. + * @param[in] residue Residue to check + * @retval true Residue is hydrophilic + * @retval false Residue is not hydrophilic + */ +static bool is_hydrophiic_residue(const char residue) { + for (char r : HYDROPHILIC_RESIDUES) { + if (residue == r) { + return true; + } + } + + return false; +} + + + +/** @brief Tells whether a sequence has a hydrophilic stretch. + * @param[in] sequence Sequence to check + * @param[in] position Position to check + * @retval true The sequence has a hydrophilic stretch + * @retval false The sequence has not hydrophilic stretches + */ +static bool has_hydrophilic_stretch(const string &sequence, const size_t position) { + size_t start = position - HYDROPHILIC_RANGE, + end = position + HYDROPHILIC_RANGE; + bool found = false; + + if (start > sequence.size()) start = 0; + if (end > sequence.size()) end = 0; + + bool previous = false; + size_t p = start, consecutives = 0; + while (!found && p < end) { + if (is_hydrophiic_residue(sequence[p])) { + if (previous) { + consecutives++; + } + previous = true; + } else { + consecutives = 0; + previous = false; + } + + found = consecutives == HYDROPHILIC_RANGE; + p++; + } + + return found; +} + + + +namespace Victor { +namespace Phylo { + const string MultipleAlignment::residues = "ARNDCQEGHILKMFPSTWYVUBZX-"; + + + MultipleAlignment::MultipleAlignment(const vector &sequences) + : sequences(sequences) { + } + + + + MultipleAlignment::MultipleAlignment(const Sequence &sequence) { + sequences.push_back(sequence); + } + + + + MultipleAlignment::MultipleAlignment() { + MultipleAlignment(vector()); + } + + + + MultipleAlignment::~MultipleAlignment() { + } + + + + void + MultipleAlignment::operator=(const MultipleAlignment &other) { + sequences = other.sequences; + } + + + + bool + MultipleAlignment::isEmpty() const { + return getSize() == 0; + } + + + + bool + MultipleAlignment::hasSequence(const string &identifier) const { + return getSequence(identifier) < getSize(); + } + + + + bool + MultipleAlignment::hasHydrophilicStretch(const size_t position) const { + bool found = false; + + size_t i = 0; + while (!found && i < getSize()) { + const string &sequence = getSequence(i).getResidues(); + found = has_hydrophilic_stretch(sequence, position); + i++; + } + + return found; + } + + + + size_t + MultipleAlignment::getSize() const { + return sequences.size(); + } + + + + size_t + MultipleAlignment::getLength() const { + return (!isEmpty()) ? getSequence(0).getResidues().size() : 0; + } + + + + Sequence + MultipleAlignment::getSequence(const size_t index) const { + return (index < getSize()) ? sequences[index] : Sequence("", ""); + } + + + + size_t + MultipleAlignment::getSequence(const string &identifier) const { + size_t index = 0; + + for (index = 0; index < getSize(); index++) { + if (getSequence(index).getIdentifier() == identifier) { + return index; + } + } + + return index; + } + + + + string & + MultipleAlignment::getResidues(const size_t position) const { + char *s = new char[getSize()]; + size_t idx = 0; + + if (position < getLength()) { + for (auto &sequence : sequences) { + s[idx++] = sequence.getResidue(position); + } + } + + return *(new string(s)); + } + + + + size_t + MultipleAlignment::getResiduesNumber(const size_t position) const { + return getResidues(position).size(); + } + + + + size_t + MultipleAlignment::getNonGapNumber(const size_t position) const { + return getResiduesNumber(position) - getGapNumber(position); + } + + + + size_t + MultipleAlignment::getGapNumber(const size_t position) const { + return getCount('-', position); + } + + + + size_t + MultipleAlignment::getCount( + const char residue, + const size_t position) const { + size_t count = 0; + + for (auto &sequence : sequences) { + count += sequence.getResidue(position) == residue; + } + + return count; + } + + + + double + MultipleAlignment::getFrequency( + const char residue, + const size_t position) const { + return (getResiduesNumber(position) != 0) + ? (double) getCount(residue, position) / (double) getResiduesNumber(position) + : 0.0; + } + + + + map & + MultipleAlignment::getFrequencies(const size_t position) const { + map *frequencies = new map(); + + for (char residue : residues) { + (*frequencies)[residue] = getFrequency(residue, position); + } + + return *frequencies; + } + + + + double + MultipleAlignment::getPercentIdentity() const { + size_t conserved = 0; + + for (size_t j = 0; j < getSize(); j++) { + const string column = getResidues(j); + size_t i = 1; + bool is_conserved = true; + while (is_conserved && i < getSize()) { + is_conserved &= column[i] == column[0]; + i++; + } + conserved += is_conserved ? 1 : 0; + } + + return (double) conserved / getLength(); + } + + + + char + MultipleAlignment::getConsensus(const size_t position) const { + char consensus = '-'; + size_t max_count = 0; + + for (char residue : residues) { + if (residue == '-') continue; + const size_t count = getCount(residue, position); + + if (count > max_count) { + max_count = count; + consensus = residue; + } + } + + return consensus; + } + + + + string & + MultipleAlignment::getConsensus() const { + string *consensus = new string(); + + for (size_t i = 0; i < getLength(); i++) { + (*consensus) += getConsensus(i); + } + + return *consensus; + } + + + + string & + MultipleAlignment::asString() const { + size_t longest_name = 0; + string *result = new string(); + vector names(getSize()); + vector positions(getSize()); + + // Finds longest name of sequence + for (size_t i = 0; i < getSize(); i++) { + const size_t length = getSequence(i).getIdentifier().size(); + longest_name = std::max(longest_name, length); + } + + // Pads names + for (size_t i = 0; i < getSize(); i++) { + const string identifier = getSequence(i).getIdentifier(); + string name = identifier; + for (size_t j = identifier.size(); j < longest_name; j++) { + name += " "; + } + name += " "; + names[i] = name; + } + + // Prints data + for (size_t j = 0; j < getLength(); j += 50) { + for (size_t i = 0; i < getSize(); i++) { + bool print_positions = false; + (*result) += names[i]; + for (size_t k = 0; k < 50 && j + k < getLength(); k++) { + const char symbol = getSequence(i).getResidues()[j + k]; + (*result) += symbol; + positions[i] += (symbol != '-'); + print_positions |= (symbol != '-'); + } + if (print_positions) { + (*result) += " " + to_string(positions[i]); + } + (*result) += "\n"; + } + (*result) += "\n\n"; + } + + return *result; + } + + + + void + MultipleAlignment::saveClustalW(ostream &output) const { + output << asString() << endl; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/MultipleAlignment.h b/Phylo/Sources/MultipleAlignment.h new file mode 100644 index 0000000..bac8253 --- /dev/null +++ b/Phylo/Sources/MultipleAlignment.h @@ -0,0 +1,225 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_MULTIPLEALIGNMENT_H_ +#define _VICTOR_PHYLO_MULTIPLEALIGNMENT_H_ + +#include +#include +#include +#include + +using std::string; +using std::pair; +using std::vector; +using std::map; + +namespace Victor { +namespace Phylo { + +/** @brief A multiple sequence alignment (MSA). + * + * MSAs holds information about alignments of a set of sequences. + * + * @author Marco Zanella + */ +class MultipleAlignment { +public: + /** @brief Builds an MSA from a set of sequences. + * @param[in] sequences Sequences in the MSA + */ + explicit MultipleAlignment(const vector &sequences); + + /** @brief Builds an MSA from a single sequence. + * @param[in] sequence Sequence + */ + explicit MultipleAlignment(const Sequence &sequence); + + /** @brief Default constructor. + * + * Produces an empty MSA. + */ + MultipleAlignment(); + + /** @brief Destructor. */ + ~MultipleAlignment(); + + + + /** @brief Assignment operator. + * @param[in] other MultipleAlignment to copy + */ + void operator=(const MultipleAlignment &other); + + + + /** @brief Tells whether the MSA is empty. + * + * An MSA is empty when it contains no sequences. + * @retval true This MSA is empty + * @retval false This MSA is not empty + */ + bool isEmpty() const; + + /** @brief Tells whether this MSA contains a sequence with given identifier. + * @param[in] identifier An identifier + * @retval true This MSA contains data about given sequence + * @retval false This MSA does not contain data about given sequence + */ + bool hasSequence(const string &identifier) const; + + /** @brief Tells whether this MSA has a hydrophilic stretch. + * @param[in] position Position to check + * @retval true This MSA contains a hydrophilic stretch + * @retval false This MSA does not contain a hydrophilic stretch + */ + bool hasHydrophilicStretch(const size_t position) const; + + + + /** @brief Returns number of sequences in this MSA. + * @return Number of sequences in this MSA. + */ + size_t getSize() const; + + /** @brief Returns length of the MSA. + * + * The length of an MSA is the length of its sequences (including gaps). + * Every sequence has the same length, by construction. + * @return Length of this multiple alignment + */ + size_t getLength() const; + + /** @brief Returns sequence at given index. + * + * If index is invalid, returns an empty sequence. + * @param[in] index Index of the sequence + * @return Sequence at given index + */ + Sequence getSequence(const size_t index) const; + + /** @brief Returns index of given sequence. + * + * Searches a sequence with given identifier and returns its index in this + * MSA. If sequence is not found, returns an invalid index (greater than + * or equal to the size of this MSA). + * @param[in] identifier Identifier of the sequence + * @return Index of the found sequence, or an invalid position + */ + size_t getSequence(const string &identifier) const; + + /** @brief Returns residues at given position. + * + * Returns a string containing residues (or gaps) at given column of this + * MSA. + * + * If position is invalid, returns an empty string. + * @param[in] position Index of the columng. + * @return Residues at given position + */ + string &getResidues(const size_t position) const; + + /** @brief Returns number of residues (or gaps) at given position. + * + * If position is invalid, returns 0. + * @param[in] position Index of the column + * @return Number of residues at given column of this MSA + */ + size_t getResiduesNumber(const size_t position) const; + + /** @brief Returns number of non-gaps at given position. + * + * If position is invalid, returns 0. + * @param[in] position Index of the column + * @return Number of non-gaps at given column of this MSA + */ + size_t getNonGapNumber(const size_t position) const; + + /** @brief Returns number of gaps at given position. + * + * If position is invalid, returns 0. + * @param[in] position Index of the column + * @return Number of gaps at given column of this MSA + */ + size_t getGapNumber(const size_t position) const; + + /** @brief Returns number of occurencies of given residues at given position. + * + * If residue or position are invalid, returns 0. + * @param[in] residue Residue to find + * @param[in] position Index of the column + * @return Number of occurencies of given residue at given position + */ + size_t getCount(const char residue, const size_t position) const; + + /** @brief Returns frequency of given residue at given position. + * + * If residue or position are invalid, returns 0. + * @param[in] residue Residue to find + * @param[in] position Index of the column + * @return Frequency of given residue at given position + */ + double getFrequency(const char residue, const size_t position) const; + + /** @brief Returns the map of frequencies for given position. + * + * Keys of the map are residues (or gap), values are their frequencies. + * + * If position is invalid, frequencies in the map are 0. + * @param[in] position Index of the column + * @return Map of frequencies + */ + map &getFrequencies(const size_t position) const; + + /** @brief Returns percent identity of this multiple alignment. + * @return Percent identity + */ + double getPercentIdentity() const; + + /** @brief Returns consensus residue. + * @param[in] position Position to use + * @return Consensus + */ + char getConsensus(const size_t position) const; + + /** @brief Returns consensus sequence. + * @return Consensus + */ + string &getConsensus() const; + + + + /** @brief Returns a string version of this multiple alignment. + * @return This multiple sequence alignment as a string + */ + string &asString() const; + + /** @brief Exports this multiple sequence alignment. + * @param[out] output Stream to write output to + */ + void saveClustalW(ostream &output) const; + + + +private: + static const string residues; ///< Every possible residue + vector sequences; ///< Sequences in the MSA +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_MULTIPLEALIGNMENT_H_ \ No newline at end of file diff --git a/Phylo/Sources/MultipleAlignmentAlgorithm.h b/Phylo/Sources/MultipleAlignmentAlgorithm.h new file mode 100644 index 0000000..bdf9b78 --- /dev/null +++ b/Phylo/Sources/MultipleAlignmentAlgorithm.h @@ -0,0 +1,61 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_MULTIPLEALIGNMENTALGORITHM_H_ +#define _VICTOR_PHYLO_MULTIPLEALIGNMENTALGORITHM_H_ + +#include +#include + +using namespace Victor::Align2; + +namespace Victor { +namespace Phylo { + +/** @brief Implements a multiple sequence alignment algorithm. + * + * Multiple sequence alignment (MSA) algorithms produce MSAs by considering + * a set of sequences. + * + * MSA algorithms are implemented as functors from an alignment to a MSA. + * + * This class follows the Strategy and the Facade Design Patterns. + * + * @author Marco Zanella + */ +class MultipleAlignmentAlgorithm { + public: + /** @brief Builds an MSA from an alignment. + * @param[in] alignment The alignment + * @return Multiple sequence alignment + */ + inline MultipleAlignment &operator()(const AlignmentBase &alignment) { + return apply(alignment); + } + + + + /** @brief Builds an MSA from an alignment. + * @param[in] alignment The alignment + * @return Multiple sequence alignment + */ + virtual MultipleAlignment &apply(const AlignmentBase &alignment) const = 0; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_MULTIPLEALIGNMENTALGORITHM_H_ \ No newline at end of file diff --git a/Phylo/Sources/NJ.cc b/Phylo/Sources/NJ.cc new file mode 100644 index 0000000..d52ed0b --- /dev/null +++ b/Phylo/Sources/NJ.cc @@ -0,0 +1,115 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include + +using std::max; + +namespace Victor { +namespace Phylo { + typedef UnrootedTree::Node Node; + + + NJ::~NJ() { + } + + + + UnrootedTree & + NJ::apply(const DistanceMatrix &matrix) const { + UnrootedTree *tree = new UnrootedTree(); + DistanceMatrix d = matrix; + set OTUs = matrix.getOTUs(); + map node_pool; + + + // Initializes leaves + for (auto OTU : OTUs) { + Node *leaf = new Node(OTU); + node_pool[OTU] = leaf; + tree->addNode(*leaf); + } + + + // Repeats until every element in the matrix is consumed + while (!d.isEmpty()) { + // Calculates matrix Q, based on current distance matrix + DistanceMatrix Q; + OTUs = d.getOTUs(); + const size_t n = OTUs.size(); + for (auto i : OTUs) { + Q.addOTU(i); + for (auto j : OTUs) { + if (i == j) continue; + double q_ij, d_ik = 0.0, d_jk = 0.0; + for (auto k : OTUs){ + d_ik += d(i, k); + d_jk += d(j, k); + } + + q_ij = (n - 2) * d(i, j) - d_ik - d_jk; + q_ij = q_ij; + Q(i, j, q_ij); + } + } + + + // Finds f, g such that Q(f, g) is minimum (i != j), then + // joins them to a new node u + const pair min_pos = Q.getMinimumPosition(); + const string f = min_pos.first, + g = min_pos.second, + u = f + "+" + g; + Node *node = new Node(); + node_pool[u] = node; + tree->addNode(*node); + + + // Calculates distances between new node and merged ones. If + // there are only two nodes left, operation is trivial + if (2 == n) { + node->addNeighbor(*node_pool[f], d(f, g) / 2.0); + node->addNeighbor(*node_pool[g], d(f, g) / 2.0); + } else { + double delta_fu, delta_gu, d_fk = 0.0, d_gk = 0.0;; + for (auto k : OTUs) { + d_fk += d(f, k); + d_gk += d(g, k); + } + delta_fu = max(0.5 * d(f, g) + (1.0 / (2.0 * (n - 2))) * (d_fk - d_gk), 0.0); + delta_gu = max(d(f, g) - delta_fu, 0.0); + node->addNeighbor(*node_pool[f], delta_fu); + node->addNeighbor(*node_pool[g], delta_gu); + } + + + // Calculates distances from each OTU to the new node + for (auto k : OTUs) { + double d_uk = 0.5 * (d(f, k) + d(g, k) - d(f, g)); + d(u, k, d_uk); + } + + + // Removes "consumed" OTUs and adds newly generated one + d.removeOTU(f) + .removeOTU(g) + .addOTU(u); + } + + return *tree; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/NJ.h b/Phylo/Sources/NJ.h new file mode 100644 index 0000000..f8cc86c --- /dev/null +++ b/Phylo/Sources/NJ.h @@ -0,0 +1,59 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_NJ_H_ +#define _VICTOR_PHYLO_NJ_H_ + +#include +#include + +namespace Victor { +namespace Phylo { + +/** @brief Implements the NJ algorithm. + * + * Implements NJ as a functor. + * NJ (Neighbor Joining) is a bottom-up agglomerative clustering method + * for the creation of phylogenetic trees. This algorithm requires + * knowledge about the distance between each pair of taxa (e.g., species + * or sequences) to form the tree. + * + * For more information see: + * - The Neighbor-joining Method: A New Method for Reconstructing + * Phylogenetic Trees (Saitou and Nei) + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class NJ: public ClusteringAlgorithm { + public: + /** @brief Destructor. */ + virtual ~NJ(); + + + + /** @brief Builds a phylogenetic tree from given distance matrix. + * @param[in] matrix Distance matrix + * @return Phylogenetic tree + */ + virtual UnrootedTree &apply(const DistanceMatrix &matrix) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_NJ_ \ No newline at end of file diff --git a/Phylo/Sources/NewickParser.cc b/Phylo/Sources/NewickParser.cc new file mode 100644 index 0000000..b0c8afc --- /dev/null +++ b/Phylo/Sources/NewickParser.cc @@ -0,0 +1,261 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include + +#define SYNTAX_ERROR -1 + +using std::stringstream; + +namespace Victor { +namespace Phylo { + static const double NA = -1.0; + + + NewickParser::~NewickParser() { + } + + + + bool + NewickParser::isEmpty() const { + return input.empty(); + } + + + + bool + NewickParser::isNext(string character_set) const { + bool is_next = false; + + if (isEmpty()) { + return false; + } + + for (auto c : character_set) { + is_next |= c == input[0]; + } + + return is_next; + } + + + + char + NewickParser::getNext() const { + return (!isEmpty()) ? input[0] : '\0'; + } + + + + char + NewickParser::shift() { + char c = getNext(); + + if (!isEmpty()){ + input = input.substr(1); + } + + return c; + } + + + + void + NewickParser::error(const string &message) const { + std::cerr << "[Victor::Phylo::NewickParser Syntax error]: " + << message + << " near: \"" << input << "\"" + << std::endl; + exit(SYNTAX_ERROR); + } + + + + RootedTree & + NewickParser::parse(const string &input) { + this->input = input; + return parseNewick(); + } + + + + RootedTree & + NewickParser::parseNewick() { + RootedTree *newick; + + // Empty Newick file + if (isNext(";")) { + newick = new RootedTree(); + } + + // Recursvely parses file + else { + newick = parseTree(); + } + + // Consumes ";" and checks for errors. + shift(); + if (!isEmpty()) { + error("Stray character after last character"); + } + + return *newick; + } + + + + RootedTree * + NewickParser::parseTree() { + RootedTree *node; + + // Subtree + if (isNext("(")) { + vector children; + + shift(); + children.push_back(parseTree()); + parseSiblings(&children); + shift(); + node = parseNode(); + + for (auto child : children) { + node->addChild(*child); + } + } + + // Length only + else if (isNext(":")) { + double length = parseLength(); + node = new RootedTree(length); + } + + // Label and length + else { + string label = parseString(); + double length = parseLength(); + + node = (length != NA) + ? new RootedTree(length, label) + : new RootedTree(label); + } + + return node; + } + + + + void + NewickParser::parseSiblings(vector *siblings) { + // No more siblings + if (isNext(")")) { + return; + } + + // One more sibling + else if (isNext(",")) { + shift(); + siblings->push_back(parseTree()); + parseSiblings(siblings); + return; + } + + // Syntax error + else { + error("Error while parsing siblings"); + } + } + + + + RootedTree * + NewickParser::parseNode() { + string label = parseLabel(); + double length = parseLength(); + RootedTree *node = (length != NA) + ? new RootedTree(length, label) + : new RootedTree(label); + return node; + } + + + + string + NewickParser::parseLabel() { + return (!isNext(";):,")) ? parseString() : ""; + } + + + + double + NewickParser::parseLength() { + // A length is specified + if (isNext(":")) { + shift(); + return parseNumber(); + } + + // No length is specified + else if (isNext(";),")) { + return NA; + } + + // Syntax error + else { + error("Error while parsing number"); + return NA; + } + } + + + + string + NewickParser::parseString() { + string buffer = ""; + + // String is enclosed by double quotes + if (isNext("\"")) { + shift(); + while (!isEmpty() && !isNext("\"")) { + buffer += shift(); + } + shift(); + } + + // String is not enclosed by double quotes + else { + while (!isEmpty() && !isNext("):, ;")) { + buffer += shift(); + } + } + + return buffer; + } + + + + double + NewickParser::parseNumber() { + char *ptr; + double length = strtod(input.c_str(), &ptr); + + input = string(ptr); + + return length; + } + +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/NewickParser.h b/Phylo/Sources/NewickParser.h new file mode 100644 index 0000000..8a5ab5f --- /dev/null +++ b/Phylo/Sources/NewickParser.h @@ -0,0 +1,145 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_NEWICKPARSER_H_ +#define _VICTOR_PHYLO_NEWICKPARSER_H_ + +#include + +namespace Victor { +namespace Phylo { + +/** @brief Implements a parser for the Newick format. + * + * This parser recognizes the following LL(1) grammar: + * \verbatim + Newick ::= Tree; + | ; + Tree ::= (Tree Siblings) Node + | string Length + | :number + Siblings ::= , Tree Siblings + | + Node ::= Label Length + Label ::= string + | + Length ::= :number + | + \endverbatim + * Where string represents any alphanumeric sequence or any sequence + * of characters enclosed by double quotes, and number represents a + * floating point number. + * + * @note There is no official newick grammar. The one proposed here was + * built with reverse engeneering techniques. + * + * @author Marco Zanella + */ +class NewickParser { + public: + /** @brief Destructor. */ + virtual ~NewickParser(); + + + + /** @brief Parses a Newick string. + * @param[in] input Input string + * @return Rooted tree + */ + RootedTree &parse(const string &input); + + + + private: + string input; ///< Input string + + + /** @brief Tells whether input string is empty. + * @retval true Input string is empty + * @retval false Input string is not empty + */ + bool isEmpty() const; + + /** @brief tells whether next input character belong to given set. + * @param[in] character_set Set of characters (as string) + * @retval True if next character belongs to given set + * @retval False if next character does not belong to given set + */ + bool isNext(string character_set = "") const; + + /** @brief Returns next character in the input string. + * @retval Next character from input string + */ + char getNext() const; + + /** @brief Consumes first input character. + * + * Removes first character from input and returns it. + * @retval Next input character + */ + char shift(); + + /** @brief Reports a parsing error and exits. */ + void error(const string &message = "Unknown error") const; + + /** @brief Parses a Newick file. + * @return Rooted tree encoded by the Newick file + */ + RootedTree &parseNewick(); + + /** @brief Parses a tree. + * @return Rooted tree + */ + RootedTree *parseTree(); + + /** @brief Parses siblings (sub)trees. + * @param[in, out] siblings Siblings parsed so far + */ + void parseSiblings(vector *siblings); + + /** @brief Parses a node. + * @return Node of a rooted tree + */ + RootedTree *parseNode(); + + /** @brief Parses a label. + * @return Label of the node + */ + string parseLabel(); + + /** @brief Parses an arc length. + * @return Arc length + */ + double parseLength(); + + /** @brief Parses a string. + * + * Strings may be either spaces-free sequences of character or any + * sequence of character enclosed by double quotes. + * @return String + */ + string parseString(); + + /** @brief Parses a number. + * @return Number (floating point) + */ + double parseNumber(); +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_NEWICKPARSER_H_ \ No newline at end of file diff --git a/Phylo/Sources/PhylogeneticAlgorithm.h b/Phylo/Sources/PhylogeneticAlgorithm.h new file mode 100644 index 0000000..7ed353b --- /dev/null +++ b/Phylo/Sources/PhylogeneticAlgorithm.h @@ -0,0 +1,37 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_PHYLOGENETICALGORITHM_H_ +#define _VICTOR_PHYLO_PHYLOGENETICALGORITHM_H_ + +namespace Victor { +namespace Phylo { + +/** @brief Implements a phylogenetic algorithm. + * + * Phylogenetic algorithms produce phylogenetic trees by aggregating, + * clustering and/or optimizing informations about alignments, profiles, + * etc.. + * + * @author Marco Zanella + */ +class PhylogeneticAlgorithm { +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_PHYLOGENETICALGORITHM_ \ No newline at end of file diff --git a/Phylo/Sources/PhylogeneticTree.cc b/Phylo/Sources/PhylogeneticTree.cc new file mode 100644 index 0000000..9f6c9b5 --- /dev/null +++ b/Phylo/Sources/PhylogeneticTree.cc @@ -0,0 +1,51 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include + +using std::stringstream; + +namespace Victor { +namespace Phylo { + PhylogeneticTree::~PhylogeneticTree() { + } + + + + void + PhylogeneticTree::loadNewick(const istream &input) { + stringstream buffer; + buffer << input.rdbuf(); + parseNewick(buffer.str()); + } + + + + void + PhylogeneticTree::saveNewick(ostream &output) const { + output << asNewick() << ";"; + } + + + + PhylogeneticTree & + PhylogeneticTree::accept(Visitor &visitor) { + visitor.visit(*this); + return *this; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/PhylogeneticTree.h b/Phylo/Sources/PhylogeneticTree.h new file mode 100644 index 0000000..383558a --- /dev/null +++ b/Phylo/Sources/PhylogeneticTree.h @@ -0,0 +1,104 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_PHYLOGENETICTREE_H_ +#define _VICTOR_PHYLO_PHYLOGENETICTREE_H_ + +#include +#include +#include +#include +#include +#include + +using std::istream; +using std::ostream; +using std::string; +using std::vector; + +namespace Victor { +namespace Phylo { + +// Forward declaration +class RootedTree; +class UnrootedTree; + +/** @brief A phylogenetic tree. + * + * A phylogenetic tree is a tree where every node may have a label, and + * arcs have a length. + * + * This class follows the Visitor Design Pattern and uses Method + * Cascading (through Method Chaining). + * + * @author Marco Zanella + */ +class PhylogeneticTree { + public: + /** @brief Destructor. */ + virtual ~PhylogeneticTree(); + + + + /** @brief Returns matrix of distances among leaves. + * @return Distance matrix + */ + virtual DistanceMatrix &getDistanceMatrix() const = 0; + + /** @brief Returns a rooted version of this tree. + * @return A rooted version of this tree + */ + virtual RootedTree &asRootedTree() const = 0; + + /** @brief Returns an unrooted version of this tree. + * @return An unrooted version of this tree + */ + virtual UnrootedTree &asUnrootedTree() const = 0; + + /** @brief Parses a string in Newick format. + * @param[in] input String in Newick format + * @return This tree itself + */ + virtual PhylogeneticTree &parseNewick(const string &input) = 0; + + /** @brief Returns a Newick version of this tree. + * @return String representing this tree in Newick format + */ + virtual string asNewick() const = 0; + + /** @brief Loads a phylogenetic tree in Newick format. + * @param[in] input Stream to read input from + */ + void loadNewick(const istream &input); + + /** @brief Saves a phylogenetic tree in Newick format. + * @param[out] output Stream to write output to + */ + void saveNewick(ostream &output) const; + + + + /** @brief Accepts a visitor. + * @param[in, out] visitor Visitor to accept + * @return This tree itself + */ + virtual PhylogeneticTree &accept(Visitor &visitor); +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_PHYLOGENETICTREE_ \ No newline at end of file diff --git a/Phylo/Sources/RootedTree.cc b/Phylo/Sources/RootedTree.cc new file mode 100644 index 0000000..6fffe28 --- /dev/null +++ b/Phylo/Sources/RootedTree.cc @@ -0,0 +1,485 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include + +using std::stringstream; + +namespace Victor { +namespace Phylo { + typedef RootedTree::Node Node; + typedef RootedTree::Subtree Subtree; + + RootedTree RootedTree::emptyTree; + const double RootedTree::NA = -1.0; + + RootedTree::RootedTree(Node *parent, const double distance, const string &label) + : parent(parent), label(label), distance(distance) { + this->previous = nullptr; + this->next = nullptr; + if (nullptr != parent) { + parent->addChild(*this); + } + } + + RootedTree::RootedTree(const double distance, const string &label): + RootedTree(nullptr, distance, label) {} + + RootedTree::RootedTree(const string &label): + RootedTree(nullptr, NA, label) {} + + + + RootedTree::~RootedTree() { + } + + + + bool + RootedTree::operator==(const Subtree &other) const { + bool equal = true; + size_t i = 0; + + // If trees point the same memory area, they are equal. + if (this == &other) { + return true; + } + + // If trees have different labels, number of children or distance, + // they are not equal. + if (label != other.label + || getChildrenNumber() != other.getChildrenNumber() + || getDistance() != other.getDistance()) { + return false; + } + + // If children of trees are equal, trees are equal. + while (equal && i < getChildrenNumber()) { + equal &= getChild(i) == other.getChild(i); + i++; + } + + return equal; + } + + + + bool + RootedTree::operator!=(const Subtree &other) const { + return !(*this == other); + } + + + + bool + RootedTree::operator<(const Node &other) const { + return isAncestor(other); + } + + + + bool + RootedTree::operator>(const Node &other) const { + return isDescendant(other); + } + + + + RootedTree & + RootedTree::operator+(Node &child) { + return addChild(child); + } + + + + Subtree & + RootedTree::operator[](const size_t index) const { + return getChild(index); + } + + + + bool + RootedTree::isLeaf() const { + return children.size() == 0; + } + + + + bool + RootedTree::hasSiblings() const { + return nullptr != previous || nullptr != next; + } + + + + bool + RootedTree::hasChildren() const { + return !isLeaf(); + } + + + + bool + RootedTree::isRoot() const { + return nullptr == parent; + } + + + + bool + RootedTree::isAncestor(const Node &node) const { + if (node.isRoot()) { + return false; + } else if (node.parent == this) { + return true; + } else { + return isAncestor(node.getParent()); + } + } + + + + bool + RootedTree::isDescendant(const Node &node) const { + return node.isAncestor(*this); + } + + + + bool + RootedTree::hasDistance() const { + return distance != NA; + } + + + + + size_t + RootedTree::getSize() const { + size_t size = 0; + + for (Node *child : children) { + size += child->getSize(); + } + + return size + 1; + } + + + + vector + RootedTree::getLeaves() const { + vector leaves; + + if (isLeaf()) { + leaves.push_back(const_cast(this)); + } + else { + for (Node *child : children) { + vector child_leaves = child->getLeaves(); + leaves.reserve(leaves.size() + child_leaves.size()); + leaves.insert(leaves.end(), child_leaves.begin(), child_leaves.end()); + } + } + + return leaves; + } + + + + size_t + RootedTree::getLeavesNumber() const { + size_t leaves = (isLeaf()) ? 1 : 0; + + for (Node *child : children) { + leaves += child->getLeavesNumber(); + } + + return leaves; + } + + + + size_t + RootedTree::getSiblingsNumber() const { + return isRoot() ? 0 : getParent().getChildrenNumber() - 1; + } + + + + size_t + RootedTree::getChildrenNumber() const { + return children.size(); + } + + + + Node & + RootedTree::getChild(const size_t index) const { + return (index < getChildrenNumber()) + ? *(children[index]) : emptyTree; + } + + + + Node & + RootedTree::getRoot() const { + return isRoot() + ? *const_cast(this) + : getParent().getRoot(); + } + + + + size_t + RootedTree::getDepth() const { + return isRoot() ? 0 : getParent().getDepth() + 1; + } + + + + size_t + RootedTree::getHeight() const { + if (isLeaf()) { + return 0; + } else { + size_t height = 0, max_height = 0; + for (Node *child : children) { + height = child->getHeight(); + if (height > max_height) { + max_height = height; + } + } + return height + 1; + } + } + + + + Node & + RootedTree::getParent() const { + return isRoot() ? emptyTree : *parent; + } + + + + double + RootedTree::getDistance() const { + return distance; + } + + + + double + RootedTree::getDistance(const Node &node) const { + if (isAncestor(node)) { + return node.getTotalDistance() - getTotalDistance(); + } else if (isDescendant(node)) { + return getTotalDistance() - node.getTotalDistance(); + } else { + Node *ancestor = parent; + while (!ancestor->isAncestor(node)) { + ancestor = ancestor->parent; + } + return getDistance(*ancestor) + node.getDistance(*ancestor); + } + } + + + + double + RootedTree::getTotalDistance() const { + return isRoot() + ? getDistance() + : getDistance() + getParent().getTotalDistance(); + } + + + + double + RootedTree::getMaxDistance() const { + double max_distance = 0.0; + + for (auto &leaf : getLeaves()) { + max_distance = std::max(max_distance, leaf->getTotalDistance()); + } + + return max_distance; + } + + + + string + RootedTree::getLabel() const { + return label; + } + + + + Node & + RootedTree::getPreviousSibling() const { + return (nullptr != previous) ? *previous : emptyTree; + } + + + + Node & + RootedTree::getNextSibling() const { + return (nullptr != next) ? *next : emptyTree; + } + + + + DistanceMatrix & + RootedTree::getDistanceMatrix() const { + DistanceMatrix *d = new DistanceMatrix(); + vector leaves = getLeaves(); + + for (auto i : leaves) { + d->addOTU(i->getLabel()); + for (auto j : leaves) { + if (i == j) { + continue; + } + (*d)(i->getLabel(), j->getLabel(), i->getDistance(*j)); + } + } + + return *d; + } + + + + RootedTree & + RootedTree::setDistance(const double distance) { + this->distance = distance; + return *this; + } + + + + RootedTree & + RootedTree::setLabel(const string &label) { + this->label = label; + return *this; + } + + + + Subtree & + RootedTree::addChild(RootedTree::Subtree &child) { + if (hasChildren()) { + children[getChildrenNumber() - 1]->next = &child; + child.previous = children[getChildrenNumber() - 1]; + } + children.push_back(&child); + child.parent = this; + return *this; + } + + + + RootedTree & + RootedTree::asRootedTree() const { + return *(const_cast(this)); + } + + + + /** @brief Recursively builds an unrooted tree. + * @param[in] root Current node + * @param[in] tree Pointer to unrooted tree built so far + * @return Unrooted version of this node + * @note This local utility function must be implemented out of the + * RootedTree class, because UnrootedTree::Node is not available + * in the class definition. This is due to a missing feature in C++: + * no forward declarations for nested class. + */ + static UnrootedTree::Node & + _buildNode(const RootedTree &root, UnrootedTree *tree = nullptr) { + // Creates tree if null + if (nullptr == tree) { + tree = new UnrootedTree(); + } + + // Adds current node to the tree + UnrootedTree::Node *node = + new UnrootedTree::Node(tree, root.getLabel()); + + // Recursively adds children of current node to the tree as neighbors + for (size_t i = 0; i < root.getChildrenNumber(); i++) { + const RootedTree child = root.getChild(i); + node->addNeighbor(_buildNode(child, tree), child.getDistance()); + } + + return *node; + } + + UnrootedTree & + RootedTree::asUnrootedTree() const { + return _buildNode(*this).getTree(); + } + + + + RootedTree & + RootedTree::parseNewick(const string &input) { + NewickParser parser; + + *this = parser.parse(input); + + return *this; + } + + string + RootedTree::asNewick() const { + stringstream output; + + // Saves data about children + if (hasChildren()) { + output << "(" << getChild(0).asNewick() << ")"; + } + + // Saves label of this node + output << getLabel(); + + // Saves data about distance + if (hasDistance()) { + output << ":" << getDistance(); + } + + // Saves data about sibling + if (next != nullptr) { + output << "," << next->asNewick(); + } + + return output.str(); + } + + + + RootedTree & + RootedTree::accept(Visitor &visitor) { + visitor.visit(*this); + return *this; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/RootedTree.h b/Phylo/Sources/RootedTree.h new file mode 100644 index 0000000..df8e889 --- /dev/null +++ b/Phylo/Sources/RootedTree.h @@ -0,0 +1,353 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_ROOTEDTREE_H_ +#define _VICTOR_PHYLO_ROOTEDTREE_H_ + +#include +#include +#include +#include + +using std::string; +using std::vector; + +namespace Victor { +namespace Phylo { + +/** @brief Implements a rooted phylogenetic tree + * + * A rooted tree is a phylogenetic tree where every node may have a + * label, arcs have a length and every node has a parent (except the + * root node). + * + * A rooted tree is implemented using a recursive structure, and a + * (sub)tree is represented by its root node. + * + * This class follows the Visitor Design Pattern and uses Method + * Cascading (through Method Chaining). + * + * @author Marco Zanella + */ +class RootedTree: public PhylogeneticTree { + public: + /** Subtree is an alias for RootedTree. */ + typedef RootedTree Subtree; + + /** Node is an alias for RootedTree. */ + typedef RootedTree Node; + + + /** Distance from parent node Not Available. */ + static const double NA; + + + /** @brief Default constructor. + * @param[in,out] parent Pointer to parent node + * @param[in] distance Distance from parent node + * @param[in] label Label of this node + */ + RootedTree( + Node *parent = nullptr, + const double distance = NA, + const string &label = ""); + + /** @brief Constructor. + * @param[in] distance Distance from parent node + * @param[in] label Label of this node + */ + explicit RootedTree(const double distance, const string &label = ""); + + /** @brief Constructor. + * @param[in] label Label of this node + */ + explicit RootedTree(const string &label); + + /** @brief Destructor. */ + virtual ~RootedTree(); + + + + /** @brief Equality test for rooted trees. + * + * Two rooted trees are equal if (they point to the same + * memory area, or) they have identical labels, distance and children. + * @param[in] other Other tree + * @retval true Trees are equal + * @retval false Trees are not equal + */ + bool operator==(const Subtree &other) const; + + /** @brief Inequality test for rooted trees. + * + * Two rooted trees are equal if (they point to the same + * memory area, or) they have identical labels, distance and children. + * @param[in] other Other tree + * @retval true Trees are not equal + * @retval false Trees are equal + */ + bool operator!=(const Subtree &other) const; + + /** @brief Tells whether this node is an ancestor of given node. + * @param[in] other Given node + * @retval true This node is an ancestor of given one + * @retval false This node is not an ancestor of given one + */ + bool operator<(const Node &other) const; + + /** @brief Tells whether this node is a descendant of given node. + * @param[in] other Given node + * @retval true This node is a descendant of given one + * @retval false This node is not a descendant of given one + */ + bool operator>(const Node &other) const; + + /** @brief Adds a child to this node. + * @param[in, out] child Child to be added + * @return This node itself + */ + RootedTree &operator+(Node &child); + + /** @brief Returns child at given index. + * + * If index is invalid, returns an empty tree. + * @param[in] index Index of the child + * @return Child at given index + */ + Subtree &operator[](const size_t index) const; + + + + /** @brief Tells whether this node is a leaf. + * @retval true This node is a leaf + * @retval false This node has at least one child + */ + bool isLeaf() const; + + /** @brief Tells whether this node has siblings. + * @retval true This node has at least one sibling + * @retval false This node does not have any siblings + */ + bool hasSiblings() const; + + /** @brief Tells whether this node has children. + * @retval true This node has at least one child + * @retval false This node does not have any child + */ + bool hasChildren() const; + + /** @brief Tells whether this node is a root node. + * @retval true This node is a root node + * @retval false This node is not a root node + */ + bool isRoot() const; + + /** @brief Tells whether this node is an ancestor of given node. + * @param[in] node Given node + * @retval true This node is an ancestor of giiven node + * @retval false This node is not an ancestor of given node + */ + bool isAncestor(const Node &node) const; + + /** @brief Tells whether this node is a descendant of given node. + * @param[in] node Given node + * @retval true This node is a descendant of given node + * @retval false This node is not a descendant of given node + */ + bool isDescendant(const Node &node) const; + + /** @brief Tells whether this node has the distance from parent node set. + * @retval true A distance was set for this node + * @retval false A distance was not set for this node + */ + bool hasDistance() const; + + + + /** @brief Returns number of nodes in this (sub)tree. + * @return Number of nodes in this (sub)tree + */ + size_t getSize() const; + + /** @brief Returns leaves of this (sub)tree. + * @return Leaves as a vector + */ + vector getLeaves() const; + + /** @brief Returns number of leaves in this (sub)tree. + * @return Number of leaves in this (sub)tree + */ + size_t getLeavesNumber() const; + + /** @brief Returns number of siblings of this node. + * @return Number of siblings + */ + size_t getSiblingsNumber() const; + + /** @brief Return number of children of this node. + * @return Number of children + */ + size_t getChildrenNumber() const; + + /** @brief Returns child at given index. + * + * By default, returns first child. + * If index is invalid, returns an empty tree. + * @param[in] index Index of the child to be returned + * @return Child node + */ + Subtree &getChild(const size_t index = 0) const; + + /** @brief Returns root node of the tree this node belongs to. + * @return Root node + */ + Node &getRoot() const; + + /** @brief Returns depth of this node. + * @return Depth of this node + */ + size_t getDepth() const; + + /** @brief Returns height of this node. + * @return Height of this node + */ + size_t getHeight() const; + + /** @brief Returns parent of this node. + * + * If this node is a root node, returns an empty tree. + * @return Parent node + */ + Node &getParent() const; + + /** @brief Returns distance from this node to its parent. + * + * Equivalently, returns the length of the arc. + * @return Distance from this node to its parent + */ + double getDistance() const; + + /** @brief Returns distance from this node to given one. + * + * @param[in] node Node + * @return Distance from this node to given one. + */ + double getDistance(const Node &node) const; + + /** @brief Returns total distance from this node to its root. + * @return Cumulative distance from this node to the root + */ + double getTotalDistance() const; + + /** @brief Returns maximum distance in this tree. + * @return Maximum cumulative distance + */ + double getMaxDistance() const; + + /** @brief Returns label of this node. + * @return Label of this node + */ + string getLabel() const; + + /** @brief Returns previous sibling of this node. + * + * If this node has no previous sibling, returns an empty tree. + * @return Previous sibling + */ + Node &getPreviousSibling() const; + + /** @brief Returns next sibling of this node. + * + * If this node has no next sibling, returns an empty tree. + * @return Next sibling + */ + Node &getNextSibling() const; + + /** @brief Returns matrix of distances among leaves. + * @return Distance matrix + */ + virtual DistanceMatrix &getDistanceMatrix() const; + + + + /** @brief Sets distance from this node to its parent. + * + * Equivalently, sets the length of the arc. + * @param[in] distance New distance from this node to its parent + * @return This node + */ + RootedTree &setDistance(const double distance = NA); + + /** @brief Sets label of this node. + * @param[in] label New label of this node + * @return This node + */ + RootedTree &setLabel(const string &label = ""); + + + + /** @brief Adds a new child to this node. + * + * New child become the last child of this node. + * @param[in, out] child New child + * @return This node + */ + Subtree &addChild(Subtree &child); + + /** @brief Returns a rooted version of this tree. + * @return A rooted version of this tree + */ + virtual RootedTree &asRootedTree() const; + + /** @brief Returns an unrooted version of this tree. + * @return An unrooted version of this tree + */ + virtual UnrootedTree &asUnrootedTree() const; + + /** @brief Parses a string in Newick format. + * @param[in] input String in Newick format + * @return This tree itself + */ + virtual RootedTree &parseNewick(const string &input); + + /** @brief Returns a Newick version of this tree. + * @return String representing this tree in Newick format + */ + virtual string asNewick() const; + + + + /** @brief Accepts a visitor. + * @param[in, out] visitor Visitor to accept + * @return This tree itself + */ + virtual RootedTree &accept(Visitor &visitor); + + private: + static RootedTree emptyTree; ///< Empty tree + + string label; ///< Label of this node + double distance; ///< Distance from parent node + Node *parent; ///< Parent of this node + vector children; ///< Children of this node + Node *previous; ///< Pointer to Previous sibling + Node *next; ///< Pointer to next sibling +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_ROOTEDTREE_H_ \ No newline at end of file diff --git a/Phylo/Sources/Sequence.cc b/Phylo/Sources/Sequence.cc new file mode 100644 index 0000000..524ac43 --- /dev/null +++ b/Phylo/Sources/Sequence.cc @@ -0,0 +1,112 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include + +namespace Victor { +namespace Phylo { + Sequence::Sequence(const string &identifier, const string &residues) + : residues(residues) { + this->identifier = Sequence::formatIdentifier(identifier); + } + + + Sequence::~Sequence() { + } + + + + vector & + Sequence::toSequences(const AlignmentBase &alignment) { + string identifier, residues; + vector *sequences = new vector(); + + // Inserts "target" sequence + identifier = alignment.getTargetName(); + residues = AlignmentBase::getPureSequence(alignment.getTarget()); + sequences->push_back(Sequence(identifier, residues)); + + // Inserts every template sequence + for (size_t i = 0; i < alignment.size(); i++) { + identifier = alignment.getTemplateName(i); + residues = AlignmentBase::getPureSequence(alignment.getTemplate(i)); + sequences->push_back(Sequence(identifier, residues)); + } + + return *sequences; + } + + + + map & + Sequence::toMap(const AlignmentBase &alignment) { + vector list = toSequences(alignment); + map *sequences = new map; + + for (auto &sequence : list) { + (*sequences)[sequence.getIdentifier()] = sequence.getResidues(); + } + + return *sequences; + } + + + + bool + Sequence::isEmpty() const { + return residues.empty(); + } + + + + string + Sequence::getIdentifier() const { + return identifier; + } + + + + string + Sequence::getID() const { + return getIdentifier(); + } + + + + char + Sequence::getResidue(const size_t position) const { + return (position < residues.size()) ? residues[position] : '\0'; + } + + + + string + Sequence::getResidues() const { + return residues; + } + + + + string + Sequence::formatIdentifier(const string &identifier) { + const string::size_type pos = identifier.find(' ', 0); + return (pos < identifier.size()) + ? identifier.substr(0, pos) + : identifier; + } + +} // namespace Phylo +} // namespace Victor diff --git a/Phylo/Sources/Sequence.h b/Phylo/Sources/Sequence.h new file mode 100644 index 0000000..5ea7851 --- /dev/null +++ b/Phylo/Sources/Sequence.h @@ -0,0 +1,116 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_SEQUENCE_H_ +#define _VICTOR_PHYLO_SEQUENCE_H_ + +#define _GLIBCXX_IOMANIP +#include +#include +#include + +using std::string; +using std::map; +using Victor::Align2::AlignmentBase; + +namespace Victor { +namespace Phylo { + +/** @brief A sequence. + * + * Contains information about a sequence. + * + * @author Marco Zanella + */ +class Sequence { + public: + /** @brief Builds a sequence with given identifier and residues + * @param[in] identifier Idenfifier of this sequence + * @param[in] residues Residues in this sequence + */ + explicit Sequence(const string &identifier, const string &residues); + + /** @brief Destructor. */ + ~Sequence(); + + + + /** Converts an alignment into a list of sequences. + * @param[in] alignment Alignment + * @return Vector of Sequence + */ + static vector &toSequences(const AlignmentBase &alignment); + + + + /** Converts an alignment into a map of sequences. + * @param[in] alignment Alignment + * @return Map of sequences: identifier => residues + */ + static map &toMap(const AlignmentBase &alignment); + + + + /** @brief Tells whether this sequence is empty. + * @retval true This sequence is empty + * @retval false This sequence is not empty + */ + bool isEmpty() const; + + + + /** @brief Returns identifier of this sequence. + * @return Identifier of this sequence. + */ + string getIdentifier() const; + + /** @brief Returns identifier of this sequence. + * @return Identifier of this sequence. + */ + string getID() const; + + /** @brief Returns residue at given position. + * @param[in] position Position of the residue to return + * @return Residue + */ + char getResidue(const size_t position) const; + + /** @brief Returns residues in this sequence. + * @return Residues in this sequence + */ + string getResidues() const; + + + + private: + string identifier; ///< Identifier of this sequence + string residues; ///< Residues in this sequence + + + + /** @brief Returns a compact version of an identifier. + * + * Strips spaces and keeps only the first word of the identifier. + * @param[in] identifier Identifier + * @return Compact identifier + */ + static string formatIdentifier(const string &identifier); +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_SEQUENCE_H_ diff --git a/Phylo/Sources/SubstitutionMatrix.cc b/Phylo/Sources/SubstitutionMatrix.cc new file mode 100644 index 0000000..37bbbe4 --- /dev/null +++ b/Phylo/Sources/SubstitutionMatrix.cc @@ -0,0 +1,405 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include +#include + +namespace Victor { +namespace Phylo { + typedef SubstitutionMatrix::Identifier Identifier; + + /** @brief Returns a precalculate matrix as a map. + * @param[in] identifier Identifier of the matrix + * @return Precalculated matrix + */ + static map> &precalculated_matrices(const Identifier identifier); + + const string SubstitutionMatrix::residues = "ARNDCEQGHILKMFPSTWYVUOBZJX"; + + + SubstitutionMatrix::SubstitutionMatrix(const map> &scores) { + const size_t size = 26; + int new_scores[26 * 26], + max_score = 0, + min_score = 0; + double avg_mismatch_score = 0.0; + map> scores_map = scores; + + for (size_t i = 0; i < size; i++) { + const char r1 = residues[i]; + for (size_t j = 0; j < size; j++) { + const char r2 = residues[j]; + const int score = scores_map[r1][r2]; + + new_scores[hash(r1) * size + hash(r2)] = score; + min_score = std::min(score, min_score); + max_score = std::max(score, max_score); + avg_mismatch_score += score; + } + } + avg_mismatch_score /= (size * size); + + memcpy(&this->scores, &new_scores, size * size * sizeof(int)); + this->min_score = min_score; + this->max_score = max_score; + this->avg_mismatch_score = avg_mismatch_score; + } + + + + SubstitutionMatrix::SubstitutionMatrix(const Identifier identifier) + : SubstitutionMatrix(precalculated_matrices(identifier)) { + } + + + + SubstitutionMatrix::SubstitutionMatrix(const SubMatrix &matrix) + : SubstitutionMatrix(SubMatrixToMap(matrix)) { + } + + + + SubstitutionMatrix::SubstitutionMatrix(const SubstitutionMatrix &matrix) + : min_score(matrix.min_score), max_score(matrix.max_score), + avg_mismatch_score(matrix.avg_mismatch_score) { + memcpy(&scores, &matrix.scores, matrix.getScoresNumber() * sizeof(int)); + } + + + + SubstitutionMatrix::~SubstitutionMatrix() { + } + + + + bool + SubstitutionMatrix::operator==(const SubstitutionMatrix &other) const { + return isEqual(other); + } + + + + int + SubstitutionMatrix::operator()(const char a, const char b) const { + return getScore(a, b); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::operator+(const int value) const { + return add(value); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::operator-(const int value) const { + return add(-value); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::operator-() const { + return multiply(-1); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::operator*(const int value) const { + return multiply(value); + } + + + + bool + SubstitutionMatrix::isEqual(const SubstitutionMatrix &other) const { + const size_t size = getScoresNumber(); + bool is_equal = true; + size_t i = 0; + + // If matrices differ in sizes, they are not equal + if (size != other.getScoresNumber()) { + return false; + } + + // Checks whether every score is equal + while (is_equal && i < size) { + is_equal &= scores[i] == other.scores[i]; + i++; + } + + return is_equal; + } + + + + size_t + SubstitutionMatrix::getSize() const { + return getResidues().size(); + } + + + + size_t + SubstitutionMatrix::getScoresNumber() const { + return getSize() * getSize(); + } + + + + string + SubstitutionMatrix::getResidues() const { + return residues; + } + + + + int + SubstitutionMatrix::getScore(const char a, const char b) const { + return scores[hash(a) * getSize() + hash(b)]; + } + + + + int + SubstitutionMatrix::getMinScore() const { + return min_score; + } + + + + int + SubstitutionMatrix::getMaxScore() const { + return max_score; + } + + + + double + SubstitutionMatrix::getAvgMismatchScore() const { + return avg_mismatch_score; + } + + + + map> & + SubstitutionMatrix::getScoresAsMap() const { + map> *scores_map = new map>(); + + for (char r1 : residues) { + for (char r2: residues) { + (*scores_map)[r1][r2] = getScore(r1, r2); + } + } + + return *scores_map; + } + + + + SubMatrix & + SubstitutionMatrix::asSubMatrix() const { + stringstream stream; + + // Saves matrix into a stream + stream << getResidues() << "\n" << getSize() << "\n"; + for (char r1 : getResidues()) { + stream << getSize(); + for (char r2 : getResidues()) { + if (getScore(r1, r2) >= 0 && getScore(r1, r2) < 10) { + stream << " "; + } + stream << " " << getScore(r1, r2) << " "; + } + stream << "\n"; + } + stream << "#" << "\n"; + + // Build SubMatrix from the stream + return *(new SubMatrix(stream)); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::add(const int value) const { + return fma(value, 1); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::multiply(const int value) const { + return fma(0, value); + } + + + + SubstitutionMatrix & + SubstitutionMatrix::fma(const int addend, const int factor) const { + map> scores_map; + + for (char r1 : residues) { + for (char r2: residues) { + scores_map[r1][r2] = addend + factor * getScore(r1, r2); + } + } + + return *(new SubstitutionMatrix(scores_map)); + } + + + + Identifier + SubstitutionMatrix::stringToIdentifier(const string &identifier) { + if (identifier == "BLOSUM30") return BLOSUM30; + if (identifier == "BLOSUM35") return BLOSUM35; + if (identifier == "BLOSUM40") return BLOSUM40; + if (identifier == "BLOSUM45") return BLOSUM45; + if (identifier == "BLOSUM50") return BLOSUM50; + if (identifier == "BLOSUM55") return BLOSUM55; + if (identifier == "BLOSUM62") return BLOSUM62; + if (identifier == "BLOSUM65") return BLOSUM65; + if (identifier == "BLOSUM70") return BLOSUM70; + if (identifier == "BLOSUM75") return BLOSUM75; + if (identifier == "BLOSUM80") return BLOSUM80; + if (identifier == "BLOSUM90") return BLOSUM90; + + if (identifier == "PAM20") return PAM20; + if (identifier == "PAM60") return PAM60; + if (identifier == "PAM120") return PAM120; + if (identifier == "PAM160") return PAM160; + if (identifier == "PAM250") return PAM250; + if (identifier == "PAM350") return PAM350; + + if (identifier == "MD40") return MD40; + if (identifier == "MD120") return MD120; + if (identifier == "MD250") return MD250; + if (identifier == "MD350") return MD350; + + if (identifier == "IDENTITY") return IDENTITY; + + if (identifier == "GON40") return GON40; + if (identifier == "GON80") return GON80; + if (identifier == "GON120") return GON120; + if (identifier == "GON160") return GON160; + if (identifier == "GON250") return GON250; + if (identifier == "GON300") return GON300; + if (identifier == "GON350") return GON350; + + return IDENTITY; + } + + + + size_t + SubstitutionMatrix::hash(const char amino) { + return (size_t) AminoAcid::letter1ToCode(amino); + } + + + + map> & + SubstitutionMatrix::SubMatrixToMap(const SubMatrix &submatrix) { + map> *scores_map = new map>(); + + for (char r1 : residues) { + for (char r2 : residues) { + (*scores_map)[r1][r2] = submatrix.score[r1][r2]; + } + } + + return *scores_map; + } + + + +//////////////////////////////////////////////////////////////////////// +// Precalculated matrices +static map> &precalculated_matrices(const Identifier identifier) { + const string residues = _residues;; + const size_t size = residues.size(); + map> *matrix = new map>(); + int *ptr; + + // Finds correct matrix + switch (identifier) { + // BLOSUM family + case SubstitutionMatrix::BLOSUM30: ptr = _blosum30; break; + case SubstitutionMatrix::BLOSUM35: ptr = _blosum35; break; + case SubstitutionMatrix::BLOSUM40: ptr = _blosum40; break; + case SubstitutionMatrix::BLOSUM45: ptr = _blosum45; break; + case SubstitutionMatrix::BLOSUM50: ptr = _blosum50; break; + case SubstitutionMatrix::BLOSUM55: ptr = _blosum55; break; + case SubstitutionMatrix::BLOSUM62: ptr = _blosum62; break; + case SubstitutionMatrix::BLOSUM65: ptr = _blosum65; break; + case SubstitutionMatrix::BLOSUM70: ptr = _blosum70; break; + case SubstitutionMatrix::BLOSUM75: ptr = _blosum75; break; + case SubstitutionMatrix::BLOSUM80: ptr = _blosum80; break; + case SubstitutionMatrix::BLOSUM90: ptr = _blosum90; break; + + // PAM family + case SubstitutionMatrix::PAM20: ptr = _pam20; break; + case SubstitutionMatrix::PAM60: ptr = _pam60; break; + case SubstitutionMatrix::PAM120: ptr = _pam120; break; + case SubstitutionMatrix::PAM160: ptr = _pam160; break; + case SubstitutionMatrix::PAM250: ptr = _pam250; break; + case SubstitutionMatrix::PAM350: ptr = _pam350; break; + + // MD family + case SubstitutionMatrix::MD40: ptr = _md40; break; + case SubstitutionMatrix::MD120: ptr = _md120; break; + case SubstitutionMatrix::MD250: ptr = _md250; break; + case SubstitutionMatrix::MD350: ptr = _md350; break; + + // Identity + case SubstitutionMatrix::IDENTITY: ptr = _idmat; break; + + // GON family + case SubstitutionMatrix::GON40: ptr = _gon40; break; + case SubstitutionMatrix::GON80: ptr = _gon80; break; + case SubstitutionMatrix::GON120: ptr = _gon120; break; + case SubstitutionMatrix::GON160: ptr = _gon160; break; + case SubstitutionMatrix::GON250: ptr = _gon250; break; + case SubstitutionMatrix::GON300: ptr = _gon300; break; + case SubstitutionMatrix::GON350: ptr = _gon350; break; + + // Default: identity + default: ptr = _idmat; + } + + // Converts raw matrix to map + for (size_t i = 0; i < size; i++) { + const char r_i = residues[i]; + for (size_t j = 0; j <= i; j++) { + const char r_j = residues[j]; + (*matrix)[r_i][r_j] = ptr[(i * i + i) / 2 + j]; + (*matrix)[r_j][r_i] = ptr[(i * i + i) / 2 + j]; + } + } + + return *matrix; +} + +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/SubstitutionMatrix.h b/Phylo/Sources/SubstitutionMatrix.h new file mode 100644 index 0000000..c1908ef --- /dev/null +++ b/Phylo/Sources/SubstitutionMatrix.h @@ -0,0 +1,274 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_SUBSTITUTIONMATRIX_H_ +#define _VICTOR_PHYLO_SUBSTITUTIONMATRIX_H_ + +#include +#include + +using std::map; +using Victor::Align2::SubMatrix; + +namespace Victor { +namespace Phylo { + +/** @brief Implements a substitution matrix. + * + * This class is similar to SubMatrix in the Align2 package. This class + * can interoperate with SubMatrix, since it offers methods to convert + * a SubMatrix to a SubstitutionMatrix and vice-versa. + * + * This class uses Method Cascading (thought Method Chaining) for its + * setter member functions. + * + * Most common substitution matrices are hardcoded, so that it is no + * longer necessary to read from a stream. + * + * Values for the precalculated matrices are taken from the official + * ClustalW implementation. + * + * @author Marco Zanella + */ +class SubstitutionMatrix { + public: + /** Identifiers of hardcoded substitution matrices. */ + typedef enum { + BLOSUM30, ///< BLOSUM 30 + BLOSUM35, ///< BLOSUM 35 + BLOSUM40, ///< BLOSUM 40 + BLOSUM45, ///< BLOSUM 45 + BLOSUM50, ///< BLOSUM 50 + BLOSUM55, ///< BLOSUM 55 + BLOSUM62, ///< BLOSUM 62 + BLOSUM65, ///< BLOSUM 65 + BLOSUM70, ///< BLOSUM 70 + BLOSUM75, ///< BLOSUM 75 + BLOSUM80, ///< BLOSUM 80 + BLOSUM90, ///< BLOSUM 90 + + PAM20, ///< PAM 20 + PAM60, ///< PAM 60 + PAM120, ///< PAM 120 + PAM160, ///< PAM 160 + PAM250, ///< PAM 250 + PAM350, ///< PAM 350 + + MD40, ///< MD 40 + MD120, ///< MD 120 + MD250, ///< MD 250 + MD350, ///< MD 350 + + IDENTITY, ///< Identity matrix + + GON40, ///< GON 40 + GON80, ///< GON 80 + GON120, ///< GON 120 + GON160, ///< GON 160 + GON250, ///< GON 250 + GON300, ///< GON 300 + GON350 ///< GON 350 + } Identifier; + + + + /** @brief Builds a subsitution matrix from a map. + * @param[in] scores Scores among residues + */ + explicit SubstitutionMatrix(const map> &scores); + + /** @brief Builds a pre-calculated substitution matrix. + * @param[in] identifer Identifier of the matrix + */ + explicit SubstitutionMatrix(const Identifier identifer); + + /** @brief Builds a substitution matrix from a SubMatrix. + * + * Converts a SubMatrix to a SubstitutionMatrix. + * @param[in] matrix SubMatrix object + */ + explicit SubstitutionMatrix(const SubMatrix &matrix); + + /** @brief Copy constructor. + * @param[in] matrix Substitution matrix + */ + explicit SubstitutionMatrix(const SubstitutionMatrix &matrix); + + /** @brief Destructor. */ + virtual ~SubstitutionMatrix(); + + + + /** @brief Tells whether this matrix is equal to given one. + * @param[in] other Other substitution matrix + */ + bool operator==(const SubstitutionMatrix &other) const; + + /** @brief Returns score between given residues. + * @param[in] a First amino acid + * @param[in] b Second amino acid + * @return Score between a and b + */ + int operator()(const char a, const char b) const; + + /** @brief Computes sum of scores and a given constant. + * @param[in] value Value to be added + * @return A new substitution matrix + */ + SubstitutionMatrix &operator+(const int value) const; + + /** @brief Computes difference between scores and a given constant. + * @param[in] value Value to be subtracted + * @return A new substitution matrix + */ + SubstitutionMatrix &operator-(const int value) const; + + /** @brief Changes signess of scores. + * @return A new substitution matrix + */ + SubstitutionMatrix &operator-() const; + + /** @brief Computes product of scores and a given constant. + * @param[in] value Value to be multiplied + * @return A new substitution matrix + */ + SubstitutionMatrix &operator*(const int value) const; + + + + /** @brief Tells whether this matrix is equal to given one. + * @param[in] other Other substitution matrix + */ + bool isEqual(const SubstitutionMatrix &other) const; + + + + /** @brief Returns size of this subsitution matrix. + * @return Size of this matrix + */ + size_t getSize() const; + + /** @brief Returns number of elements in this matrix. + * @return Number of scores in this matrix. + */ + size_t getScoresNumber() const; + + /** @brief Returns residues in this substitution matrix. + * @return Residues + */ + string getResidues() const; + + /** @brief Returns score between given residues. + * @param[in] a First amino acid + * @param[in] b Second amino acid + * @return Score between a and b + */ + int getScore(const char a, const char b) const; + + /** @brief Returns minimum score in this matrix. + * @return Minimum score + */ + int getMinScore() const; + + /** @brief Returns maximum score in this matrix. + * @return Maximum score + */ + int getMaxScore() const; + + /** @brief Returns average mismatch score. + * @return Average mismatch score + */ + double getAvgMismatchScore() const; + + /** @brief Returns scores as a map. + * @return Scores as a map + */ + map> &getScoresAsMap() const; + + /** @brief Returns a SubMatrix reference. + * + * Converts this substitution matrix to a SubMatrix object. + * @return This substitution matrix as a SubMatrix + */ + SubMatrix &asSubMatrix() const; + + + + /** @brief Computes sum of scores and a given constant. + * @param[in] value Value to be added + * @return A new substitution matrix + */ + SubstitutionMatrix &add(const int value) const; + + /** @brief Computes product of scores and a given constant. + * @param[in] value Value to be multiplied + * @return A new substitution matrix + */ + SubstitutionMatrix &multiply(const int value) const; + + /** @brief Performs a fused multiply-add (fma) operation. + * + * Multiplies this matrix by given factor, then adds given addend to + * the result at once. This is more efficient than a + b * M. + * @param[in] addend Value to be added + * @param[in] factor Value to be multiplied + * @return A new substitution matrix + */ + SubstitutionMatrix &fma(const int addend, const int factor) const; + + + + private: + static const string residues; ///< Residues + + int scores[26 * 26]; ///< Scores + double avg_mismatch_score; ///< Average mismatch score + int min_score; ///< Minimum score + int max_score; ///< Maximum score + + + /** @brief Converts a string into an identifier. + * + * If conversion fails, returns the identity identifier. + * @param[in] identifier Identifier as a string + * @return Identifier + */ + static Identifier stringToIdentifier(const string &identifier); + + /** @brief Returns an hased version of an amino acid. + * + * Hash function maps amino acids into the interval [0, 25], minimizing + * entropy. + * @param[in] amino Amino acid + * @return Hash value + */ + static size_t hash(const char amino); + + /** @brief Returns a SubMatrix as a map. + * + * Converts a SubMatrix object into a map of scores. + * @param[in] submatrix SubMatrix object + * @return Score map + */ + static map> &SubMatrixToMap(const SubMatrix &submatrix); +}; + + + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_SUBSTITUTIONMATRIX_H_ \ No newline at end of file diff --git a/Phylo/Sources/UPGMA.cc b/Phylo/Sources/UPGMA.cc new file mode 100644 index 0000000..14a2fd5 --- /dev/null +++ b/Phylo/Sources/UPGMA.cc @@ -0,0 +1,111 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include + +/** Returns union of sets. + * @param[in] A First set + * @param[in] B Second set + * @return Set union between A and B: A U B + */ +template +set set_union(const set &A, const set &B) { + set C = A; + C.insert(B.begin(), B.end()); + return C; +} + + + +namespace Victor { +namespace Phylo { + UPGMA::~UPGMA() { + } + + + + RootedTree & + UPGMA::apply(const DistanceMatrix &matrix) const { + map node_pool; + map cumulative; + map> components; + RootedTree *tree; + DistanceMatrix DM = matrix; + set OTUs = matrix.getOTUs(); + + + // Initializes auxilary data structures + for (auto &label : OTUs) { + node_pool[label] = new RootedTree(label); + cumulative[label] = 0.0; + components[label].insert(label); + } + + while (!DM.isEmpty()) { + // Takes minimum from distance matrix and computes new label and + // distance + pair min = DM.getMinimumPosition(); + string i = min.first, + j = min.second, + new_label = i + "+" + j; + double new_distance = DM(i, j) / 2.0; + + // Creates a new node for this joining + tree = new RootedTree(); + tree->addChild(*node_pool[i]); + tree->addChild(*node_pool[j]); + + // Sets distance between new joining node and children + node_pool[i]->setDistance(new_distance - cumulative[i]); + node_pool[j]->setDistance(new_distance - cumulative[j]); + + // Updates auxiliary data structures + node_pool[new_label] = tree; + cumulative[new_label] = new_distance; + components[new_label] = set_union(components[i], components[j]); + + + // Updates distance matrix with new distances + OTUs = DM.getOTUs(); + for (auto &l : OTUs) { + // Does not update entries about consumed labels + if (l == i || l == j) { + continue; + } + + // Computes average distance + double average_distance = 0.0; + for (auto &a : components[new_label]) { + for (auto &b : components[l]) { + average_distance += matrix(a, b); + } + } + average_distance /= (components[new_label].size() * components[l].size()); + + // Updates matrix + DM(l, new_label, average_distance); + } + + // Adds new OTU to the distance matrix, and removes consumed ones + DM.addOTU(new_label) + .removeOTU(i) + .removeOTU(j); + } + return *tree; + } + +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/UPGMA.h b/Phylo/Sources/UPGMA.h new file mode 100644 index 0000000..288ceb5 --- /dev/null +++ b/Phylo/Sources/UPGMA.h @@ -0,0 +1,60 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_UPGMA_H_ +#define _VICTOR_PHYLO_UPGMA_H_ + +#include +#include + +namespace Victor { +namespace Phylo { + +/** @brief Implements the UPGMA algorithm. + * + * Implements UPGMA as a functor. + * UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is an + * agglomerative, bottom-up hierarchical clustering method. + * The UPGMA algorithm constructs a rooted tree (dendrogram) that + * reflects the structure present in a pairwise similarity matrix + * (or a dissimilarity matrix). + * + * For more information see: + * - A quantitative approach to a problem in classification + * (Michanel and Sockal) + * + * This class follows the Strategy Design Pattern. + * + * @author Marco Zanella + */ +class UPGMA: public ClusteringAlgorithm { + public: + /** @brief Destructor. */ + virtual ~UPGMA(); + + + + /** @brief Builds a phylogenetic tree from given distance matrix. + * @param[in] matrix Distance matrix + * @return Phylogenetic tree + */ + virtual RootedTree &apply(const DistanceMatrix &matrix) const; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_UPGMA_ \ No newline at end of file diff --git a/Phylo/Sources/UnrootedTree.cc b/Phylo/Sources/UnrootedTree.cc new file mode 100644 index 0000000..0ac2bdb --- /dev/null +++ b/Phylo/Sources/UnrootedTree.cc @@ -0,0 +1,608 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include + +using std::stringstream; + +namespace Victor { +namespace Phylo { + typedef UnrootedTree::Node Node; + + UnrootedTree UnrootedTree::emptyTree; + Node Node::emptyNode; + const double Node::NA = -1.0; + size_t Node::next_ID = 0; + + //////////////////////////////////////////////////////////////////// + // UnrootedTree::Node + Node::Node(UnrootedTree *tree, const string &label) + : tree(tree), label(label) { + this->ID = getNextIdentifier(); + + if (nullptr != tree) { + tree->addNode(*this); + } + } + + + + Node::Node(const string &label) : Node(nullptr, label) { + } + + + + bool + Node::operator==(const Node &other) const { + return getIdentifier() == other.getIdentifier(); + } + + + bool + Node::operator!=(const Node &other) const { + return !(*this == other); + } + + + + bool + Node::isLeaf() const { + return getSize() < 2; + } + + + + bool + Node::hasNeighbors() const { + return !neighbors.empty(); + } + + + + bool + Node::isNeighbor(const size_t identifier) const { + return neighbors.find(identifier) != neighbors.end(); + } + + + + bool + Node::isNeighbor(const Node &node) const { + return isNeighbor(node.getIdentifier()); + } + + + + bool + Node::hasPath(const size_t identifier, const Node *previous) const { + if (isNeighbor(identifier)) { + return true; + } + + bool has_path = false; + for (auto neighbor : getNeighbors()) { + if (neighbor == previous) { + continue; + } + + has_path |= neighbor->hasPath(identifier, this); + } + + return has_path; + } + + + + bool + Node::hasPath(const Node &node) const { + return hasPath(node.getIdentifier()); + } + + + + bool + Node::belongsTo(const UnrootedTree &tree) const { + return this->tree == &tree || getTree() == tree; + } + + + + size_t + Node::getIdentifier() const { + return ID; + } + + + + size_t + Node::getID() const { + return getIdentifier(); + } + + + + size_t + Node::getSize() const { + return neighbors.size(); + } + + + + size_t + Node::getNeighborsNumber() const { + return getSize(); + } + + + + Node & + Node::getNeighbor(const size_t identifier) const { + return (isNeighbor(identifier)) + ? *(neighbors.find(identifier)->second.first) + : emptyNode; + } + + + + Node & + Node::getClosestNeighbor() const { + Node *closest = const_cast(this); + double distance = std::numeric_limits::max(); + + for (auto neighbor : getNeighbors()) { + if (getDistance(*neighbor) < distance) { + distance = getDistance(*neighbor); + closest = neighbor; + } + } + + return *closest; + } + + + + Node & + Node::getNeighborClosestTo(const Node &target, const Node *avoid) const { + Node *closest = const_cast(this); + double distance = std::numeric_limits::max(); + + for (auto neighbor : getNeighbors()) { + if (avoid != nullptr && *avoid == *neighbor) continue; + if (neighbor->getDistance(target) < distance) { + distance = neighbor->getDistance(target); + closest = neighbor; + } + } + + return *closest; + } + + + + vector + Node::getNeighbors() const { + vector neighbors; + + for (auto entry : this->neighbors) { + neighbors.push_back(entry.second.first); + } + + return neighbors; + } + + + + double + UnrootedTree::Node::getDistance(const size_t identifier, const Node *previous) const { + // If nodes are neighbors, returns distance directly + if (isNeighbor(identifier)) { + return neighbors.find(identifier)->second.second; + } + + // If nodes are not neighbors, finds a path + double distance = NA; + vector neighbors = getNeighbors(); + + for (auto neighbor : neighbors) { + double to_neighbor = getDistance(*neighbor), + path_length; + + // Avoids infinite loops + if (previous == neighbor || NA == to_neighbor) { + continue; + } + + path_length = neighbor->getDistance(identifier, this); + + // Exits the loop if the path was found + if (path_length != NA) { + distance = to_neighbor + path_length; + break; + } + } + + return distance; + } + + + + double + UnrootedTree::Node::getDistance(const Node &node) const { + return getDistance(node.getIdentifier()); + } + + + + UnrootedTree & + Node::getTree() const { + return (nullptr != tree) ? *tree : emptyTree; + } + + + + string + Node::getLabel() const { + return label; + } + + + + Node & + Node::setLabel(const string &label) { + this->label = label; + return *this; + } + + + Node & + Node::setDistance(const size_t identifier, const double distance) { + if (isNeighbor(identifier)) { + neighbors.find(identifier)->second.second = distance; + } + return *this; + } + + + Node & + Node::setDistance(Node &node, const double distance) { + return setDistance(node.getIdentifier(), distance); + } + + + + Node & + Node::addNeighbor(Node &node, const double distance) { + // If nodes do not belong to the same tree, nothing happens + if (!node.belongsTo(getTree())) { + return *this; + } + + neighbors[node.getIdentifier()] = make_pair(&node, distance); + node.neighbors[getIdentifier()] = make_pair(this, distance); + + return *this; + } + + + + Node & + Node::addBetween(Node &neighbor, Node &node, const double distance) { + // If node do not belong to the same tree, or are not neighbors, + // nothing happens + if (!node.belongsTo(getTree()) || !isNeighbor(neighbor)) { + return *this; + } + + const double d_ac = distance, + d_bc = getDistance(neighbor) - d_ac; + + addNeighbor(node, d_ac); + neighbor.addNeighbor(node, d_bc); + removeNeighbor(neighbor); + + return *this; + } + + + + Node & + Node::removeNeighbor(Node &node) { + neighbors.erase(node.getIdentifier()); + node.neighbors.erase(getIdentifier()); + + return *this; + } + + + RootedTree & + Node::asRootedTree() const { + return getTree().asRootedTree(getIdentifier()); + } + + + + size_t + Node::getNextIdentifier() { + return next_ID++; + } + + + + + + //////////////////////////////////////////////////////////////////// + // UnrootedTree + UnrootedTree::UnrootedTree() { + } + + + + UnrootedTree::~UnrootedTree() { + } + + + + bool + UnrootedTree::operator==(const UnrootedTree &other) const { + // If trees point the same memory area, they are trivially equal + if (this == &other) { + return true; + } + + // If trees have a different number of nodes, they cannot be equal + if (getSize() != other.getSize()) { + return false; + } + + // Trees are equal if their nodes are equal + bool equal = true; + for (auto &entry : nodes) { + equal &= getNode(entry.first) == other.getNode(entry.first); + } + + return equal; + } + + + + bool + UnrootedTree::operator!=(const UnrootedTree &other) const { + return !(*this == other); + } + + + + UnrootedTree & + UnrootedTree::operator+(Node &node) { + return addNode(node); + } + + + + Node & + UnrootedTree::operator[](const size_t identifier) const { + return getNode(identifier); + } + + + + bool + UnrootedTree::isEmpty() const { + return getSize() == 0; + } + + + + bool + UnrootedTree::hasNode(const size_t ID) const { + return nodes.find(ID) != nodes.end(); + } + + + + bool + UnrootedTree::hasNode(const Node &node) const { + return hasNode(node.getIdentifier()); + } + + + + size_t + UnrootedTree::getSize() const { + return nodes.size(); + } + + + + Node & + UnrootedTree::getNode(const size_t identifier) const { + return hasNode(identifier) + ? *(nodes.find(identifier)->second) + : Node::emptyNode; + } + + + + vector + UnrootedTree::getNodes() const { + vector nodes; + + for (auto entry : this->nodes) { + nodes.push_back(entry.second); + } + + return nodes; + } + + + + vector + UnrootedTree::getLeaves() const { + vector leaves; + + for (auto entry : nodes) { + Node *node = entry.second; + if (node->isLeaf()) { + leaves.push_back(node); + } + } + + return leaves; + } + + + + DistanceMatrix & + UnrootedTree::getDistanceMatrix() const { + vector leaves = getLeaves(); + DistanceMatrix *d = new DistanceMatrix(); + + for (auto i : leaves) { + d->addOTU(i->getLabel()); + for (auto j : leaves) { + if (i == j) { + continue; + } + (*d)(i->getLabel(), j->getLabel(), i->getDistance(*j)); + } + } + + return *d; + } + + + + UnrootedTree & + UnrootedTree::addNode(Node &node) { + nodes[node.getIdentifier()] = &node; + return *this; + } + + + + RootedTree & + UnrootedTree::midpointRoot() const { + map node_pool; + + UnrootedTree tree = *this; + DistanceMatrix d = tree.getDistanceMatrix(); + + // Initializes node pool + for (auto node : tree.getLeaves()) { + node_pool[node->getLabel()] = node; + } + + // Finds most distant nodes A and B + pair max = d.getMaximumPosition(); + Node *A = node_pool[max.first], + *B = node_pool[max.second]; + double max_distance = d(max.first, max.second); + + // Finds adjacent nodes between which new root will be placed + Node *current = A, + *previous = B; + double path_distance = max_distance; + + while (path_distance >= max_distance / 2.0 && !current->isNeighbor(*B)) { + Node *avoid = previous; + previous = current; + current = ¤t->getNeighborClosestTo(*B, avoid); + path_distance = current->getDistance(*B); + } + + // Adds new root node between current and previous + Node *root = new Node(); + tree.addNode(*root); + current->addBetween(*previous, *root, max_distance / 2.0 - path_distance); + + return tree.asRootedTree(*root); + } + + + + RootedTree & + UnrootedTree::asRootedTree() const { + return midpointRoot(); + } + + + + RootedTree & + UnrootedTree::asRootedTree(const size_t root) const { + return asRootedTree(getNode(root)); + } + + + + RootedTree & + UnrootedTree::asRootedTree(Node &root, const Node *parent) const { + RootedTree *root_node = new RootedTree(root.getLabel()); + + // Sets distance from parent, if parent is not null + if (nullptr != parent) { + root_node->setDistance(root.getDistance(*parent)); + } + + // Recursively adds children + for (auto &entry : root.neighbors) { + Node *neighbor = entry.second.first; + if (neighbor != parent) { + root_node->addChild(asRootedTree(*neighbor, &root)); + } + } + + return *root_node; + } + + + + UnrootedTree & + UnrootedTree::asUnrootedTree() const { + return *(const_cast(this)); + } + + + + UnrootedTree & + UnrootedTree::parseNewick(const string &input) { + RootedTree tree; + + tree.parseNewick(input); + + *this = tree.asUnrootedTree(); + + return *this; + } + + + + string + UnrootedTree::asNewick() const { + return asRootedTree().asNewick(); + } + + + + UnrootedTree & + UnrootedTree::accept(Visitor &visitor) { + visitor.visit(*this); + return *this; + } +} // namespace Phylo +} // namespace Victor \ No newline at end of file diff --git a/Phylo/Sources/UnrootedTree.h b/Phylo/Sources/UnrootedTree.h new file mode 100644 index 0000000..c54fd57 --- /dev/null +++ b/Phylo/Sources/UnrootedTree.h @@ -0,0 +1,473 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_UNROOTEDTREE_H_ +#define _VICTOR_PHYLO_UNROOTEDTREE_H_ + +#include +#include +#include +#include +#include +#include + +using std::string; +using std::vector; +using std::map; +using std::pair; +using std::make_pair; + +namespace Victor { +namespace Phylo { + +/** @brief Implements an unrooted tree. + * + * An unrooted tree is a phylogenetic tree where every node may have a + * label, arcs have a length and nodes may have neighbors. + * + * This class follows the Visitor Design Pattern and uses Method + * Cascading (through Method Chaining). + * + * @author Marco Zanella + */ +class UnrootedTree: public PhylogeneticTree { + public: + /** @brief Implements a node in an unrooted tree. */ + class Node { + friend class UnrootedTree; + public: + /** @brief Builds a node and inserts it into a tree. + * @param[in, out] tree Tree this node belongs to + * @param[in] label Label of this node + */ + explicit Node(UnrootedTree *tree, const string &label = ""); + + /** @brief Default constructor. + * @param[in] label Label of this node + */ + Node(const string &label = ""); + + + + /** @brief Tells whether two nodes are equal. + * + * Two nodes are equal when they have the same identifier. + * @param[in] other Other node + * @retval true Nodes are equal + * @retval false Nodes are not equal + */ + bool operator==(const Node &other) const; + + /** @brief Tells whether two nodes are not equal. + * + * Two nodes are equal when they have the same identifier. + * @param[in] other Other node + * @retval true Nodes are not equal + * @retval false Nodes are equal + */ + bool operator!=(const Node &other) const; + + + + /** @brief Tells whether this node is a leaf. + * @retval true This node is a leaf + * @retval false This node has at least two neighbors + */ + bool isLeaf() const; + + /** @brief Tells whether this node has neighbors. + * @retval true This node has at least one neighbor + * @retval false This node does not have any neighbors + */ + bool hasNeighbors() const; + + /** @brief Tells whether this node is a neighbor of given node. + * @param[in] identifier Identifier of given node + * @retval true This node is a neighbor of giiven node + * @retval false This node is not a neighbor of given node + */ + bool isNeighbor(const size_t identifier) const; + + /** @brief Tells whether this node is a neighbor of given node. + * @param[in] node Given node + * @retval true This node is a neighbor of given node + * @retval false This node is not a neighbor of given node + */ + bool isNeighbor(const Node &node) const; + + /** @brief Tells whether a path exists from this node to given node. + * @param[in] identifier Identifier of given node + * @param[in] previous Previously visited node + * @retval true A path between this node and given one exists + * @retval false A path between this node and given one does not exist + */ + bool hasPath(const size_t identifier, const Node *previous = nullptr) const; + + /** @brief Tells whether a path exists from this node to given node. + * @param[in] node Given node + * @retval true A path between this node and given one exists + * @retval false A path between this node and given one does not exist + */ + bool hasPath(const Node &node) const; + + /** @brief Tells whether this node belongs to given tree + * @param[in] tree Given tree + * @retval true This node belongs to given tree + * @retval false This node does not belong to given tree + */ + bool belongsTo(const UnrootedTree &tree) const; + + + + /** @brief Returns identifier of this node. + * @return Identifier of this node + */ + size_t getIdentifier() const; + + /** @brief Returns identifier of this node. + * @return Identifier of this node + */ + size_t getID() const; + + /** @brief Returns number of neighbors of this node. + * @return Number of neighbors of this node + */ + size_t getSize() const; + + /** @brief Returns number of neighbors of this node. + * @return Number of neighbors of this node + */ + size_t getNeighborsNumber() const; + + /** @brief Returns neighbor at given index. + * + * If node is not a neighbor, returns an empty node. + * @param[in] identifier Identifier of the neighbor + * @return Child node + */ + Node &getNeighbor(const size_t identifier) const; + + /** @brief Returns neighbor closest to this node. + * + * If more than one neighbor share minimal distance, choses one + * in non-deterministic way. + * + * If this node has no neighbors, returns this node itself. + * @return Closest neighbor + */ + Node &getClosestNeighbor() const; + + /** @brief Returns neighbor closest to target node. + * + * If more than one neighbor share minimal distance, choses one + * in non-deterministic way. + * + * If this node has no neighbors, or target node is not reachable, + * returns this node. + * @param[in] target Target node + * @param[in] avoid Node to be avoided + * @return Neighbor closest to target + */ + Node &getNeighborClosestTo(const Node &target, const Node *avoid = nullptr) const; + + /** @brief Returns neighbors of this node. + * @return Neighbors as a vector + */ + vector getNeighbors() const; + + /** @brief Returns distance from this node to given one. + * @param[in] identifier Identifier of the node + * @param[in] previous Neighbor which has been already visited + * @return Distance from this node to given one. + */ + double getDistance(const size_t identifier, const Node *previous = nullptr) const; + + /** @brief Returns distance from this node to given one. + * @param[in] node Node + * @return Distance from this node to given one. + */ + double getDistance(const Node &node) const; + + /** @brief Returns unrooted tree this node belongs to. + * @return Unrooted tree this node belongs to + */ + UnrootedTree &getTree() const; + + /** @brief Returns label of this node. + * @return Label of this node + */ + string getLabel() const; + + + + /** @brief Sets label of this node. + * @param[in] label New label of this node + * @return This node + */ + Node &setLabel(const string &label = ""); + + /** @brief Sets distance between this node and given one. + * + * If given node is not a neighbor of this node, nothing happens. + * @param[in, out] identifier Identifier of given node + * @param[in] distance New distance + * @return This node + */ + Node &setDistance(const size_t identifier, const double distance = NA); + + /** @brief Sets distance between this node and given one. + * + * If given node is not a neighbor of this node, nothing happens. + * @param[in, out] node Given node + * @param[in] distance New distance + * @return This node + */ + Node &setDistance(Node &node, const double distance = NA); + + + + /** @brief Adds a neighbor to this node. + * + * Neighbor node must belong to the same tree. If it does not + * belong to the same tree, nothing happens. + * @param[in, out] node New neighbor + * @param[in] distance Distance of new neighbor + * @return This node + */ + Node &addNeighbor(Node &node, const double distance = NA); + + /** @brief Adds a node between this node and one neighbor of its. + * + * If new node does not belong to the tree, or given node is + * not a neighbor, nothing happens. + * @param[in] neighbor Old neighbor + * @param[in] node New neighbor + * @param[in] distance Distance from this node + * @return This node itself + */ + Node &addBetween(Node &neighbor, Node &node, const double distance); + + /** @brief Removes a neighbor from this node. + * + * If node is not a neighbor of this node, nothing happens. + * @param[in, out] node Neighbor to remove + * @return This node + */ + Node &removeNeighbor(Node &node); + + + /** @brief Returns a rooted tree rooted in this node. + * @return A rooted tree version of the tree this node belongs to + */ + RootedTree &asRootedTree() const; + + + + private: + static Node emptyNode; ///< Empty node + static size_t next_ID; ///< Next available identifier for a node + static const double NA; ///< Distance Not Available + + size_t ID; ///< Identifier of this node + string label; ///< Label of this node + map> neighbors; ///< Neighbors of this node + UnrootedTree *tree; ///< Unrooted tree this node belongs to + + + /** Returns next available identifier for a node. + * @return Next available identifier + */ + static size_t getNextIdentifier(); + }; + + + + /** @brief Default constructor. + * + * Produces an empty unrooted tree. + */ + UnrootedTree(); + + /** @brief Destructor. */ + virtual ~UnrootedTree(); + + + + /** @brief Equality test for unrooted trees. + * + * Two unrooted trees are equal if (they point to the same + * memory area, or) they have the same nodes. + * @param[in] other Other tree + * @retval true Trees are equal + * @retval false Trees are not equal + */ + bool operator==(const UnrootedTree &other) const; + + /** @brief Inequality test for unrooted trees. + * + * Two unrooted trees are equal if (they point to the same + * memory area, or) they have the same nodes. + * @param[in] other Other tree + * @retval true Trees are not equal + * @retval false Trees are equal + */ + bool operator!=(const UnrootedTree &other) const; + + /** @brief Adds a node to this tree. + * @param[in, out] node Node to be added + * @return This tree itself + */ + UnrootedTree &operator+(Node &node); + + /** @brief Returns node with given identifier. + * + * If indentifier is invalid, returns an empty node. + * @param[in] identifier Index of the node + * @return Node with given identifier + */ + Node &operator[](const size_t identifier) const; + + + + /** @brief Tells whether this tree is empty. + * @retval true This tree is empty + * @retval false There is at least one node in this tree + */ + bool isEmpty() const; + + /** @brief Tells whether a node belongs to this tree. + * @param[in] ID Identifier of given node + * @retval true Node belongs to this tree + * @retval false Node does not belong to this tree + */ + bool hasNode(const size_t ID) const; + + /** @brief Tells whether a node belongs to this tree. + * @param[in] node Given node + * @retval true Node belongs to this tree + * @retval false Node does not belong to this tree + */ + bool hasNode(const Node &node) const; + + + + /** @brief Returns number of nodes in this unrooted tree + * @return Number of nodes in this tree + */ + size_t getSize() const; + + /** @brief Returns node with given identifier. + * + * If identifier is invalid, returns an empty node. + * @param[in] identifier Identifier of the node + * @return Node with given identifier + */ + Node &getNode(const size_t identifier) const; + + /** @brief Returns every node in this tree. + * @return Nodes as a vector + */ + vector getNodes() const; + + /** @brief Returns leaves in this tree. + * @return Leaves as a vector + */ + vector getLeaves() const; + + /** @brief Returns matrix of distances among leaves. + * @return Distance matrix + */ + virtual DistanceMatrix &getDistanceMatrix() const; + + + + /** @brief Adds a node into this tree. + * @param[in] node Node to insert + * @return This tree itself + */ + UnrootedTree &addNode(Node &node); + + + + /** @brief Returns a rooted version of this tree. + * + * Root node is chosen using the midpoint rooting strategy. + * @return A rooted version of this tree + */ + virtual RootedTree &midpointRoot() const; + + /** @brief Returns a rooted version of this tree. + * + * Root node is chosen with a midpoint strategy. + * @return A rooted version of this tree + */ + virtual RootedTree &asRootedTree() const; + + /** @brief Returns a rooted version of this tree. + * + * Tree is rooted in one node of its. + * @param[in] root Identifier of the root node + * @return A rooted version of this tree + */ + virtual RootedTree &asRootedTree(const size_t root) const; + + /** @brief Returns a rooted version of this tree. + * + * Tree is rooted in one node of its. + * @param[in] root Node that will become root + * @param[in] parent Pointer to parent node + * @return A rooted version of this tree + */ + virtual RootedTree &asRootedTree(Node &root, const Node *parent = nullptr) const; + + /** @brief Returns an unrooted version of this tree. + * @return An unrooted version of this tree + */ + virtual UnrootedTree &asUnrootedTree() const; + + /** @brief Parses a string in Newick format. + * @param[in] input String in Newick format + * @return This tree itself + */ + virtual UnrootedTree &parseNewick(const string &input); + + /** @brief Returns a Newick version of this tree. + * @return String representing this tree in Newick format + */ + virtual string asNewick() const; + + + + /** @brief Accepts a visitor. + * @param[in, out] visitor Visitor to accept + * @return This tree itself + */ + virtual UnrootedTree &accept(Visitor &visitor); + + + + private: + /** Empty tree. */ + static UnrootedTree emptyTree; + + /** Nodes in this tree. */ + map nodes; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_UNROOTEDTREE_H_ \ No newline at end of file diff --git a/Phylo/Sources/Visitor.h b/Phylo/Sources/Visitor.h new file mode 100644 index 0000000..80bb3fe --- /dev/null +++ b/Phylo/Sources/Visitor.h @@ -0,0 +1,63 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_VISITOR_H_ +#define _VICTOR_PHYLO_VISITOR_H_ + +namespace Victor { +namespace Phylo { + +// Forward class declaration +class PhylogeneticTree; +class RootedTree; +class UnrootedTree; + +/** @brief A visitor for the phylogenetic tree hierarchy. + * + * This class defines the interface of a visitor for the phylogenetic + * tree hierarchy: PhylogeneticTree, RootedTree and UnrootedTree. + * + * This class follows the Visitor Design Pattern. + * + * @author Marco Zanella + */ +class Visitor { + public: + /** @brief Destructor. */ + virtual ~Visitor() = 0; + + + + /** @brief Visits a phylogenetic tree. + * @param[in, out] tree Phylogenetic tree to visit + */ + virtual void visit(PhylogeneticTree &tree) = 0; + + /** @brief Visits a rooted tree. + * @param[in, out] tree Rooted tree to visit + */ + virtual void visit(RootedTree &tree) = 0; + + /** @brief Visits an unrooted tree. + * @param[in, out] tree Unrooted tree to visit + */ + virtual void visit(UnrootedTree &tree) = 0; +}; + +} // namespace Phylo +} // namespace Victor + +#endif // _VICTOR_PHYLO_VISITOR_H_ \ No newline at end of file diff --git a/Phylo/Sources/phylo.h b/Phylo/Sources/phylo.h new file mode 100644 index 0000000..c0dde03 --- /dev/null +++ b/Phylo/Sources/phylo.h @@ -0,0 +1,58 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#ifndef _VICTOR_PHYLO_PHYLO_ +#define _VICTOR_PHYLO_PHYLO_ + + +namespace Victor { +/** @brief Molecular PHYLOgenenesys package. + * + * @author Marco Zanella + */ +namespace Phylo {} +} + +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +#include + +#include +#include +#include + +#include + +#endif // _VICTOR_PHYLO_PHYLO_ \ No newline at end of file diff --git a/Phylo/Sources/precalculated_matrices.h b/Phylo/Sources/precalculated_matrices.h new file mode 100644 index 0000000..ef10b5f --- /dev/null +++ b/Phylo/Sources/precalculated_matrices.h @@ -0,0 +1,864 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +/* These matrices are extracted form the official ClustalW implementation. + * Credits go to Mark Larkin, Copyright (c) 2007 Des Higgins, Julie Thompson + * and Toby Gibson. + */ + +#ifndef _VICTOR_PHYLO_PRECOMPUTED_MATRICES_H_ +#define _VICTOR_PHYLO_PRECOMPUTED_MATRICES_H_ + +#include + +using std::string; + +namespace Victor { +namespace Phylo { + +/** Sorted residues used in precalculated matrices. */ +const string _residues = "ABCDEFGHIKLMNPQRSTVWXYZ"; + + + +//////////////////////////////////////////////////////////////////////// +// BLOSUM family +int _blosum30[] = { + 4, + 0, 5, + -3, -2, 17, + 0, 5, -3, 9, + 0, 0, 1, 1, 6, + -2, -3, -3, -5, -4, 10, + 0, 0, -4, -1, -2, -3, 8, + -2, -2, -5, -2, 0, -3, -3, 14, + 0, -2, -2, -4, -3, 0, -1, -2, 6, + 0, 0, -3, 0, 2, -1, -1, -2, -2, 4, + -1, -1, 0, -1, -1, 2, -2, -1, 2, -2, 4, + 1, -2, -2, -3, -1, -2, -2, 2, 1, 2, 2, 6, + 0, 4, -1, 1, -1, -1, 0, -1, 0, 0, -2, 0, 8, + -1, -2, -3, -1, 1, -4, -1, 1, -3, 1, -3, -4, -3, 11, + 1, -1, -2, -1, 2, -3, -2, 0, -2, 0, -2, -1, -1, 0, 8, + -1, -2, -2, -1, -1, -1, -2, -1, -3, 1, -2, 0, -2, -1, 3, 8, + 1, 0, -2, 0, 0, -1, 0, -1, -1, 0, -2, -2, 0, -1, -1, -1, 4, + 1, 0, -2, -1, -2, -2, -2, -2, 0, -1, 0, 0, 1, 0, 0, -3, 2, 5, + 1, -2, -2, -2, -3, 1, -3, -3, 4, -2, 1, 0, -2, -4, -3, -1, -1, 1, 5, + -5, -5, -2, -4, -1, 1, 1, -5, -3, -2, -2, -3, -7, -3, -1, 0, -3, -5, -3, 20, + 0, -1, -2, -1, -1, -1, -1, -1, 0, 0, 0, 0, 0, -1, 0, -1, 0, 0, 0, -2, -1, + -4, -3, -6, -1, -2, 3, -3, 0, -1, -1, 3, -1, -4, -2, -1, 0, -2, -1, 1, 5, -1, 9, + 0, 0, 0, 0, 5, -4, -2, 0, -3, 1, -1, -1, -1, 0, 4, 0, -1, -1, -3, -1, 0, -2, 4 +}; + +int _blosum35[] = { + 5, + -1, 5, + -2, -2, 15, + -1, 5, -3, 8, + -1, 0, -1, 2, 6, + -2, -2, -4, -3, -3, 8, + 0, 0, -3, -2, -2, -3, 7, + -2, 0, -4, 0, -1, -3, -2, 12, + -1, -2, -4, -3, -3, 1, -3, -3, 5, + 0, 0, -2, -1, 1, -1, -1, -2, -2, 5, + -2, -2, -2, -2, -1, 2, -3, -2, 2, -2, 5, + 0, -2, -4, -3, -2, 0, -1, 1, 1, 0, 3, 6, + -1, 4, -1, 1, -1, -1, 1, 1, -1, 0, -2, -1, 7, + -2, -1, -4, -1, 0, -4, -2, -1, -1, 0, -3, -3, -2, 10, + 0, 0, -3, -1, 2, -4, -2, -1, -2, 0, -2, -1, 1, 0, 7, + -1, -1, -3, -1, -1, -1, -2, -1, -3, 2, -2, 0, -1, -2, 2, 8, + 1, 0, -3, -1, 0, -1, 1, -1, -2, 0, -2, -1, 0, -2, 0, -1, 4, + 0, -1, -1, -1, -1, -1, -2, -2, -1, 0, 0, 0, 0, 0, 0, -2, 2, 5, + 0, -2, -2, -2, -2, 1, -3, -4, 4, -2, 2, 1, -2, -3, -3, -1, -1, 1, 5, + -2, -3, -5, -3, -1, 1, -1, -4, -1, 0, 0, 1, -2, -4, -1, 0, -2, -2, -2, 16, + 0, -1, -2, -1, -1, -1, -1, -1, 0, 0, 0, 0, 0, -1, -1, -1, 0, 0, 0, -1, -1, + -1, -2, -5, -2, -1, 3, -2, 0, 0, -1, 0, 0, -2, -3, 0, 0, -1, -2, 0, 3, -1, 8, + -1, 0, -2, 1, 5, -3, -2, -1, -3, 1, -2, -2, 0, 0, 4, 0, 0, -1, -2, -1, 0, -1, 4 +}; + +int _blosum40[] = { + 5, + -1, 5, + -2, -2, 16, + -1, 6, -2, 9, + -1, 1, -2, 2, 7, + -3, -3, -2, -4, -3, 9, + 1, -1, -3, -2, -3, -3, 8, + -2, 0, -4, 0, 0, -2, -2, 13, + -1, -3, -4, -4, -4, 1, -4, -3, 6, + -1, 0, -3, 0, 1, -3, -2, -1, -3, 6, + -2, -3, -2, -3, -2, 2, -4, -2, 2, -2, 6, + -1, -3, -3, -3, -2, 0, -2, 1, 1, -1, 3, 7, + -1, 4, -2, 2, -1, -3, 0, 1, -2, 0, -3, -2, 8, + -2, -2, -5, -2, 0, -4, -1, -2, -2, -1, -4, -2, -2, 11, + 0, 0, -4, -1, 2, -4, -2, 0, -3, 1, -2, -1, 1, -2, 8, + -2, -1, -3, -1, -1, -2, -3, 0, -3, 3, -2, -1, 0, -3, 2, 9, + 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -3, -2, 1, -1, 1, -1, 5, + 0, 0, -1, -1, -1, -1, -2, -2, -1, 0, -1, -1, 0, 0, -1, -2, 2, 6, + 0, -3, -2, -3, -3, 0, -4, -4, 4, -2, 2, 1, -3, -3, -3, -2, -1, 1, 5, + -3, -4, -6, -5, -2, 1, -2, -5, -3, -2, -1, -2, -4, -4, -1, -2, -5, -4, -3, 19, + 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, 0, -1, -2, -1, -1, 0, 0, -1, -2, -1, + -2, -3, -4, -3, -2, 4, -3, 2, 0, -1, 0, 1, -2, -3, -1, -1, -2, -1, -1, 3, -1, 9, + -1, 2, -3, 1, 5, -4, -2, 0, -4, 1, -2, -2, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 5 +}; + +int _blosum45[] = { + 5, + -1, 4, + -1, -2, 12, + -2, 5, -3, 7, + -1, 1, -3, 2, 6, + -2, -3, -2, -4, -3, 8, + 0, -1, -3, -1, -2, -3, 7, + -2, 0, -3, 0, 0, -2, -2, 10, + -1, -3, -3, -4, -3, 0, -4, -3, 5, + -1, 0, -3, 0, 1, -3, -2, -1, -3, 5, + -1, -3, -2, -3, -2, 1, -3, -2, 2, -3, 5, + -1, -2, -2, -3, -2, 0, -2, 0, 2, -1, 2, 6, + -1, 4, -2, 2, 0, -2, 0, 1, -2, 0, -3, -2, 6, + -1, -2, -4, -1, 0, -3, -2, -2, -2, -1, -3, -2, -2, 9, + -1, 0, -3, 0, 2, -4, -2, 1, -2, 1, -2, 0, 0, -1, 6, + -2, -1, -3, -1, 0, -2, -2, 0, -3, 3, -2, -1, 0, -2, 1, 7, + 1, 0, -1, 0, 0, -2, 0, -1, -2, -1, -3, -2, 1, -1, 0, -1, 4, + 0, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, + 0, -3, -1, -3, -3, 0, -3, -3, 3, -2, 1, 1, -3, -3, -3, -2, -1, 0, 5, + -2, -4, -5, -4, -3, 1, -2, -3, -2, -2, -2, -2, -4, -3, -2, -2, -4, -3, -3, 15, + 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, -1, -2, -1, + -2, -2, -3, -2, -2, 3, -3, 2, 0, -1, 0, 0, -2, -3, -1, -1, -2, -1, -1, 3, -1, 8, + -1, 2, -3, 1, 4, -3, -2, 0, -3, 1, -2, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 4 +}; + +int _blosum50[] = { + 5, + -2, 5, + -1, -3, 13, + -2, 5, -4, 8, + -1, 1, -3, 2, 6, + -3, -4, -2, -5, -3, 8, + 0, -1, -3, -1, -3, -4, 8, + -2, 0, -3, -1, 0, -1, -2, 10, + -1, -4, -2, -4, -4, 0, -4, -4, 5, + -1, 0, -3, -1, 1, -4, -2, 0, -3, 6, + -2, -4, -2, -4, -3, 1, -4, -3, 2, -3, 5, + -1, -3, -2, -4, -2, 0, -3, -1, 2, -2, 3, 7, + -1, 4, -2, 2, 0, -4, 0, 1, -3, 0, -4, -2, 7, + -1, -2, -4, -1, -1, -4, -2, -2, -3, -1, -4, -3, -2, 10, + -1, 0, -3, 0, 2, -4, -2, 1, -3, 2, -2, 0, 0, -1, 7, + -2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 7, + 1, 0, -1, 0, -1, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5, + 0, 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, + 0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -3, -3, -3, -3, -2, 0, 5, + -3, -5, -5, -5, -3, 1, -3, -3, -3, -3, -2, -1, -4, -4, -1, -3, -4, -3, -3, 15, + -1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, 0, -1, -3, -1, + -2, -3, -3, -3, -2, 4, -3, 2, -1, -2, -1, 0, -2, -3, -1, -1, -2, -2, -1, 2, -1, 8, + -1, 2, -3, 1, 5, -4, -2, 0, -3, 1, -3, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 5 +}; + +int _blosum55[] = { + 5, + -2, 5, + 0, -4, 13, + -2, 5, -4, 8, + -1, 1, -4, 2, 7, + -3, -5, -3, -5, -4, 9, + 0, -1, -3, -2, -3, -4, 8, + -2, 0, -4, -1, -1, -1, -2, 11, + -2, -4, -2, -4, -4, 0, -5, -4, 6, + -1, 0, -4, -1, 1, -4, -2, 0, -4, 6, + -2, -4, -2, -5, -4, 1, -5, -3, 2, -3, 6, + -1, -3, -2, -4, -3, 0, -3, -2, 2, -2, 3, 8, + -2, 4, -3, 2, 0, -4, 0, 1, -4, 0, -4, -3, 8, + -1, -2, -3, -2, -1, -5, -3, -3, -3, -1, -4, -3, -2, 10, + -1, 0, -4, 0, 2, -4, -2, 1, -4, 2, -3, 0, 0, -1, 7, + -2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 8, + 2, 0, -1, 0, 0, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5, + 0, -1, -1, -1, -1, -3, -2, -2, -1, -1, -2, -1, 0, -1, -1, -1, 2, 6, + 0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -4, -3, -3, -3, -2, 0, 5, + -4, -5, -4, -5, -3, 2, -3, -3, -3, -4, -3, -2, -5, -5, -2, -3, -4, -3, -4, 15, + -1, -1, -2, -2, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1, + -2, -3, -3, -3, -2, 4, -4, 2, -1, -2, -1, -1, -2, -4, -1, -2, -2, -2, -2, 3, -1, 9, + -1, 2, -4, 1, 5, -4, -3, 0, -4, 1, -3, -2, 0, -1, 4, 0, 0, -1, -3, -3, -1, -2, 5 +}; + +int _blosum62[] = { + 4, + -2, 4, + 0, -3, 9, + -2, 4, -3, 6, + -1, 1, -4, 2, 5, + -2, -3, -2, -3, -3, 6, + 0, -1, -3, -1, -2, -3, 6, + -2, 0, -3, -1, 0, -1, -2, 8, + -1, -3, -1, -3, -3, 0, -4, -3, 4, + -1, 0, -3, -1, 1, -3, -2, -1, -3, 5, + -1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 4, + -1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, + -2, 3, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, + -1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, + -1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, + -1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, + 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, + 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, + 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, + -3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, + 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, -1, + -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 7, + -1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4 +}; + +int _blosum65[] = { + 4, + -2, 4, + 0, -3, 9, + -2, 4, -4, 6, + -1, 1, -4, 2, 5, + -2, -3, -2, -4, -3, 6, + 0, -1, -3, -1, -2, -3, 6, + -2, 0, -3, -1, 0, -1, -2, 8, + -1, -3, -1, -3, -3, 0, -4, -3, 4, + -1, 0, -3, -1, 1, -3, -2, -1, -3, 5, + -2, -4, -1, -4, -3, 0, -4, -3, 2, -3, 4, + -1, -3, -2, -3, -2, 0, -3, -2, 1, -2, 2, 6, + -2, 3, -3, 1, 0, -3, -1, 1, -3, 0, -4, -2, 6, + -1, -2, -3, -2, -1, -4, -2, -2, -3, -1, -3, -3, -2, 8, + -1, 0, -3, 0, 2, -3, -2, 1, -3, 1, -2, 0, 0, -1, 6, + -1, -1, -4, -2, 0, -3, -2, 0, -3, 2, -2, -2, 0, -2, 1, 6, + 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -3, -2, 1, -1, 0, -1, 4, + 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, + 0, -3, -1, -3, -3, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, + -3, -4, -2, -5, -3, 1, -3, -2, -2, -3, -2, -2, -4, -4, -2, -3, -3, -3, -3, 10, + -1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -2, -1, + -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -2, -2, -2, -2, -1, 2, -1, 7, + -1, 1, -4, 1, 4, -3, -2, 0, -3, 1, -3, -2, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4 +}; + +int _blosum70[] = { + 4, + -2, 4, + -1, -4, 9, + -2, 4, -4, 6, + -1, 1, -4, 1, 5, + -2, -4, -2, -4, -4, 6, + 0, -1, -3, -2, -2, -4, 6, + -2, -1, -4, -1, 0, -1, -2, 8, + -2, -4, -1, -4, -4, 0, -4, -4, 4, + -1, -1, -4, -1, 1, -3, -2, -1, -3, 5, + -2, -4, -2, -4, -3, 0, -4, -3, 2, -3, 4, + -1, -3, -2, -3, -2, 0, -3, -2, 1, -2, 2, 6, + -2, 3, -3, 1, 0, -3, -1, 0, -4, 0, -4, -2, 6, + -1, -2, -3, -2, -1, -4, -3, -2, -3, -1, -3, -3, -2, 8, + -1, 0, -3, -1, 2, -3, -2, 1, -3, 1, -2, 0, 0, -2, 6, + -2, -1, -4, -2, 0, -3, -3, 0, -3, 2, -3, -2, -1, -2, 1, 6, + 1, 0, -1, 0, 0, -3, -1, -1, -3, 0, -3, -2, 0, -1, 0, -1, 4, + 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -2, -1, 0, -1, -1, -1, 1, 5, + 0, -3, -1, -4, -3, -1, -4, -3, 3, -3, 1, 1, -3, -3, -2, -3, -2, 0, 4, + -3, -4, -3, -5, -4, 1, -3, -2, -3, -3, -2, -2, -4, -4, -2, -3, -3, -3, -3, 11, + -1, -1, -2, -2, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1, + -2, -3, -3, -4, -3, 3, -4, 2, -1, -2, -1, -1, -2, -3, -2, -2, -2, -2, -2, 2, -2, 7, + -1, 0, -4, 1, 4, -4, -2, 0, -3, 1, -3, -2, 0, -1, 3, 0, 0, -1, -3, -3, -1, -2, 4 +}; + +int _blosum75[] = { + 4, + -2, 4, + -1, -4, 9, + -2, 4, -4, 6, + -1, 1, -5, 1, 5, + -3, -4, -2, -4, -4, 6, + 0, -1, -3, -2, -3, -4, 6, + -2, -1, -4, -1, 0, -2, -2, 8, + -2, -4, -1, -4, -4, 0, -5, -4, 4, + -1, -1, -4, -1, 1, -4, -2, -1, -3, 5, + -2, -4, -2, -4, -4, 0, -4, -3, 1, -3, 4, + -1, -3, -2, -4, -2, 0, -3, -2, 1, -2, 2, 6, + -2, 3, -3, 1, -1, -4, -1, 0, -4, 0, -4, -3, 6, + -1, -2, -4, -2, -1, -4, -3, -2, -3, -1, -3, -3, -3, 8, + -1, 0, -3, -1, 2, -4, -2, 1, -3, 1, -3, 0, 0, -2, 6, + -2, -1, -4, -2, 0, -3, -3, 0, -3, 2, -3, -2, -1, -2, 1, 6, + 1, 0, -1, -1, 0, -3, -1, -1, -3, 0, -3, -2, 0, -1, 0, -1, 5, + 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -2, -1, 0, -1, -1, -1, 1, 5, + 0, -4, -1, -4, -3, -1, -4, -4, 3, -3, 1, 1, -3, -3, -2, -3, -2, 0, 4, + -3, -5, -3, -5, -4, 1, -3, -2, -3, -4, -2, -2, -4, -5, -2, -3, -3, -3, -3, 11, + -1, -2, -2, -2, -1, -2, -2, -1, -2, -1, -1, -1, -1, -2, -1, -1, -1, -1, -1, -3, -1, + -2, -3, -3, -4, -3, 3, -4, 2, -2, -2, -1, -2, -3, -4, -2, -2, -2, -2, -2, 2, -2, 7, + -1, 0, -4, 1, 4, -4, -2, 0, -4, 1, -3, -2, 0, -2, 3, 0, 0, -1, -3, -3, -1, -3, 4 +}; + +int _blosum80[] = { + 7, + -3, 6, + -1, -6, 13, + -3, 6, -7, 10, + -2, 1, -7, 2, 8, + -4, -6, -4, -6, -6, 10, + 0, -2, -6, -3, -4, -6, 9, + -3, -1, -7, -2, 0, -2, -4, 12, + -3, -6, -2, -7, -6, -1, -7, -6, 7, + -1, -1, -6, -2, 1, -5, -3, -1, -5, 8, + -3, -7, -3, -7, -6, 0, -7, -5, 2, -4, 6, + -2, -5, -3, -6, -4, 0, -5, -4, 2, -3, 3, 9, + -3, 5, -5, 2, -1, -6, -1, 1, -6, 0, -6, -4, 9, + -1, -4, -6, -3, -2, -6, -5, -4, -5, -2, -5, -4, -4, 12, + -2, -1, -5, -1, 3, -5, -4, 1, -5, 2, -4, -1, 0, -3, 9, + -3, -2, -6, -3, -1, -5, -4, 0, -5, 3, -4, -3, -1, -3, 1, 9, + 2, 0, -2, -1, -1, -4, -1, -2, -4, -1, -4, -3, 1, -2, -1, -2, 7, + 0, -1, -2, -2, -2, -4, -3, -3, -2, -1, -3, -1, 0, -3, -1, -2, 2, 8, + -1, -6, -2, -6, -4, -2, -6, -5, 4, -4, 1, 1, -5, -4, -4, -4, -3, 0, 7, + -5, -8, -5, -8, -6, 0, -6, -4, -5, -6, -4, -3, -7, -7, -4, -5, -6, -5, -5, 16, + -1, -3, -4, -3, -2, -3, -3, -2, -2, -2, -2, -2, -2, -3, -2, -2, -1, -1, -2, -5, -2, + -4, -5, -5, -6, -5, 4, -6, 3, -3, -4, -2, -3, -4, -6, -3, -4, -3, -3, -3, 3, -3, 11, + -2, 0, -7, 1, 6, -6, -4, 0, -6, 1, -5, -3, -1, -2, 5, 0, -1, -2, -4, -5, -1, -4, 6 +}; + +int _blosum85[] = { + 5, + -2, 4, + -1, -4, 9, + -2, 4, -5, 7, + -1, 0, -5, 1, 6, + -3, -4, -3, -4, -4, 7, + 0, -1, -4, -2, -3, -4, 6, + -2, -1, -5, -2, -1, -2, -3, 8, + -2, -5, -2, -5, -4, -1, -5, -4, 5, + -1, -1, -4, -1, 0, -4, -2, -1, -3, 6, + -2, -5, -2, -5, -4, 0, -5, -3, 1, -3, 4, + -2, -4, -2, -4, -3, -1, -4, -3, 1, -2, 2, 7, + -2, 4, -4, 1, -1, -4, -1, 0, -4, 0, -4, -3, 7, + -1, -3, -4, -2, -2, -4, -3, -3, -4, -2, -4, -3, -3, 8, + -1, -1, -4, -1, 2, -4, -3, 1, -4, 1, -3, 0, 0, -2, 6, + -2, -2, -4, -2, -1, -4, -3, 0, -4, 2, -3, -2, -1, -2, 1, 6, + 1, 0, -2, -1, -1, -3, -1, -1, -3, -1, -3, -2, 0, -1, -1, -1, 5, + 0, -1, -2, -2, -1, -3, -2, -2, -1, -1, -2, -1, 0, -2, -1, -2, 1, 5, + -1, -4, -1, -4, -3, -1, -4, -4, 3, -3, 0, 0, -4, -3, -3, -3, -2, 0, 5, + -3, -5, -4, -6, -4, 0, -4, -3, -3, -5, -3, -2, -5, -5, -3, -4, -4, -4, -3, 11, + -1, -2, -3, -2, -1, -2, -2, -2, -2, -1, -2, -1, -2, -2, -1, -2, -1, -1, -1, -3, -2, + -3, -4, -3, -4, -4, 3, -5, 2, -2, -3, -2, -2, -3, -4, -2, -3, -2, -2, -2, 2, -2, 7, + -1, 0, -5, 1, 4, -4, -3, 0, -4, 1, -4, -2, -1, -2, 4, 0, -1, -1, -3, -4, -1, -3, 4 +}; + +int _blosum90[] = { + 5, + -2, 4, + -1, -4, 9, + -3, 4, -5, 7, + -1, 0, -6, 1, 6, + -3, -4, -3, -5, -5, 7, + 0, -2, -4, -2, -3, -5, 6, + -2, -1, -5, -2, -1, -2, -3, 8, + -2, -5, -2, -5, -4, -1, -5, -4, 5, + -1, -1, -4, -1, 0, -4, -2, -1, -4, 6, + -2, -5, -2, -5, -4, 0, -5, -4, 1, -3, 5, + -2, -4, -2, -4, -3, -1, -4, -3, 1, -2, 2, 7, + -2, 4, -4, 1, -1, -4, -1, 0, -4, 0, -4, -3, 7, + -1, -3, -4, -3, -2, -4, -3, -3, -4, -2, -4, -3, -3, 8, + -1, -1, -4, -1, 2, -4, -3, 1, -4, 1, -3, 0, 0, -2, 7, + -2, -2, -5, -3, -1, -4, -3, 0, -4, 2, -3, -2, -1, -3, 1, 6, + 1, 0, -2, -1, -1, -3, -1, -2, -3, -1, -3, -2, 0, -2, -1, -1, 5, + 0, -1, -2, -2, -1, -3, -3, -2, -1, -1, -2, -1, 0, -2, -1, -2, 1, 6, + -1, -4, -2, -5, -3, -2, -5, -4, 3, -3, 0, 0, -4, -3, -3, -3, -2, -1, 5, + -4, -6, -4, -6, -5, 0, -4, -3, -4, -5, -3, -2, -5, -5, -3, -4, -4, -4, -3, 11, + -1, -2, -3, -2, -2, -2, -2, -2, -2, -1, -2, -1, -2, -2, -1, -2, -1, -1, -2, -3, -2, + -3, -4, -4, -4, -4, 3, -5, 1, -2, -3, -2, -2, -3, -4, -3, -3, -3, -2, -3, 2, -2, 8, + -1, 0, -5, 0, 4, -4, -3, 0, -4, 1, -4, -2, -1, -2, 4, 0, -1, -1, -3, -4, -1, -3, 4 +}; + + + +//////////////////////////////////////////////////////////////////////// +// PAM family +int _pam20[] = { + 6, + -5, 6, + -8,-14, 10, + -4, 6,-16, 8, + -3, 0,-16, 2, 8, + -9,-12,-15,-17,-16, 9, + -3, -4,-11, -4, -5,-10, 7, + -8, -2, -8, -5, -6, -7,-10, 9, + -6, -7, -7, -9, -6, -3,-13,-11, 9, + -8, -3,-16, -6, -5,-16, -8, -8, -7, 7, + -7,-10,-17,-15,-10, -4,-12, -7, -2, -9, 7, + -6,-12,-16,-13, -8, -5,-10,-13, -2, -3, 0, 11, + -5, 6,-13, 1, -3,-10, -4, -1, -6, -2, -8,-11, 8, + -2, -8, -9, -9, -7,-11, -7, -5,-10, -8, -8, -9, -7, 8, + -5, -4,-16, -4, 0,-15, -8, 0, -9, -4, -6, -5, -5, -4, 9, + -8, -9, -9,-12,-11,-10,-11, -3, -6, -1,-10, -5, -7, -5, -2, 9, + -1, -2, -4, -5, -5, -7, -3, -7, -8, -5, -9, -6, -1, -3, -6, -4, 7, + -1, -4, -9, -6, -7,-10, -7, -8, -3, -4, -8, -5, -3, -5, -7, -8, 0, 7, + -3, -9, -7, -9, -8, -9, -7, -7, 1,-10, -3, -2, -9, -7, -8, -9, -8, -4, 7, + -16,-11,-18,-17,-19, -6,-17, -8,-16,-14, -7,-15, -9,-16,-15, -3, -6,-15,-18, 13, + -4, -6,-11, -7, -6, -9, -6, -6, -6, -6, -7, -6, -4, -6, -6, -7, -4, -5, -6,-13, -6, + -9, -7, -5,-13, -9, 1,-16, -4, -7,-10, -8,-13, -5,-16,-14,-11, -8, -7, -8, -6, -9, 10, + -4, -1,-16, 0, 6,-16, -6, -2, -7, -5, -8, -6, -4, -5, 7, -5, -6, -7, -8,-17, -6,-11, 6 +}; + +int _pam60[] = { + 5, + -2, 5, + -5, -9, 9, + -2, 5,-10, 7, + -1, 2,-10, 3, 7, + -6, -8, -9,-11,-10, 8, + 0, -2, -7, -2, -2, -7, 6, + -5, 0, -6, -2, -3, -4, -6, 8, + -3, -4, -4, -5, -4, -1, -7, -6, 7, + -5, -1,-10, -2, -3,-10, -5, -4, -4, 6, + -4, -7,-11, -9, -7, -1, -8, -4, 0, -6, 6, + -3, -6,-10, -7, -5, -2, -6, -7, 1, 0, 2, 10, + -2, 5, -7, 2, 0, -6, -1, 1, -4, 0, -5, -6, 6, + 0, -4, -6, -5, -3, -7, -4, -2, -6, -4, -5, -6, -4, 7, + -3, -1,-10, -1, 2, -9, -5, 2, -5, -1, -3, -2, -2, -1, 7, + -5, -5, -6, -6, -6, -7, -7, 0, -4, 2, -6, -2, -3, -2, 0, 8, + 1, 0, -1, -2, -2, -5, 0, -4, -4, -2, -6, -4, 1, 0, -3, -2, 5, + 1, -2, -5, -3, -4, -6, -3, -5, -1, -2, -5, -2, -1, -2, -4, -4, 1, 6, + -1, -5, -4, -6, -4, -5, -4, -5, 3, -6, -1, 0, -5, -4, -5, -5, -4, -1, 6, + -10, -8,-12,-11,-12, -3,-11, -5,-10, -8, -4, -9, -6,-10, -9, 0, -4, -9,-11, 13, + -2, -3, -6, -3, -3, -5, -3, -3, -3, -3, -4, -3, -2, -3, -3, -4, -2, -2, -3, -8, -3, + -6, -5, -2, -8, -7, 3,-10, -2, -4, -7, -5, -7, -3,-10, -8, -8, -5, -5, -5, -3, -5, 9, + -2, 1,-10, 2, 5,-10, -3, 0, -4, -2, -5, -4, -1, -2, 6, -2, -3, -4, -5,-11, -3, -7, 5 +}; + +int _pam120[] = { + 3, + 0, 4, + -3, -6, 9, + 0, 4, -7, 5, + 0, 3, -7, 3, 5, + -4, -5, -6, -7, -7, 8, + 1, 0, -4, 0, -1, -5, 5, + -3, 1, -4, 0, -1, -3, -4, 7, + -1, -3, -3, -3, -3, 0, -4, -4, 6, + -2, 0, -7, -1, -1, -7, -3, -2, -3, 5, + -3, -4, -7, -5, -4, 0, -5, -3, 1, -4, 5, + -2, -4, -6, -4, -3, -1, -4, -4, 1, 0, 3, 8, + -1, 3, -5, 2, 1, -4, 0, 2, -2, 1, -4, -3, 4, + 1, -2, -4, -3, -2, -5, -2, -1, -3, -2, -3, -3, -2, 6, + -1, 0, -7, 1, 2, -6, -3, 3, -3, 0, -2, -1, 0, 0, 6, + -3, -2, -4, -3, -3, -5, -4, 1, -2, 2, -4, -1, -1, -1, 1, 6, + 1, 0, 0, 0, -1, -3, 1, -2, -2, -1, -4, -2, 1, 1, -2, -1, 3, + 1, 0, -3, -1, -2, -4, -1, -3, 0, -1, -3, -1, 0, -1, -2, -2, 2, 4, + 0, -3, -3, -3, -3, -3, -2, -3, 3, -4, 1, 1, -3, -2, -3, -3, -2, 0, 5, + -7, -6, -8, -8, -8, -1, -8, -3, -6, -5, -3, -6, -4, -7, -6, 1, -2, -6, -8, 12, + -1, -1, -4, -2, -1, -3, -2, -2, -1, -2, -2, -2, -1, -2, -1, -2, -1, -1, -1, -5, -2, + -4, -3, -1, -5, -5, 4, -6, -1, -2, -5, -2, -4, -2, -6, -5, -5, -3, -3, -3, -2, -3, 8, + -1, 2, -7, 3, 4, -6, -2, 1, -3, -1, -3, -2, 0, -1, 4, -1, -1, -2, -3, -7, -1, -5, 4 +}; + +int _pam160[] = { + 2, + 0, 3, + -2, -4, 9, + 0, 3, -5, 4, + 0, 2, -5, 3, 4, + -3, -4, -5, -6, -5, 7, + 1, 0, -3, 0, 0, -4, 4, + -2, 1, -3, 0, 0, -2, -3, 6, + -1, -2, -2, -3, -2, 0, -3, -3, 5, + -2, 0, -5, 0, -1, -5, -2, -1, -2, 4, + -2, -4, -6, -4, -3, 1, -4, -2, 2, -3, 5, + -1, -3, -5, -3, -2, 0, -3, -3, 2, 0, 3, 7, + 0, 2, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 3, + 1, -1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -2, -1, 5, + -1, 1, -5, 1, 2, -5, -2, 2, -2, 0, -2, -1, 0, 0, 5, + -2, -1, -3, -2, -2, -4, -3, 1, -2, 3, -3, -1, -1, -1, 1, 6, + 1, 0, 0, 0, 0, -3, 1, -1, -2, -1, -3, -2, 1, 1, -1, -1, 2, + 1, 0, -2, -1, -1, -3, -1, -2, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, + 0, -2, -2, -3, -2, -2, -2, -2, 3, -3, 1, 1, -2, -2, -2, -3, -1, 0, 4, + -5, -5, -7, -6, -7, -1, -7, -3, -5, -4, -2, -4, -4, -5, -5, 1, -2, -5, -6, 12, + 0, -1, -3, -1, -1, -3, -1, -1, -1, -1, -2, -1, 0, -1, -1, -1, 0, 0, -1, -4, -1, + -3, -3, 0, -4, -4, 5, -5, 0, -2, -4, -2, -3, -2, -5, -4, -4, -3, -3, -3, -1, -3, 8, + 0, 2, -5, 2, 3, -5, -1, 1, -2, 0, -3, -2, 1, -1, 3, 0, -1, -1, -2, -6, -1, -4, 3 +}; + +int _pam250[] = { + 2, + 0, 3, + -2, -4, 12, + 0, 3, -5, 4, + 0, 3, -5, 3, 4, + -3, -4, -4, -6, -5, 9, + 1, 0, -3, 1, 0, -5, 5, + -1, 1, -3, 1, 1, -2, -2, 6, + -1, -2, -2, -2, -2, 1, -3, -2, 5, + -1, 1, -5, 0, 0, -5, -2, 0, -2, 5, + -2, -3, -6, -4, -3, 2, -4, -2, 2, -3, 6, + -1, -2, -5, -3, -2, 0, -3, -2, 2, 0, 4, 6, + 0, 2, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 2, + 1, -1, -3, -1, -1, -5, 0, 0, -2, -1, -3, -2, 0, 6, + 0, 1, -5, 2, 2, -5, -1, 3, -2, 1, -2, -1, 1, 0, 4, + -2, -1, -4, -1, -1, -4, -3, 2, -2, 3, -3, 0, 0, 0, 1, 6, + 1, 0, 0, 0, 0, -3, 1, -1, -1, 0, -3, -2, 1, 1, -1, 0, 2, + 1, 0, -2, 0, 0, -3, 0, -1, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, + 0, -2, -2, -2, -2, -1, -1, -2, 4, -2, 2, 2, -2, -1, -2, -2, -1, 0, 4, + -6, -5, -8, -7, -7, 0, -7, -3, -5, -3, -2, -4, -4, -6, -5, 2, -2, -5, -6, 17, + 0, -1, -3, -1, -1, -2, -1, -1, -1, -1, -1, -1, 0, -1, -1, -1, 0, 0, -1, -4, -1, + -3, -3, 0, -4, -4, 7, -5, 0, -1, -4, -1, -2, -2, -5, -4, -4, -3, -3, -2, 0, -2, 10, + 0, 2, -5, 3, 3, -5, 0, 2, -2, 0, -3, -2, 1, 0, 3, 0, 0, -1, -2, -6, -1, -4, 3 +}; + +int _pam350[] = { + 2, + 1, 3, + -2, -5, 18, + 1, 3, -6, 4, + 1, 3, -6, 4, 4, + -4, -5, -5, -6, -6, 13, + 2, 1, -4, 1, 1, -6, 5, + -1, 1, -4, 1, 1, -2, -2, 7, + 0, -2, -3, -2, -2, 2, -2, -2, 5, + -1, 1, -6, 1, 0, -6, -1, 1, -2, 5, + -2, -4, -7, -4, -4, 3, -4, -2, 4, -3, 8, + -1, -2, -6, -3, -2, 1, -3, -2, 3, 0, 5, 6, + 0, 2, -4, 2, 2, -4, 1, 2, -2, 1, -3, -2, 2, + 1, 0, -3, 0, 0, -5, 0, 0, -2, -1, -3, -2, 0, 6, + 0, 2, -6, 2, 3, -5, -1, 3, -2, 1, -2, -1, 1, 1, 4, + -1, 0, -4, -1, 0, -5, -2, 2, -2, 4, -3, 0, 1, 0, 2, 7, + 1, 1, 0, 1, 0, -4, 1, -1, -1, 0, -3, -2, 1, 1, 0, 0, 1, + 1, 0, -2, 0, 0, -3, 1, -1, 0, 0, -2, -1, 1, 1, 0, -1, 1, 2, + 0, -2, -2, -2, -2, -1, -1, -2, 4, -2, 3, 2, -2, -1, -2, -3, -1, 0, 5, + -7, -6,-10, -8, -8, 1, -8, -3, -6, -4, -2, -5, -5, -7, -5, 4, -3, -6, -7, 27, + 0, 0, -3, -1, 0, -2, -1, 0, 0, -1, -1, 0, 0, 0, 0, -1, 0, 0, 0, -5, -1, + -4, -4, 1, -5, -5, 11, -6, 0, 0, -5, 0, -2, -3, -6, -5, -5, -3, -3, -2, 1, -2, 14, + 0, 2, -6, 3, 3, -6, 0, 2, -2, 1, -3, -2, 2, 0, 3, 1, 0, 0, -2, -7, 0, -5, 3 +}; + + + +//////////////////////////////////////////////////////////////////////// +// MD family +int _md40[] = { + 9, + 0, 0, + -7, 0, 16, + -6, 0,-13, 11, + -5, 0,-15, 3, 11, + -11, 0, -5,-15,-16, 13, + -3, 0, -7, -4, -4,-15, 10, + -9, 0, -6, -4, -8, -7,-10, 14, + -6, 0,-11,-12,-12, -5,-13,-11, 11, + -8, 0,-12, -8, -3,-16, -9, -6,-11, 11, + -9, 0,-10,-14,-13, -1,-14, -7, -1,-12, 9, + -6, 0, -9,-12,-11, -7,-12, -9, 1, -7, 1, 14, + -6, 0, -8, 1, -5,-12, -5, 0, -8, -1,-12, -9, 12, + -2, 0,-11,-11,-11,-11, -9, -4,-11,-10, -5,-10, -9, 12, + -7, 0,-12, -6, 0,-14, -9, 2,-12, -1, -6, -8, -5, -3, 12, + -7, 0, -5,-10, -8,-15, -4, 0,-10, 3, -9, -8, -6, -6, 0, 11, + 0, 0, -2, -6, -8, -6, -2, -6, -8, -7, -7, -8, 1, -1, -7, -5, 9, + 1, 0, -7, -8, -8,-11, -7, -7, -2, -5, -9, -2, -2, -4, -7, -6, 1, 10, + -1, 0, -7, -9, -8, -6, -8,-12, 4,-12, -2, 0,-10, -9,-11,-11, -7, -4, 10, + -14, 0, -4,-15,-15, -7, -7,-13,-13,-13, -8,-11,-14,-14,-11, -4, -9,-12,-10, 18, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -13, 0, -2, -8,-14, 2,-13, 2, -9,-13, -9,-11, -6,-13, -9,-10, -7,-10,-11, -6, 0, 14, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +int _md120[] = { + 6, + 0, 0, + -3, 0, 14, + -2, 0, -7, 8, + -2, 0, -8, 5, 8, + -6, 0, -2, -9,-10, 11, + 0, 0, -3, 0, -1, -9, 8, + -4, 0, -2, -1, -3, -2, -4, 11, + -1, 0, -5, -7, -7, -1, -6, -6, 7, + -4, 0, -6, -2, 0, -9, -4, -1, -6, 8, + -4, 0, -5, -8, -8, 2, -8, -4, 2, -6, 7, + -2, 0, -5, -7, -6, -2, -6, -5, 3, -4, 3, 10, + -1, 0, -3, 3, -1, -6, -1, 2, -4, 1, -6, -5, 8, + 0, 0, -5, -5, -5, -5, -4, -1, -5, -4, -2, -5, -3, 9, + -3, 0, -6, -1, 2, -7, -4, 4, -6, 2, -3, -4, -1, 0, 9, + -3, 0, -2, -4, -3, -8, -1, 2, -6, 4, -5, -4, -2, -2, 2, 8, + 2, 0, 0, -2, -3, -3, 0, -2, -3, -3, -3, -3, 2, 1, -3, -2, 5, + 2, 0, -3, -3, -4, -6, -2, -3, 0, -2, -4, 0, 1, 0, -3, -3, 2, 6, + 1, 0, -3, -5, -5, -2, -4, -6, 5, -6, 1, 2, -5, -4, -6, -6, -3, 0, 7, + -8, 0, 0, -9, -9, -3, -3, -6, -7, -6, -4, -6, -8, -8, -6, -1, -5, -7, -6, 17, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -7, 0, 2, -4, -7, 5, -8, 4, -5, -7, -4, -6, -2, -7, -4, -5, -3, -6, -6, -2, 0, 12, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +int _md250[] = { + 2, + 0, 0, + -1, 0, 11, + -1, 0, -3, 5, + -1, 0, -4, 4, 5, + -3, 0, 0, -5, -5, 8, + 1, 0, -1, 1, 1, -5, 5, + -2, 0, 0, 0, 0, 0, -2, 6, + 0, 0, -2, -3, -3, 0, -3, -3, 4, + -1, 0, -3, 0, 1, -5, -1, 1, -3, 5, + -1, 0, -2, -4, -4, 2, -4, -2, 2, -3, 5, + 0, 0, -2, -3, -3, 0, -3, -2, 3, -2, 3, 6, + 0, 0, -1, 2, 1, -3, 0, 1, -2, 1, -3, -2, 3, + 1, 0, -2, -2, -2, -2, -1, 0, -2, -1, 0, -2, -1, 6, + -1, 0, -3, 0, 2, -4, -1, 3, -3, 2, -2, -2, 0, 0, 5, + -1, 0, -1, -1, 0, -4, 0, 2, -3, 4, -3, -2, 0, -1, 2, 5, + 1, 0, 1, 0, -1, -2, 1, -1, -1, -1, -2, -1, 1, 1, -1, -1, 2, + 2, 0, -1, -1, -1, -2, 0, -1, 1, -1, -1, 0, 1, 1, -1, -1, 1, 2, + 1, 0, -2, -3, -2, 0, -2, -3, 4, -3, 2, 2, -2, -1, -3, -3, -1, 0, 4, + -4, 0, 1, -5, -5, -1, -1, -3, -4, -3, -2, -3, -4, -4, -3, 0, -3, -4, -3, 15, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -3, 0, 2, -2, -4, 5, -4, 4, -2, -3, -1, -3, -1, -3, -2, -2, -1, -3, -3, 0, 0, 9, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +int _md350[] = { + 1, + 0, 0, + 0, 0, 9, + 0, 0, -2, 3, + 0, 0, -2, 3, 3, + -2, 0, 1, -3, -4, 6, + 1, 0, 0, 1, 1, -3, 4, + -1, 0, 0, 0, 0, 0, -1, 3, + 0, 0, -1, -2, -2, 1, -2, -2, 3, + -1, 0, -1, 0, 1, -3, 0, 1, -2, 3, + -1, 0, -1, -3, -3, 2, -2, -1, 2, -2, 3, + 0, 0, -1, -2, -2, 1, -2, -1, 2, -2, 2, 3, + 0, 0, -1, 1, 1, -2, 0, 1, -1, 1, -2, -1, 2, + 1, 0, -1, -1, -1, -2, -1, 0, -1, -1, 0, -1, 0, 4, + -1, 0, -2, 1, 1, -2, 0, 2, -2, 2, -1, -1, 0, 0, 3, + -1, 0, 0, 0, 0, -3, 0, 1, -2, 3, -2, -1, 0, 0, 2, 3, + 1, 0, 0, 0, 0, -1, 1, 0, -1, 0, -1, -1, 1, 1, 0, 0, 1, + 1, 0, 0, 0, -1, -1, 0, -1, 0, 0, -1, 0, 0, 1, -1, 0, 1, 1, + 0, 0, -1, -2, -2, 0, -1, -2, 2, -2, 1, 2, -1, -1, -2, -2, 0, 0, 2, + -3, 0, 1, -4, -3, 0, -1, -2, -3, -2, -1, -2, -3, -3, -2, 0, -2, -3, -2, 14, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -2, 0, 2, -2, -2, 5, -3, 3, -1, -2, 0, -1, -1, -2, -1, -1, -1, -2, -2, 0, 0, 7, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + + + +//////////////////////////////////////////////////////////////////////// +// Identity matrix +int _idmat[] = { + 1, + 0, 1, + 0, 0, 1, + 0, 0, 0, 1, + 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 +}; + + + +//////////////////////////////////////////////////////////////////////// +// GON family +int _gon40[] = { + 92, + 0, 0, + -31, 0, 163, + -56, 0,-135, 111, + -37, 0,-140, 16, 105, + -92, 0, -64,-152,-143, 126, + -32, 0, -91, -51, -76,-152, 105, + -65, 0, -67, -41, -40, -50, -81, 145, + -76, 0, -87,-150,-106, -39,-158, -94, 104, + -54, 0,-132, -47, -13,-127, -79, -34, -86, 103, + -68, 0, -85,-155,-108, -13,-141, -85, 5, -85, 89, + -45, 0, -63,-130, -80, -16,-114, -60, 10, -57, 16, 140, + -62, 0, -83, 6, -38,-104, -40, -7, -99, -20,-112, -91, 115, + -37, 0,-137, -69, -60,-128, -87, -71,-108, -62, -83,-119, -78, 124, + -43, 0,-113, -32, 10,-100, -71, 0, -91, 2, -60, -35, -25, -46, 118, + -61, 0, -86, -77, -50,-130, -69, -31,-103, 19, -84, -81, -47, -73, -6, 112, + 0, 0, -35, -36, -41,-111, -37, -48, -95, -43, -95, -64, -11, -35, -35, -51, 99, + -25, 0, -59, -47, -52, -90, -85, -46, -51, -34, -78, -44, -27, -42, -39, -52, 13, 100, + -22, 0, -43,-133, -74, -58,-122, -98, 28, -82, -18, -22,-103, -86, -79, -88, -74, -25, 97, + -120, 0, -68,-171,-131, -6,-108, -70, -93,-127, -71, -72,-119,-149, -87, -63, -98,-120,-115, 181, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -95, 0, -56, -98,-107, 31,-129, 5, -76, -88, -64, -66, -62,-106, -81, -75, -69, -87, -73, 1, 0, 135, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + +int _gon80[] = { + 75, + 0, 0, + -10, 0, 154, + -31, 0, -93, 96, + -17, 0, -94, 31, 88, + -64, 0, -39,-111,-102, 114, + -11, 0, -61, -26, -47,-115, 97, + -39, 0, -43, -17, -17, -26, -53, 127, + -43, 0, -54,-106, -73, -15,-114, -64, 86, + -30, 0, -88, -21, 4, -89, -50, -12, -59, 85, + -43, 0, -55,-109, -75, 7,-104, -57, 22, -58, 77, + -26, 0, -39, -88, -53, 3, -83, -38, 25, -37, 31, 117, + -34, 0, -55, 21, -13, -75, -18, 9, -71, -2, -79, -62, 97, + -16, 0, -93, -42, -35, -93, -58, -45, -75, -37, -58, -78, -48, 114, + -22, 0, -76, -9, 23, -70, -44, 14, -60, 17, -39, -19, -6, -24, 95, + -36, 0, -60, -44, -23, -90, -43, -10, -71, 33, -58, -53, -22, -45, 11, 97, + 14, 0, -15, -14, -19, -77, -16, -25, -62, -20, -64, -41, 5, -14, -15, -27, 78, + -5, 0, -34, -24, -27, -62, -52, -24, -28, -15, -49, -25, -7, -20, -18, -27, 25, 81, + -6, 0, -21, -89, -51, -31, -86, -65, 41, -54, 3, 1, -69, -57, -51, -60, -43, -9, 80, + -87, 0, -43,-124, -98, 16, -81, -43, -63, -89, -44, -45, -86,-112, -62, -41, -72, -87, -80, 173, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -65, 0, -32, -69, -74, 49, -94, 21, -47, -60, -35, -37, -39, -76, -53, -50, -46, -58, -47, 23, 0, 123, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + +int _gon120[] = { + 59, + 0, 0, + -1, 0, 144, + -18, 0, -69, 82, + -9, 0, -68, 35, 72, + -48, 0, -26, -87, -78, 102, + -3, 0, -45, -14, -31, -92, 90, + -26, 0, -31, -7, -6, -14, -37, 110, + -27, 0, -36, -80, -55, -3, -87, -48, 72, + -19, 0, -64, -8, 11, -67, -34, -2, -44, 69, + -30, 0, -39, -82, -57, 15, -82, -42, 28, -44, 66, + -17, 0, -26, -64, -40, 11, -65, -28, 29, -27, 34, 95, + -20, 0, -41, 26, -1, -58, -7, 14, -55, 5, -61, -46, 80, + -6, 0, -68, -28, -22, -72, -41, -31, -56, -24, -44, -56, -32, 105, + -12, 0, -56, 1, 25, -53, -30, 17, -43, 20, -30, -14, 1, -14, 74, + -23, 0, -45, -27, -10, -68, -30, -1, -53, 36, -44, -38, -10, -30, 16, 83, + 16, 0, -7, -5, -9, -58, -6, -14, -44, -10, -47, -29, 10, -5, -7, -15, 60, + 2, 0, -21, -13, -15, -47, -35, -14, -17, -6, -34, -16, 0, -10, -9, -16, 26, 64, + 0, 0, -11, -65, -38, -17, -65, -47, 42, -39, 13, 10, -50, -42, -36, -44, -28, -3, 65, + -68, 0, -29, -96, -78, 27, -66, -28, -46, -68, -29, -31, -68, -89, -49, -30, -57, -67, -59, 166, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -48, 0, -20, -53, -56, 55, -74, 26, -31, -44, -20, -22, -28, -59, -38, -37, -35, -42, -33, 33, 0, 111, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +int _gon160[] = { + 46, + 0, 0, + 3, 0, 135, + -11, 0, -53, 70, + -4, 0, -52, 34, 59, + -38, 0, -18, -70, -62, 91, + 2, 0, -34, -7, -21, -76, 82, + -18, 0, -23, -1, -1, -7, -27, 93, + -18, 0, -25, -62, -43, 3, -70, -37, 59, + -12, 0, -48, -1, 13, -53, -24, 2, -35, 55, + -22, 0, -29, -65, -45, 19, -67, -32, 30, -34, 57, + -12, 0, -19, -50, -31, 14, -52, -21, 29, -21, 34, 76, + -12, 0, -31, 26, 5, -47, -2, 15, -44, 8, -48, -36, 65, + -1, 0, -52, -19, -14, -58, -30, -22, -43, -16, -35, -42, -22, 96, + -7, 0, -42, 6, 23, -41, -21, 17, -32, 20, -24, -12, 5, -8, 56, + -16, 0, -35, -16, -3, -53, -21, 3, -41, 35, -35, -29, -4, -21, 17, 71, + 16, 0, -2, 0, -3, -45, -1, -8, -33, -4, -36, -23, 11, 0, -2, -9, 44, + 5, 0, -14, -6, -8, -36, -24, -8, -12, -2, -24, -11, 3, -4, -4, -9, 23, 50, + 1, 0, -6, -49, -30, -8, -52, -35, 40, -30, 17, 14, -38, -32, -27, -34, -20, 0, 53, + -55, 0, -21, -78, -64, 32, -55, -19, -34, -54, -20, -22, -55, -74, -40, -24, -47, -54, -45, 158, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -37, 0, -13, -42, -44, 56, -60, 27, -20, -35, -11, -13, -22, -48, -29, -29, -28, -32, -24, 38, 0, 100, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + +int _gon250[] = { + 24, + 0, 0, + 5, 0, 115, + -3, 0, -32, 47, + 0, 0, -30, 27, 36, + -23, 0, -8, -45, -39, 70, + 5, 0, -20, 1, -8, -52, 66, + -8, 0, -13, 4, 4, -1, -14, 60, + -8, 0, -11, -38, -27, 10, -45, -22, 40, + -4, 0, -28, 5, 12, -33, -11, 6, -21, 32, + -12, 0, -15, -40, -28, 20, -44, -19, 28, -21, 40, + -7, 0, -9, -30, -20, 16, -35, -13, 25, -14, 28, 43, + -3, 0, -18, 22, 9, -31, 4, 12, -28, 8, -30, -22, 38, + 3, 0, -31, -7, -5, -38, -16, -11, -26, -6, -23, -24, -9, 76, + -2, 0, -24, 9, 17, -26, -10, 12, -19, 15, -16, -10, 7, -2, 27, + -6, 0, -22, -3, 4, -32, -10, 6, -24, 27, -22, -17, 3, -9, 15, 47, + 11, 0, 1, 5, 2, -28, 4, -2, -18, 1, -21, -14, 9, 4, 2, -2, 22, + 6, 0, -5, 0, -1, -22, -11, -3, -6, 1, -13, -6, 5, 1, 0, -2, 15, 25, + 1, 0, 0, -29, -19, 1, -33, -20, 31, -17, 18, 16, -22, -18, -15, -20, -10, 0, 34, + -36, 0, -10, -52, -43, 36, -40, -8, -18, -35, -7, -10, -36, -50, -27, -16, -33, -35, -26, 142, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -22, 0, -5, -28, -27, 51, -40, 22, -7, -21, 0, -2, -14, -31, -17, -18, -19, -19, -11, 41, 0, 78, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +int _gon300[] = { + 16, + 0, 0, + 5, 0, 104, + -1, 0, -24, 37, + 1, 0, -23, 23, 27, + -18, 0, -5, -37, -31, 60, + 5, 0, -15, 3, -4, -42, 58, + -6, 0, -10, 5, 4, 0, -10, 45, + -6, 0, -7, -30, -21, 11, -36, -16, 33, + -2, 0, -21, 6, 11, -26, -7, 5, -17, 24, + -9, 0, -10, -32, -22, 19, -36, -14, 25, -17, 33, + -5, 0, -6, -24, -16, 15, -28, -10, 22, -11, 24, 31, + -1, 0, -14, 18, 9, -25, 5, 10, -22, 8, -24, -17, 27, + 3, 0, -23, -4, -2, -30, -11, -8, -20, -3, -18, -19, -6, 66, + -1, 0, -18, 9, 14, -20, -6, 9, -15, 13, -13, -8, 7, -1, 18, + -4, 0, -17, 0, 5, -25, -6, 6, -19, 22, -18, -13, 4, -6, 13, 37, + 8, 0, 1, 5, 3, -22, 4, -1, -14, 2, -17, -11, 7, 4, 2, 0, 15, + 5, 0, -3, 1, 1, -17, -7, -1, -4, 2, -9, -5, 4, 2, 1, -1, 11, 17, + 0, 0, 1, -23, -15, 4, -26, -15, 26, -13, 17, 15, -17, -14, -12, -15, -8, 0, 26, + -29, 0, -7, -42, -36, 36, -34, -5, -13, -28, -4, -6, -30, -41, -23, -14, -27, -28, -19, 132, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -17, 0, -3, -22, -22, 46, -33, 18, -3, -17, 3, 1, -12, -25, -14, -14, -15, -15, -7, 40, 0, 67, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +int _gon350[] = { + 10, + 0, 0, + 4, 0, 93, + 0, 0, -19, 29, + 1, 0, -17, 19, 20, + -14, 0, -3, -30, -25, 51, + 5, 0, -12, 4, -2, -35, 51, + -4, 0, -8, 5, 4, 1, -7, 33, + -4, 0, -5, -24, -17, 11, -29, -13, 27, + -1, 0, -16, 6, 9, -21, -4, 5, -13, 18, + -7, 0, -7, -25, -18, 18, -30, -11, 22, -14, 28, + -4, 0, -4, -19, -13, 14, -23, -8, 19, -9, 21, 23, + 0, 0, -11, 15, 9, -20, 5, 8, -18, 7, -19, -14, 20, + 3, 0, -18, -2, 0, -25, -7, -5, -16, -2, -15, -14, -3, 56, + 0, 0, -14, 8, 11, -16, -4, 7, -11, 10, -11, -7, 6, 0, 12, + -2, 0, -13, 2, 6, -20, -4, 6, -15, 18, -14, -11, 4, -4, 10, 28, + 6, 0, 1, 5, 3, -18, 5, 0, -11, 2, -13, -9, 6, 4, 2, 1, 10, + 4, 0, -2, 2, 1, -13, -5, -1, -3, 2, -7, -4, 4, 2, 1, 0, 8, 11, + 0, 0, 2, -18, -12, 5, -21, -11, 22, -10, 16, 14, -13, -11, -9, -12, -6, 0, 21, + -24, 0, -4, -35, -29, 35, -30, -3, -9, -23, -1, -3, -24, -34, -19, -12, -22, -23, -14, 124, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + -14, 0, -1, -18, -17, 42, -27, 15, -1, -14, 5, 2, -10, -20, -11, -12, -12, -12, -4, 39, 0, 57, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 +}; + +} // namespace Victor +} // namespace Phylo + +#endif // _VICTOR_PHYLO_PRECOMPUTED_MATRICES_H_ \ No newline at end of file diff --git a/Phylo/Tests/Makefile b/Phylo/Tests/Makefile new file mode 100644 index 0000000..3a380f5 --- /dev/null +++ b/Phylo/Tests/Makefile @@ -0,0 +1,59 @@ +#--*- makefile -*-------------------------------------------------------------- +# +# Standard makefile +# +#------------------------------------------------------------------------------ + +# Path to project directory +PROJECT_ROOT = ../.. +BINPATH = $(PROJECT_ROOT)/bin/ +LIBPATH = $(PROJECT_ROOT)/lib/ +UPDIR = $(PROJECT_ROOT) +SUBDIR = + + + +# +# Libraries and paths (which are not defined globally). +# + +LIBS = -lPhylo -lAlign2 -ltools -L/usr/lib/ -lm -ldl -lcppunit +INC_PATH = -I. -I ../../Phylo/Sources -I../../tools/ -I../../Align2/Sources +LIB_PATH = -L. + + + +# +# Objects and headers +# + +SOURCES = TestPhylo.cc TestTree.h TestDistanceMatrix.h TestClustering.h TestMSA.h +OBJECTS = $(SOURCES:.cpp=.o) +TARGETS = TestPhylo +EXECS = TestPhylo +LIBRARY = TESTlibPhylo.a + + + +# +# Install rule +# + +compile: all + +all: install + +install: $(LIBRARY) $(TARGETS) + mv $(EXECS) $(UPDIR)/bin + mv $(LIBRARY) $(UPDIR)/lib + + + +# +# Call global Makefile to do the job. +# + +include ../../Makefile.global + +# Overriding to use C++11 +STANDARDFLAGS = -Wall -Wextra -pedantic -std=c++0x -DNEXCEPTIONS -DLINUX -c \ No newline at end of file diff --git a/Phylo/Tests/TestClustering.h b/Phylo/Tests/TestClustering.h new file mode 100644 index 0000000..710d2e0 --- /dev/null +++ b/Phylo/Tests/TestClustering.h @@ -0,0 +1,142 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +using namespace Victor; +using namespace Victor::Phylo; + +/** @brief Test on phylogenetic trees. + * @author Marco Zanella + */ +class TestClustering: public CppUnit::TestFixture { + public: + TestClustering() { + } + + + + /** @brief Builds a suite of tests. */ + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestClustering"); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test1 - UPGMA.", + &TestClustering::Test_A) + ); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test2 - Nighbor joining.", + &TestClustering::Test_B) + ); + + return suiteOfTests; + } + + + + /** @brief Setup method. */ + void setUp() { + } + + + + /** @brief Teardown method. */ + void tearDown() { + } + + + + protected: + /** @brief Test for UPGMA. */ + void Test_A() { + DistanceMatrix D; + D.addOTU("Human") + .addOTU("Chimp") + .addOTU("Gorilla") + .addOTU("Orang"); + + D("Human", "Chimp", 0.095); + D("Human", "Gorilla", 0.113); + D("Human", "Orang", 0.183); + D("Chimp", "Gorilla", 0.118); + D("Chimp", "Orang", 0.201); + D("Gorilla", "Orang", 0.195); + + UPGMA upgma; + RootedTree tree = upgma(D).asRootedTree(); + const string result = tree.asNewick(); + + CPPUNIT_ASSERT(result == "(((Chimp:0.0475,Human:0.0475):0.01025,Gorilla:0.05775):0.03875,Orang:0.0965)"); + } + + + + /** @brief Test for neighbor joining. */ + void Test_B() { + DistanceMatrix D; + D.addOTU("A") + .addOTU("B") + .addOTU("C") + .addOTU("D") + .addOTU("E") + .addOTU("F") + .addOTU("G") + .addOTU("H"); + + D("A", "B", 7); + D("A", "C", 8); + D("A", "D", 11); + D("A", "E", 13); + D("A", "F", 16); + D("A", "G", 13); + D("A", "H", 17); + D("B", "C", 5); + D("B", "D", 8); + D("B", "E", 10); + D("B", "F", 13); + D("B", "G", 10); + D("B", "H", 14); + D("C", "D", 5); + D("C", "E", 7); + D("C", "F", 10); + D("C", "G", 7); + D("C", "H", 11); + D("D", "E", 8); + D("D", "F", 11); + D("D", "G", 8); + D("D", "H", 12); + D("E", "F", 5); + D("E", "G", 6); + D("E", "H", 10); + D("F", "G", 9); + D("F", "H", 13); + D("G", "H", 8); + + NJ nj; + UnrootedTree tree = nj(D).asUnrootedTree(); + const string result = tree.asNewick(); + + CPPUNIT_ASSERT(result == "(((E:1,F:4):2,(G:2,H:6):1):1.5,(D:3,(C:1,((A:5,B:2):1):1):1):0.5)"); + } +}; \ No newline at end of file diff --git a/Phylo/Tests/TestDistanceMatrix.h b/Phylo/Tests/TestDistanceMatrix.h new file mode 100644 index 0000000..936391b --- /dev/null +++ b/Phylo/Tests/TestDistanceMatrix.h @@ -0,0 +1,122 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +using namespace Victor; +using namespace Victor::Phylo; + +/** @brief Test on phylogenetic trees. + * @author Marco Zanella + */ +class TestDistanceMatrix: public CppUnit::TestFixture { + public: + TestDistanceMatrix() { + } + + + + /** @brief Builds a suite of tests. */ + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestDistanceMatrix"); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test1 - Builds a matrix.", + &TestDistanceMatrix::Test_A) + ); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test2 - Get maximum value.", + &TestDistanceMatrix::Test_B) + ); + + return suiteOfTests; + } + + + + /** @brief Setup method. */ + void setUp() { + } + + + + /** @brief Teardown method. */ + void tearDown() { + } + + + + protected: + /** @brief Test for creation. */ + void Test_A() { + vector OTUs; + OTUs.push_back("A"); + OTUs.push_back("B"); + OTUs.push_back("C"); + + const double ab = 0.1, ac = 9.5, bc = 0.333; + + DistanceMatrix d; + d.addOTU(OTUs[0]) + .addOTU(OTUs[1]) + .addOTU(OTUs[2]); + + d("A", "B", ab); + d("A", "C", ac); + d("B", "C", bc); + + CPPUNIT_ASSERT( + d.getSize() == 3 && + d("A", "B") == ab && + d("B", "C") == bc && + d("A", "C") == ac + ); + } + + + + /** @brief Test for get values. */ + void Test_B() { + vector OTUs; + OTUs.push_back("A"); + OTUs.push_back("B"); + OTUs.push_back("C"); + + const double ab = 0.1, ac = 9.5, bc = 0.333; + + DistanceMatrix d; + d.addOTU(OTUs[0]) + .addOTU(OTUs[1]) + .addOTU(OTUs[2]); + + d("A", "B", ab); + d("A", "C", ac); + d("B", "C", bc); + + CPPUNIT_ASSERT( + d.getMaximum() == 9.5 && + d.getMinimum() == 0.1 + ); + } +}; \ No newline at end of file diff --git a/Phylo/Tests/TestMSA.h b/Phylo/Tests/TestMSA.h new file mode 100644 index 0000000..763f651 --- /dev/null +++ b/Phylo/Tests/TestMSA.h @@ -0,0 +1,117 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +using namespace Victor; +using namespace Victor::Phylo; + +/** @brief Test on phylogenetic trees. + * @author Marco Zanella + */ +class TestMSA: public CppUnit::TestFixture { + public: + TestMSA() { + } + + + + /** @brief Builds a suite of tests. */ + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestMSA"); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test1 - Feng-Doolittle.", + &TestMSA::Test_A) + ); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test2 - ClustalW.", + &TestMSA::Test_B) + ); + + return suiteOfTests; + } + + + + /** @brief Setup method. */ + void setUp() { + } + + + + /** @brief Teardown method. */ + void tearDown() { + } + + + +protected: + /** @brief Test for Feng-Doolittle. */ + void Test_A() { + stringstream input; + + input << ">Seq1\nMAAAAATLRGAMVGPRGAGLP\n" + << ">Seq2\nMAAAAASLRGVVLGPRGAGL\n" + << ">Seq3\nMTEFKAGSAKKGATLFKTRCL\n" + << ">Seq4\nMAAAAASLRRTVLGPRGVGLPGASAPGLL\n" + << ">Seq5\nMFSQKLLANGKLLSKLAIVSGVVG\n" + << "\n"; + + Alignment alignment; + alignment.loadFasta(input); + FengDoolittle feng_doolittle; + MultipleAlignment MSA = feng_doolittle(alignment); + + CPPUNIT_ASSERT(MSA.getConsensus() == "MAAFKAAASLRGAVLGPRGAGLAGASAPGLG"); + } + + + + /** @brief Test for ClustalW. */ + void Test_B() { + stringstream input; + + input << ">Seq1\nMAAAAATLRGAMVGPRGAGLP\n" + << ">Seq2\nMAAAAASLRGVVLGPRGAGL\n" + << ">Seq3\nMTEFKAGSAKKGATLFKTRCL\n" + << ">Seq4\nMAAAAASLRRTVLGPRGVGLPGASAPGLL\n" + << ">Seq5\nMFSQKLLANGKLLSKLAIVSGVVG\n" + << "\n"; + + Alignment alignment; + alignment.loadFasta(input); + + SubMatrix matrix(SubstitutionMatrix(SubstitutionMatrix::BLOSUM62).asSubMatrix()); + AGPFunction gap_function(10.0, 0.2); + IdentityPercentage build_matrix(matrix, gap_function); + NJ build_tree; + ClustalW clustalw(build_matrix, build_tree, ClustalW::BLOSUM); + + MultipleAlignment MSA = clustalw(alignment); + + CPPUNIT_ASSERT(MSA.getConsensus() == "MAAAAASLRGKVLGPRGAGLPGASAGCLG"); + } +}; \ No newline at end of file diff --git a/Phylo/Tests/TestPhylo.cc b/Phylo/Tests/TestPhylo.cc new file mode 100644 index 0000000..e4603aa --- /dev/null +++ b/Phylo/Tests/TestPhylo.cc @@ -0,0 +1,43 @@ +/* This file is part of Victor. + + Victor is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + Victor is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Victor. If not, see . +*/ + +#include +#include +#include +#include +#include +#include +#include + +using namespace::std; +using namespace::Victor; + +int main(int argc, char *argv[]) { + CppUnit::TextUi::TestRunner runner; + + cout << "Creating Test Suite:" << endl; + runner.addTest(TestTree::suite()); + runner.addTest(TestDistanceMatrix::suite()); + runner.addTest(TestClustering::suite()); + runner.addTest(TestMSA::suite()); + cout << "Running the unit tests:" << endl; + runner.run(); + + (void) argc; + (void) argv; + + return 0; +} \ No newline at end of file diff --git a/Phylo/Tests/TestPhylo.o b/Phylo/Tests/TestPhylo.o new file mode 100644 index 0000000000000000000000000000000000000000..950c22c6fbbefddde5b17b0ce3624b1aba2d6d12 GIT binary patch literal 157008 zcmeFa33ye-`9FS=%Sj?aZa_rb;DXU&MNHVystFZ~+Y=Tp%?hF}XpsE}`PmTuPMn_u;kn}cJP6Mh z=Zz3966e2%a54NIhTkIsYl5&@oL>Oph2s1o2wTMY#SpfN^Cb{273Y^gxJ;ZchwxHy zei?+9i}Mu_ULnq}gzzeHel>*Gz;6xw{wA<%A^ZdU{ttc+3hX)vuZQ1i`2AI2e}wP` 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z|N5X8rXN2nnl0*$&o_Mj>U=!^+ErQpvSO5M`yUj^KR4)O`Rg^meSd41jn04GCi>j{ znIatC8Wr!qRfl-~yy`vQzi$!rvG(usfz+z;`mw_TWSi6K)raISOZ0yR(U+^<@>nBy z{}n+W^FKuW4^W}>A6e4p{a-`!S8Dz+ylzx{{&_@So!I`51%1qaO{D$hl7{!cg5wpGy3%jrf-- z3GaV8$zQMeJD}O{I`7^;OZ0^~8L`~)3-0}V;=k}wFdNED<;(Z~$nfX=e@XJ!Y5pOq zx2J-=(B}q{f0gEMP@d#JGm^h^m}d*{M#rzhLz%FkdVBKkcMbaH;X{uv`BuavqW_+U%|bn`Q#3zsyDY{`UgOU#Iz-s{b=2|H#j>{8;~U zBKaFg{@f#(?>blCf_uN3Ub{hX!CJY}pD%n=a`kZ|5 zzUmv1!kb%F?{U)`{;leDH#ay}qxw2`0%5+5_;t|7`fqMsmZ==(KQ4*1U)vC. +*/ + +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +using namespace Victor; +using namespace Victor::Phylo; + +/** @brief Test on phylogenetic trees. + * @author Marco Zanella + */ +class TestTree: public CppUnit::TestFixture { + public: + TestTree() { + } + + + + /** @brief Builds a suite of tests. */ + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite("TestTree"); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test1 - Parses a Newick string.", + &TestTree::TestTree_A) + ); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test2 - Count leaves.", + &TestTree::TestTree_B) + ); + + suiteOfTests->addTest( + new CppUnit::TestCaller("Test3 - Distances.", + &TestTree::TestTree_C) + ); + + return suiteOfTests; + } + + + + /** @brief Setup method. */ + void setUp() { + } + + + + /** @brief Teardown method. */ + void tearDown() { + } + + + + protected: + /** @brief Test for parse/write. */ + void TestTree_A() { + RootedTree tree; + const string load_newick = "(A:0.5,B:0.25):0.36;"; + tree.parseNewick(load_newick); + const string save_newick = tree.asNewick() + ";"; + + CPPUNIT_ASSERT(load_newick == save_newick); + } + + + + /** @brief Test for number of leaves. */ + void TestTree_B() { + RootedTree tree; + const string load_newick = "(A:0.5,B:0.25):0.36;"; + tree.parseNewick(load_newick); + const size_t leaves = tree.getLeavesNumber(); + + CPPUNIT_ASSERT(leaves == 2); + } + + + + /** @brief Test for distance. */ + void TestTree_C() { + RootedTree tree; + const string load_newick = "(A:0.5,B:0.25):0.36;"; + tree.parseNewick(load_newick); + const double max_distance = tree.getMaxDistance(); + + CPPUNIT_ASSERT(max_distance == 0.86); + } +}; \ No newline at end of file From 7c1ca4a5f9a212146dae55abc008b60fd70c1553 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:18:26 +0200 Subject: [PATCH 02/25] Create test.md --- wiki/test.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 wiki/test.md diff --git a/wiki/test.md b/wiki/test.md new file mode 100644 index 0000000..fc83c13 --- /dev/null +++ b/wiki/test.md @@ -0,0 +1 @@ +hello world '''a''' From b2251c6647e296b5f20df2e6500ed834440850bc Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:20:45 +0200 Subject: [PATCH 03/25] Rename test.md to Test.md --- wiki/{test.md => Test.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename wiki/{test.md => Test.md} (100%) diff --git a/wiki/test.md b/wiki/Test.md similarity index 100% rename from wiki/test.md rename to wiki/Test.md From c6a06ca2fa4b009aa3f3ad9f29e443739874ac88 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:22:02 +0200 Subject: [PATCH 04/25] Rename Test.md to Test.mediawiki --- wiki/{Test.md => Test.mediawiki} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename wiki/{Test.md => Test.mediawiki} (100%) diff --git a/wiki/Test.md b/wiki/Test.mediawiki similarity index 100% rename from wiki/Test.md rename to wiki/Test.mediawiki From cb86e7b1b8f32aad006974e3971316a9cd853c32 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:22:16 +0200 Subject: [PATCH 05/25] Delete Test.mediawiki --- wiki/Test.mediawiki | 1 - 1 file changed, 1 deletion(-) delete mode 100644 wiki/Test.mediawiki diff --git a/wiki/Test.mediawiki b/wiki/Test.mediawiki deleted file mode 100644 index fc83c13..0000000 --- a/wiki/Test.mediawiki +++ /dev/null @@ -1 +0,0 @@ -hello world '''a''' From 31f947d3ed17111712505e2ce5dab313e6122941 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:23:28 +0200 Subject: [PATCH 06/25] Create Introduction.mediawiki --- wiki/Introduction.mediawiki | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 wiki/Introduction.mediawiki diff --git a/wiki/Introduction.mediawiki b/wiki/Introduction.mediawiki new file mode 100644 index 0000000..8027f0c --- /dev/null +++ b/wiki/Introduction.mediawiki @@ -0,0 +1,26 @@ +== Phylo == +The '''Phylo''' package allows building and manipulating phylogenetic trees and multiple sequence alignments. It relies on the ''Align2'' package, with which shares the modular object oriented design. This package is written in C++11 and follows the Strategy Pattern. + +[[File:Phyltree.svg|thumb|upright=1.3|alt=Phylogenetic tree overview|Overview of the phylogenetic tree building process.]] + +There are three main components in the packages are: +*'''DistanceMatrix''' - stores information about sequences and distances among them +*'''PhylogeneticTree''' - represents a phylogenetic tree, where leaves are sequences; there are two interchangeable types of trees: ''RootedTree'' and ''UnrootedTree''. It is possible to switch from the latter to the former transparently (the underling rooting techniques is the ''midpoint rooting''), or by manually specifying a root node. The Visitor Design Pattern is available for this tree hierarchy +*'''MultipleAlignment''' - a multiple sequence alignment + +There are several strategies to construct each of the main components: +*'''DistanceMatrixBuilder''' - builds a '''DistanceMatrix''' from a set of sequences: +**''IdentityPercentage'' - estimates a distance as the percent identity after a global alignment +**''LevenshteinDistance'' - uses the [https://en.wikipedia.org/wiki/Levenshtein_distance Levenshtein distance] metrics +**''FengDolittleDistance'' - distance metrics proposed by Feng and Doolittle Feng, Da-Fei, Doolittle, RussellF. ''Progressive sequence alignment as a prerequisitet to correct phylogenetic trees''. Journal of Molecular Evolution, 1987, p. 351-360. +*'''ClusteringAlgorithm''': produces a '''PhylogeneticTree''' from a '''DistanceMatrix''': +**''UPGMA'' +**''Fitch-Margoliash'' +**''Neihbor Joining'' +*'''MultipleAlignmentAlgorithm''' - produces a '''MultipleAlignment''' from a set of sequences: +**''Feng-Doolittle'' +**''ClustalW'' + +For a more detailed overview, please refer to the [[Features]] page. + +[[File:Msa.svg|thumb|upright=2.8|center|alt=Multiple alignment overview|Overview of the multiple sequence alignment process.]] From 2a03ed788f07e4253cf74ed3ac73ce57d48552f2 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:24:26 +0200 Subject: [PATCH 07/25] Added wiki --- wiki/Features.mediawiki | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 wiki/Features.mediawiki diff --git a/wiki/Features.mediawiki b/wiki/Features.mediawiki new file mode 100644 index 0000000..510390a --- /dev/null +++ b/wiki/Features.mediawiki @@ -0,0 +1,45 @@ += Phylo library = + +The Phylo library is about phylogenetic trees and multiple sequence alignments. For an overview and explanation of Phylo classes, please refer to the [http://protein.bio.unipd.it/victor_doxygen/index.html Doxygen documentation]. The key items in the Phylo library are the distance matrix, phylogenetic tree and multiple sequence alignment. + +In order to build a distance matrix from an alignment, a distance metric must be specified. There are three available metrics: +* Percent identity: distance for each pair of sequences is estimated as one minus the percent identity divided by one hundred, after a global alignment is performed +* Levensthein distance: distance is estimated as the minimum number of substitutions (without taking in account properties of the residues, such as mutation probability) +* Feng-Doolittle distance: distance metric proposed by Feng and Doolittle + +Phylogenetics tree can be built from a distance matrix using a clustering algorithm. There are three available clustering algorithms: +* UPGMA +* Fitch-Margoliash +* Neighbor Joining + +Multiple sequence alignments can be built from set of sequences. There are two multiple sequence alignment algorithms supported: +* Feng-Doolittle +* ClustalW + + + +== Building a phylogenetic tree == +'''phyltree''' allows to generate a phylogenetic tree from an alignment. + + phyltree --in path/to/alignment.fasta + +The behaviour of the program can be tuned with optional parameters (such as the distance metrics or the clustering algorithm). The complete documentation for these additional parameters can be viewed with + + phyltree -h + +By default, the resulting phylogenetic tree is printed on screen. For more information, see the [[Tutorial]]. + + + +== Building a multiple alignment == +'''fengdoolittle''' is an implementation of the omonymous multiple sequence alignment algorithm. '''clustalw''' is a clone of the original (but now unsupported) ClustalW program, an improved version of Clustal which allows to build a multiple sequence alignment from a set of sequences using some advance features, such as position-specific gap opening and extension penalties, sequence weighting and use of different substitution matrices as the alignment procedes. + +The easiest way to compute a multiple sequence alignment is by running the command: + + clustalw --in path/to/alignment.fasta -m /path/to/substitution_matrix.dat + +which will output the resulting multiple alignment on the screen. The behaviour of the alignment can be changed trhough optional paramters. For a complete reference, launch + + clustalw -h + +For a complete documentation, see the [[Tutorial]]. From 8d9da8127ccfcdbb43fc2bc105d6e34691ffa514 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:26:53 +0200 Subject: [PATCH 08/25] Added the wiki --- wiki/Tutorial.mediawiki | 167 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 167 insertions(+) create mode 100644 wiki/Tutorial.mediawiki diff --git a/wiki/Tutorial.mediawiki b/wiki/Tutorial.mediawiki new file mode 100644 index 0000000..c6e5ecf --- /dev/null +++ b/wiki/Tutorial.mediawiki @@ -0,0 +1,167 @@ += Building a phylogenetic tree = +The '''phyltree''' tool allows to build phylogenetic trees. Some optional parameters can be used to tune the process: + + --in Path to input FASTA file + --out Path to output Newick file (default: to screen + -m Path to substitution matrix file (default: blosum62.dat) + -o Open gap penalty (default: 10.0) + -e Extension gap penalty (default: 0.1) + -d <0|1|2> Distance matrix builder criterion (default: 0) + -d 0: Distance as 1 - percentage of identity + -d 1: Use Levenshtein distance + -d 2: Use Feng-Doolittle distance + -c <0|1|2> Clustering algorithm (default:2) + -c 0: UPGMA + -c 1: Fitch-Margoliash + -c 2: Neighbor Joining + -v Verbose (default: no) + +The resulting phylogenetic tree is saved in Newick format. + +== Example == +[[File:Phyltree.png|thumb|upright=1.5|right|Output of ''phyltree'', rendered with [http://etetoolkit.org/treeview/ TreeView].]] + +The following example is obtained using a library of CYC1 Cytochrome genes from various species simply running the command: + + phyltree --in /home/victor/cyc1_input.fasta -m /home/victor/data/blosum62.dat -d 2 + + (((sp|Q0JF02|CPS4_ORYSJ:0,(sp|P30183|CCB11_ARATH:0,sp|Q54D07|CY1_DICDI:0):0.528361):1.6686,((sp|P08574|CY1_HUMAN:0, + (sp|P00125|CY1_BOVIN:0.0429261,sp|Q9D0M3|CY1_MOUSE:0):0.297808):1.55218,(sp|P41179|CCN1_TRYBB:0,(sp|P74917|CY552_ACIFR:0, + sp|Q9K499|CYC1_STRCO:0):0.732572):1.10758):0.382313):0.0823948,(sp|P00048|CYC_NEUCR:0,((sp|Q6C9Q0|CYC_YARLI:0, + (sp|Q6Q4H8|CYC_PICPA:0,(sp|Q06374|CG1_COLGL:0,sp|Q6E7D7|CPS4_ORYSI:0.308501):0):0.582973):0.342549,(sp|O13393|CYC_PICST:0, + (sp|P53698|CYC_CANAL:0,(((sp|P00043|CYC_DEBHA:0.0802929,(sp|O93863|CYC_PACTA:0.0723514,sp|P00041|CYC_ISSOR:0.0505152):0.0294868) + :0.0185369,(sp|Q753F4|CYC_ASHGO:0.0858857,(sp|P19681|CYC_SCHOC:0.0293847,(sp|P00044|CYC1_YEAST:0.0370127, + (sp|P25400|CYC_CANGA:0.05915,(sp|P00046|CYC_SCHPO:0.0113562,(sp|Q4HVX7|CYC_GIBZE:0,(sp|P15451|CYC_CHLRE:0, + sp|Q9AJE4|CYC1_KITGR:0.179574):0.32777):0.166349):0.106052):0.039459):0.0937627):0.0511101):0.00528961) + :0.0434401):0.0434401):0.104043):0.169192):0.810171):0.217969); + +The output Newick string was used as input for the [http://etetoolkit.org/treeview/ TreeView] online tool, producing a visual representation of the tree. + +== Extending the code == +The '''phylo''' API can be used within a C++ project. + + + + #include + + using namespace Victor; + using namespace Victor::Align2; + using namespace Victor::Phylo; + + int main(int argc, char *argv[]) { + // Loads an alignment + ifstream fasta_file("path/to/alignment.fasta"); + Alignment alignment; + alignment.loadFasta(fasta_file); + + + // Loads a substitution matrix, i.e. BLOSUM62 + ifstream matrix_file("path/to/blosum62.dat"); + SubMatrix substitution_matrix(matrix_file); + + + // Prepares a gap function + AGPFunction gap_function(10.0, 0.1); + + // Distance metrics, i.e. percent identity + IdentityPercentage build_matrix(substitution_matrix, gap_function); + + + // Custering algorithm, i.e. neighbor joining + NJ build_tree; + + + // Computes distance matrix and phylogenetic tree + DistanceMatrix d = build_matrix(alignment); + RootedTree tree = build_tree(d).asRootedTree(); + + + // Saves the result + ofstream newick_file("path/to/output.newick"); + tree.saveNewick(newick_file); + + return 0; + } + + +Please refer to the [http://protein.bio.unipd.it/victor_doxygen/index.html Doxygen documentation] for more detailed information. + += Building a multiple sequence alignment - Feng-Doolittle = +The '''fengdoolittle''' algorithm is one of the oldest and most mature methods to produce a multiple sequence alignment from a library of sequences. There are very vew tunable parameters, hence it is the easiest tool for this purpose: + + --in Name of input FASTA file + --out Name of output alignment file (default: to screen) + -o Open gap penalty (default: 10.0) + -e Extension gap penalty (default: 0.1) + -v Verbose (default: no) + + + += Building a multiple sequence alignment - ClustalW = +The '''clustalw''' tool can be used to generate a multiple alignment from a set of sequence. Like the ''phyltree'' program, many options are available to the user: + + --in Path to input FASTA file + --out Path to output ClustalW file (default: to screen) + -m Path to substitution matrix file (default: blosum62.dat) + -o Open gap penalty (default: 10.0) + -e Extension gap penalty (default: 0.1) + -d <0|1|2> Distance matrix builder criterion (default: 0) + -d 0: Distance as 1 - percentage of identity + -d 1: Use Levenshtein distance + -d 2: Use Feng-Doolittle distance + -c <0|1|2> Clustering algorithm (default:2) + -c 0: UPGMA + -c 1: Fitch-Margoliash + -c 2: Neighbor Joining + -n <0|1> Substitution matrix family for multiple alignment (default: 1) + -w 0: PAM series + -w 1: BLOSUM series + -wo Initial open gap penalty for ClustalW (default: 10.0) + -we Initial extension gap penalty for ClustalW (default: 0.2) + -v Verbose (default: no) + +The resulting multiple alignment is saved in clustal format. + + + +== Example == + +The following example is obtained using a library of CYC1 Cytochrome genes from various species simply running the command: + + clustalw --in /home/victor/cyc1_input.fasta --out /home/victor/output.aln -m /home/victor/data/blosum62.dat -d 2 + +The output clustal string was used as input for the [http://www.jalview.org/ Jalview] tool, producing a visual representation of the alignment, along with its consensus sequence and quality. + +[[File:Msa.png|thumb|upright=2.5|center|Output of ''clustalw'', rendered with [http://www.jalview.org/ Jalview].]] + +== Extending the code == +The '''phylo''' API can be used within a C++ project. + + + + #include + + using namespace Victor; + using namespace Victor::Align2; + using namespace Victor::Phylo; + + int main(int argc, char *argv[]) { + // Loads alignment and prepares stuffs + ... + LevenshteinDistance levenshtein_distance; + UPGMA upgma; + + + // Computes multiple alignment + MultipleAlignment MSA = ClustalW(levenshtein_distance, upgma, ClustalW::BLOSUM); + + + // Saves the result + ofstream msa_file("path/to/output.clustalw"); + MSA.saveClustalW(newick_file); + + return 0; + } + + +Please refer to the [http://protein.bio.unipd.it/victor_doxygen/index.html Doxygen documentation] for more detailed information. 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0000000..09d5666 --- /dev/null +++ b/wiki/phyltree.svg @@ -0,0 +1,226 @@ + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + Alignment + + DistanceMatrix + + PhylogeneticTree + + DistanceMatrixBuilder + + ClusteringAlgorithm + + From d25b35d288ad5e3b4a5bb7ef07eee4e05ac328c4 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 12:38:49 +0200 Subject: [PATCH 10/25] Added the wiki --- wiki/{msa.png => Msa.png} | Bin wiki/{msa.svg => Msa.svg} | 0 wiki/{phyltree.png => Phyltree.png} | Bin wiki/{phyltree.svg => Phyltree.svg} | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename wiki/{msa.png => Msa.png} (100%) rename wiki/{msa.svg => Msa.svg} (100%) rename wiki/{phyltree.png => Phyltree.png} (100%) rename wiki/{phyltree.svg => Phyltree.svg} (100%) diff --git a/wiki/msa.png b/wiki/Msa.png similarity index 100% rename from wiki/msa.png rename to wiki/Msa.png diff --git a/wiki/msa.svg b/wiki/Msa.svg similarity index 100% rename from wiki/msa.svg rename to wiki/Msa.svg diff --git a/wiki/phyltree.png b/wiki/Phyltree.png similarity index 100% rename from wiki/phyltree.png rename to wiki/Phyltree.png diff --git a/wiki/phyltree.svg b/wiki/Phyltree.svg similarity index 100% rename from wiki/phyltree.svg rename to wiki/Phyltree.svg From 3974e581397a8da16e0f825230bf4dbf2e4f6a07 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Mon, 13 Jul 2015 13:02:24 +0200 Subject: [PATCH 11/25] Added the wiki --- {wiki => Phylo/wiki}/Features.mediawiki | 0 {wiki => Phylo/wiki}/Introduction.mediawiki | 0 {wiki => Phylo/wiki}/Msa.png | Bin {wiki => Phylo/wiki}/Msa.svg | 0 {wiki => Phylo/wiki}/Phyltree.png | Bin {wiki => Phylo/wiki}/Phyltree.svg | 0 {wiki => Phylo/wiki}/Tutorial.mediawiki | 0 7 files changed, 0 insertions(+), 0 deletions(-) rename {wiki => Phylo/wiki}/Features.mediawiki (100%) rename {wiki => Phylo/wiki}/Introduction.mediawiki (100%) rename {wiki => Phylo/wiki}/Msa.png (100%) rename {wiki => Phylo/wiki}/Msa.svg (100%) rename {wiki => Phylo/wiki}/Phyltree.png (100%) rename {wiki => Phylo/wiki}/Phyltree.svg (100%) rename {wiki => Phylo/wiki}/Tutorial.mediawiki (100%) diff --git a/wiki/Features.mediawiki b/Phylo/wiki/Features.mediawiki similarity index 100% rename from wiki/Features.mediawiki rename to Phylo/wiki/Features.mediawiki diff --git a/wiki/Introduction.mediawiki b/Phylo/wiki/Introduction.mediawiki similarity index 100% rename from wiki/Introduction.mediawiki rename to Phylo/wiki/Introduction.mediawiki diff --git a/wiki/Msa.png b/Phylo/wiki/Msa.png similarity index 100% rename from wiki/Msa.png rename to Phylo/wiki/Msa.png diff --git a/wiki/Msa.svg b/Phylo/wiki/Msa.svg similarity index 100% rename from wiki/Msa.svg rename to Phylo/wiki/Msa.svg diff --git a/wiki/Phyltree.png b/Phylo/wiki/Phyltree.png similarity index 100% rename from wiki/Phyltree.png rename to Phylo/wiki/Phyltree.png diff --git a/wiki/Phyltree.svg b/Phylo/wiki/Phyltree.svg similarity index 100% rename from wiki/Phyltree.svg rename to Phylo/wiki/Phyltree.svg diff --git a/wiki/Tutorial.mediawiki b/Phylo/wiki/Tutorial.mediawiki similarity index 100% rename from wiki/Tutorial.mediawiki rename to Phylo/wiki/Tutorial.mediawiki From af7733078880dada557b1d19ffafde4b1e60e6ea Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Tue, 14 Jul 2015 16:36:05 +0200 Subject: [PATCH 12/25] Delete Features.mediawiki --- Phylo/wiki/Features.mediawiki | 45 ----------------------------------- 1 file changed, 45 deletions(-) delete mode 100644 Phylo/wiki/Features.mediawiki diff --git a/Phylo/wiki/Features.mediawiki b/Phylo/wiki/Features.mediawiki deleted file mode 100644 index 510390a..0000000 --- a/Phylo/wiki/Features.mediawiki +++ /dev/null @@ -1,45 +0,0 @@ -= Phylo library = - -The Phylo library is about phylogenetic trees and multiple sequence alignments. For an overview and explanation of Phylo classes, please refer to the [http://protein.bio.unipd.it/victor_doxygen/index.html Doxygen documentation]. The key items in the Phylo library are the distance matrix, phylogenetic tree and multiple sequence alignment. - -In order to build a distance matrix from an alignment, a distance metric must be specified. There are three available metrics: -* Percent identity: distance for each pair of sequences is estimated as one minus the percent identity divided by one hundred, after a global alignment is performed -* Levensthein distance: distance is estimated as the minimum number of substitutions (without taking in account properties of the residues, such as mutation probability) -* Feng-Doolittle distance: distance metric proposed by Feng and Doolittle - -Phylogenetics tree can be built from a distance matrix using a clustering algorithm. There are three available clustering algorithms: -* UPGMA -* Fitch-Margoliash -* Neighbor Joining - -Multiple sequence alignments can be built from set of sequences. There are two multiple sequence alignment algorithms supported: -* Feng-Doolittle -* ClustalW - - - -== Building a phylogenetic tree == -'''phyltree''' allows to generate a phylogenetic tree from an alignment. - - phyltree --in path/to/alignment.fasta - -The behaviour of the program can be tuned with optional parameters (such as the distance metrics or the clustering algorithm). The complete documentation for these additional parameters can be viewed with - - phyltree -h - -By default, the resulting phylogenetic tree is printed on screen. For more information, see the [[Tutorial]]. - - - -== Building a multiple alignment == -'''fengdoolittle''' is an implementation of the omonymous multiple sequence alignment algorithm. '''clustalw''' is a clone of the original (but now unsupported) ClustalW program, an improved version of Clustal which allows to build a multiple sequence alignment from a set of sequences using some advance features, such as position-specific gap opening and extension penalties, sequence weighting and use of different substitution matrices as the alignment procedes. - -The easiest way to compute a multiple sequence alignment is by running the command: - - clustalw --in path/to/alignment.fasta -m /path/to/substitution_matrix.dat - -which will output the resulting multiple alignment on the screen. The behaviour of the alignment can be changed trhough optional paramters. For a complete reference, launch - - clustalw -h - -For a complete documentation, see the [[Tutorial]]. From 90912c77df04113b7033e933f80297e8fcda7357 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Tue, 14 Jul 2015 16:36:23 +0200 Subject: [PATCH 13/25] Delete Introduction.mediawiki --- Phylo/wiki/Introduction.mediawiki | 26 -------------------------- 1 file changed, 26 deletions(-) delete mode 100644 Phylo/wiki/Introduction.mediawiki diff --git a/Phylo/wiki/Introduction.mediawiki b/Phylo/wiki/Introduction.mediawiki deleted file mode 100644 index 8027f0c..0000000 --- a/Phylo/wiki/Introduction.mediawiki +++ /dev/null @@ -1,26 +0,0 @@ -== Phylo == -The '''Phylo''' package allows building and manipulating phylogenetic trees and multiple sequence alignments. It relies on the ''Align2'' package, with which shares the modular object oriented design. This package is written in C++11 and follows the Strategy Pattern. - -[[File:Phyltree.svg|thumb|upright=1.3|alt=Phylogenetic tree overview|Overview of the phylogenetic tree building process.]] - -There are three main components in the packages are: -*'''DistanceMatrix''' - stores information about sequences and distances among them -*'''PhylogeneticTree''' - represents a phylogenetic tree, where leaves are sequences; there are two interchangeable types of trees: ''RootedTree'' and ''UnrootedTree''. It is possible to switch from the latter to the former transparently (the underling rooting techniques is the ''midpoint rooting''), or by manually specifying a root node. The Visitor Design Pattern is available for this tree hierarchy -*'''MultipleAlignment''' - a multiple sequence alignment - -There are several strategies to construct each of the main components: -*'''DistanceMatrixBuilder''' - builds a '''DistanceMatrix''' from a set of sequences: -**''IdentityPercentage'' - estimates a distance as the percent identity after a global alignment -**''LevenshteinDistance'' - uses the [https://en.wikipedia.org/wiki/Levenshtein_distance Levenshtein distance] metrics -**''FengDolittleDistance'' - distance metrics proposed by Feng and Doolittle Feng, Da-Fei, Doolittle, RussellF. ''Progressive sequence alignment as a prerequisitet to correct phylogenetic trees''. Journal of Molecular Evolution, 1987, p. 351-360. -*'''ClusteringAlgorithm''': produces a '''PhylogeneticTree''' from a '''DistanceMatrix''': -**''UPGMA'' -**''Fitch-Margoliash'' -**''Neihbor Joining'' -*'''MultipleAlignmentAlgorithm''' - produces a '''MultipleAlignment''' from a set of sequences: -**''Feng-Doolittle'' -**''ClustalW'' - -For a more detailed overview, please refer to the [[Features]] page. - -[[File:Msa.svg|thumb|upright=2.8|center|alt=Multiple alignment overview|Overview of the multiple sequence alignment process.]] From 7b66ce97c5df14ffd0fac4396e921452738d6665 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Tue, 14 Jul 2015 16:36:33 +0200 Subject: [PATCH 14/25] Delete Msa.png --- Phylo/wiki/Msa.png | Bin 71341 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 Phylo/wiki/Msa.png diff --git a/Phylo/wiki/Msa.png b/Phylo/wiki/Msa.png deleted file mode 100644 index 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zIkc5WL8>Q#xOgGXP~fB^j`Xq3$0A|C?(IGVgR+5S6)C_yl&_`0$ucmExXEl*QU3{ttlilXQU)tt7~&{ou3-Zoc=XGH>j zVaj?Stim;5i4{{zV6YDXPI|r1|3R#O(mx8ED0OuSq#Z7tdaRqHY3l041*TOANnot? zf;XreSo4I}+pDla6hMIIcL05J^8mC`o9szkNhRWa9WN%A_DfLkYjFk>(+0iAIgQU^ zpvg)WJrXrnv%6!k=Qz#1SA3uL%=f_*vwiXy#1x}?(5v@h_Owq89A__nX|nw#2Kc>3 zZ>n%8dI$mbLcIWtHznI=&Jb3s=-d=E4us?`btH^^Xg2!U79Id2Y$d^Kc`H*ooZItGR_^zWnr5c;0+X4416t^+q9uT>Q8 z$k`cIi9Zm)&s**9#Thf=G2v{1NSSf^h%Wx(gZMKDp@<+h>6-xRh@}X-M*Z1he_rx9 zet+UoeK3zZkqH8UU}}4SkJdaM6CTu4oc&n!9Oi1h%g%~@k_m*&PrEiG680>3cfAsu z&iwnGJ{|K9(yND=fE3_P`?Za5^z|j3(SdV$w>H3=Yd{$uAM%;Djuffx>-V%?M}pco zxcngCb0_62YW-dfyXpMtg??V8{K`Sh4Ni+cuM-rU&121ZT^Uqj*2-awpJX(n{&O{S11CRvud5bIT13)GV zU9PeHYl(3XepBbLjARV-0`u)zBN*D&s49Pax&2WDBi4JCod$51I>FCa3shp7 z-kAW_RS7+=+bsFqnUb)%>iX;P|8sN+5#G-W1}J~^ukDnBkRev#(YQX1;#B&-%VOjX zWIhEnIsSn0f4@c^9DsWA|Leo&Aex*wg8YA17(ad$_~{e>AAfqoJo)5XFvyuh?}0xW Ms%KS-lq>@N4+v94cK`qY From 1e26507ec09450f1a4873284165f06bcfe271735 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Tue, 14 Jul 2015 16:37:05 +0200 Subject: [PATCH 17/25] Delete Phyltree.svg --- Phylo/wiki/Phyltree.svg | 226 ---------------------------------------- 1 file changed, 226 deletions(-) delete mode 100644 Phylo/wiki/Phyltree.svg diff --git a/Phylo/wiki/Phyltree.svg b/Phylo/wiki/Phyltree.svg deleted file mode 100644 index 09d5666..0000000 --- a/Phylo/wiki/Phyltree.svg +++ /dev/null @@ -1,226 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - - Alignment - - DistanceMatrix - - PhylogeneticTree - - DistanceMatrixBuilder - - ClusteringAlgorithm - - From 3e210ceb8734db4481d3b052b581d88528790a57 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Tue, 14 Jul 2015 16:37:16 +0200 Subject: [PATCH 18/25] Delete Tutorial.mediawiki --- Phylo/wiki/Tutorial.mediawiki | 167 ---------------------------------- 1 file changed, 167 deletions(-) delete mode 100644 Phylo/wiki/Tutorial.mediawiki diff --git a/Phylo/wiki/Tutorial.mediawiki b/Phylo/wiki/Tutorial.mediawiki deleted file mode 100644 index c6e5ecf..0000000 --- a/Phylo/wiki/Tutorial.mediawiki +++ /dev/null @@ -1,167 +0,0 @@ -= Building a phylogenetic tree = -The '''phyltree''' tool allows to build phylogenetic trees. Some optional parameters can be used to tune the process: - - --in Path to input FASTA file - --out Path to output Newick file (default: to screen - -m Path to substitution matrix file (default: blosum62.dat) - -o Open gap penalty (default: 10.0) - -e Extension gap penalty (default: 0.1) - -d <0|1|2> Distance matrix builder criterion (default: 0) - -d 0: Distance as 1 - percentage of identity - -d 1: Use Levenshtein distance - -d 2: Use Feng-Doolittle distance - -c <0|1|2> Clustering algorithm (default:2) - -c 0: UPGMA - -c 1: Fitch-Margoliash - -c 2: Neighbor Joining - -v Verbose (default: no) - -The resulting phylogenetic tree is saved in Newick format. - -== Example == -[[File:Phyltree.png|thumb|upright=1.5|right|Output of ''phyltree'', rendered with [http://etetoolkit.org/treeview/ TreeView].]] - -The following example is obtained using a library of CYC1 Cytochrome genes from various species simply running the command: - - phyltree --in /home/victor/cyc1_input.fasta -m /home/victor/data/blosum62.dat -d 2 - - (((sp|Q0JF02|CPS4_ORYSJ:0,(sp|P30183|CCB11_ARATH:0,sp|Q54D07|CY1_DICDI:0):0.528361):1.6686,((sp|P08574|CY1_HUMAN:0, - (sp|P00125|CY1_BOVIN:0.0429261,sp|Q9D0M3|CY1_MOUSE:0):0.297808):1.55218,(sp|P41179|CCN1_TRYBB:0,(sp|P74917|CY552_ACIFR:0, - sp|Q9K499|CYC1_STRCO:0):0.732572):1.10758):0.382313):0.0823948,(sp|P00048|CYC_NEUCR:0,((sp|Q6C9Q0|CYC_YARLI:0, - (sp|Q6Q4H8|CYC_PICPA:0,(sp|Q06374|CG1_COLGL:0,sp|Q6E7D7|CPS4_ORYSI:0.308501):0):0.582973):0.342549,(sp|O13393|CYC_PICST:0, - (sp|P53698|CYC_CANAL:0,(((sp|P00043|CYC_DEBHA:0.0802929,(sp|O93863|CYC_PACTA:0.0723514,sp|P00041|CYC_ISSOR:0.0505152):0.0294868) - :0.0185369,(sp|Q753F4|CYC_ASHGO:0.0858857,(sp|P19681|CYC_SCHOC:0.0293847,(sp|P00044|CYC1_YEAST:0.0370127, - (sp|P25400|CYC_CANGA:0.05915,(sp|P00046|CYC_SCHPO:0.0113562,(sp|Q4HVX7|CYC_GIBZE:0,(sp|P15451|CYC_CHLRE:0, - sp|Q9AJE4|CYC1_KITGR:0.179574):0.32777):0.166349):0.106052):0.039459):0.0937627):0.0511101):0.00528961) - :0.0434401):0.0434401):0.104043):0.169192):0.810171):0.217969); - -The output Newick string was used as input for the [http://etetoolkit.org/treeview/ TreeView] online tool, producing a visual representation of the tree. - -== Extending the code == -The '''phylo''' API can be used within a C++ project. - - - - #include - - using namespace Victor; - using namespace Victor::Align2; - using namespace Victor::Phylo; - - int main(int argc, char *argv[]) { - // Loads an alignment - ifstream fasta_file("path/to/alignment.fasta"); - Alignment alignment; - alignment.loadFasta(fasta_file); - - - // Loads a substitution matrix, i.e. BLOSUM62 - ifstream matrix_file("path/to/blosum62.dat"); - SubMatrix substitution_matrix(matrix_file); - - - // Prepares a gap function - AGPFunction gap_function(10.0, 0.1); - - // Distance metrics, i.e. percent identity - IdentityPercentage build_matrix(substitution_matrix, gap_function); - - - // Custering algorithm, i.e. neighbor joining - NJ build_tree; - - - // Computes distance matrix and phylogenetic tree - DistanceMatrix d = build_matrix(alignment); - RootedTree tree = build_tree(d).asRootedTree(); - - - // Saves the result - ofstream newick_file("path/to/output.newick"); - tree.saveNewick(newick_file); - - return 0; - } - - -Please refer to the [http://protein.bio.unipd.it/victor_doxygen/index.html Doxygen documentation] for more detailed information. - -= Building a multiple sequence alignment - Feng-Doolittle = -The '''fengdoolittle''' algorithm is one of the oldest and most mature methods to produce a multiple sequence alignment from a library of sequences. There are very vew tunable parameters, hence it is the easiest tool for this purpose: - - --in Name of input FASTA file - --out Name of output alignment file (default: to screen) - -o Open gap penalty (default: 10.0) - -e Extension gap penalty (default: 0.1) - -v Verbose (default: no) - - - -= Building a multiple sequence alignment - ClustalW = -The '''clustalw''' tool can be used to generate a multiple alignment from a set of sequence. Like the ''phyltree'' program, many options are available to the user: - - --in Path to input FASTA file - --out Path to output ClustalW file (default: to screen) - -m Path to substitution matrix file (default: blosum62.dat) - -o Open gap penalty (default: 10.0) - -e Extension gap penalty (default: 0.1) - -d <0|1|2> Distance matrix builder criterion (default: 0) - -d 0: Distance as 1 - percentage of identity - -d 1: Use Levenshtein distance - -d 2: Use Feng-Doolittle distance - -c <0|1|2> Clustering algorithm (default:2) - -c 0: UPGMA - -c 1: Fitch-Margoliash - -c 2: Neighbor Joining - -n <0|1> Substitution matrix family for multiple alignment (default: 1) - -w 0: PAM series - -w 1: BLOSUM series - -wo Initial open gap penalty for ClustalW (default: 10.0) - -we Initial extension gap penalty for ClustalW (default: 0.2) - -v Verbose (default: no) - -The resulting multiple alignment is saved in clustal format. - - - -== Example == - -The following example is obtained using a library of CYC1 Cytochrome genes from various species simply running the command: - - clustalw --in /home/victor/cyc1_input.fasta --out /home/victor/output.aln -m /home/victor/data/blosum62.dat -d 2 - -The output clustal string was used as input for the [http://www.jalview.org/ Jalview] tool, producing a visual representation of the alignment, along with its consensus sequence and quality. - -[[File:Msa.png|thumb|upright=2.5|center|Output of ''clustalw'', rendered with [http://www.jalview.org/ Jalview].]] - -== Extending the code == -The '''phylo''' API can be used within a C++ project. - - - - #include - - using namespace Victor; - using namespace Victor::Align2; - using namespace Victor::Phylo; - - int main(int argc, char *argv[]) { - // Loads alignment and prepares stuffs - ... - LevenshteinDistance levenshtein_distance; - UPGMA upgma; - - - // Computes multiple alignment - MultipleAlignment MSA = ClustalW(levenshtein_distance, upgma, ClustalW::BLOSUM); - - - // Saves the result - ofstream msa_file("path/to/output.clustalw"); - MSA.saveClustalW(newick_file); - - return 0; - } - - -Please refer to the [http://protein.bio.unipd.it/victor_doxygen/index.html Doxygen documentation] for more detailed information. From 373289ddf6663e48485a982659de2db68d8508ab Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Fri, 17 Jul 2015 11:59:14 +0200 Subject: [PATCH 19/25] Added a comment to gap computation Added a comment to make clearer the meaning of the way to calculate gap penalties --- Phylo/Sources/ClustalW.cc | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index 14c6638..99b7e72 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -237,21 +237,23 @@ namespace Phylo { size_t hgaps = 1, vgaps = 1; for (size_t i = 1; i <= N; i++) { for (size_t j = 1; j <= M; j++) { - double vgap = 0.9; - double hgap = 0.9; + double vgap = 0.0; + double hgap = 0.0; + /* Documentation is unclear about gaps values. hgap = getPositionSpecificGOP(A, B, ss, j - 1) + hgaps * getPositionSpecificGEP(A, B, j - 1); vgap = getPositionSpecificGOP(B, A, ss, i - 1) + vgaps * getPositionSpecificGEP(B, A, i - 1); + */ -hgap = (direction[i][j - 1] != LEFT) - ? getPositionSpecificGOP(A, B, ss, j - 1) - : getPositionSpecificGEP(A, B, j - 1); -vgap = (direction[i - 1][j] != UP) - ? getPositionSpecificGOP(B, A, ss, i - 1) - : getPositionSpecificGEP(B, A, i - 1); + hgap = (direction[i][j - 1] != LEFT) + ? getPositionSpecificGOP(A, B, ss, j - 1) + : getPositionSpecificGEP(A, B, j - 1); + vgap = (direction[i - 1][j] != UP) + ? getPositionSpecificGOP(B, A, ss, i - 1) + : getPositionSpecificGEP(B, A, i - 1); const double d = score[i-1][j-1] + S(A, B, i, j, ss, weights), u = score[i - 1][j] - vgap, @@ -562,4 +564,4 @@ static vector join( } return sequences; -} \ No newline at end of file +} From afc29e97e59f78546ac0e2f6c9721563d744e5a7 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Wed, 22 Jul 2015 18:10:30 +0200 Subject: [PATCH 20/25] Fixed memory leaks --- Phylo/Sources/ClustalW.cc | 40 ++++++++++++++++-------------- Phylo/Sources/ClustalW.h | 2 +- Phylo/Sources/FengDoolittle.cc | 40 +++++++++++++++--------------- Phylo/Sources/FengDoolittle.h | 2 +- Phylo/Sources/MultipleAlignment.cc | 6 +++-- Phylo/Sources/MultipleAlignment.h | 2 +- 6 files changed, 48 insertions(+), 44 deletions(-) diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index 99b7e72..0366d72 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -125,7 +125,7 @@ namespace Phylo { Weights weights = getWeights(guide_tree); // Progressive alignments - return align(sequences, guide_tree, weights); + return *align(sequences, guide_tree, weights); } @@ -160,7 +160,7 @@ namespace Phylo { - MultipleAlignment & + MultipleAlignment * ClustalW::align( Sequences &sequences, const RootedTree &node, @@ -171,7 +171,7 @@ namespace Phylo { if (node.isLeaf()) { const string identifier = node.getLabel(); const string residues = sequences[identifier]; - return *(new MultipleAlignment(Sequence(identifier, residues))); + return (new MultipleAlignment(Sequence(identifier, residues))); } @@ -184,11 +184,11 @@ namespace Phylo { //////////////////////////////////////////////////////////////// // Two sequences: performs alignment - const MultipleAlignment A = align(sequences, node[0], weights), - B = align(sequences, node[1], weights); + const MultipleAlignment *A = align(sequences, node[0], weights), + *B = align(sequences, node[1], weights); const SubstitutionMatrix ss(getSubstitutionMatrix(node)); - const size_t M = A.getLength(), - N = B.getLength(); + const size_t M = A->getLength(), + N = B->getLength(); #if VERBOSE==1 @@ -217,8 +217,8 @@ namespace Phylo { score[0][0] = 0; direction[0][0] = NONE; for (size_t j = 1; j <= M; j++) { - const double GOP = getPositionSpecificGOP(A, B, ss, 0); - const double GEP = getPositionSpecificGEP(A, B, j - 1); + const double GOP = getPositionSpecificGOP(*A, *B, ss, 0); + const double GEP = getPositionSpecificGEP(*A, *B, j - 1); score[0][j] = -(GOP + GEP * (j - 1)); direction[0][j] = LEFT; } @@ -226,8 +226,8 @@ namespace Phylo { // Initializes first column for (size_t i = 1; i <= N; i++) { - const double GOP = getPositionSpecificGOP(B, A, ss, 0), - GEP = getPositionSpecificGEP(B, A, i - 1); + const double GOP = getPositionSpecificGOP(*B, *A, ss, 0), + GEP = getPositionSpecificGEP(*B, *A, i - 1); score[i][0] = -(GOP + GEP * (i - 1)); direction[i][0] = UP; } @@ -249,13 +249,13 @@ namespace Phylo { */ hgap = (direction[i][j - 1] != LEFT) - ? getPositionSpecificGOP(A, B, ss, j - 1) - : getPositionSpecificGEP(A, B, j - 1); + ? getPositionSpecificGOP(*A, *B, ss, j - 1) + : getPositionSpecificGEP(*A, *B, j - 1); vgap = (direction[i - 1][j] != UP) - ? getPositionSpecificGOP(B, A, ss, i - 1) - : getPositionSpecificGEP(B, A, i - 1); + ? getPositionSpecificGOP(*B, *A, ss, i - 1) + : getPositionSpecificGEP(*B, *A, i - 1); - const double d = score[i-1][j-1] + S(A, B, i, j, ss, weights), + const double d = score[i-1][j-1] + S(*A, *B, i, j, ss, weights), u = score[i - 1][j] - vgap, l = score[i][j - 1] - hgap; @@ -271,15 +271,17 @@ namespace Phylo { // Traceback - vector residues = traceback(A, B, direction); + vector residues = traceback(*A, *B, direction); // Builds sequences - vector joint = join(A, B, residues); + vector joint = join(*A, *B, residues); // Returns multiple alignment - return *(new MultipleAlignment(joint)); + delete A; + delete B; + return (new MultipleAlignment(joint)); } diff --git a/Phylo/Sources/ClustalW.h b/Phylo/Sources/ClustalW.h index 59990cc..9486c22 100644 --- a/Phylo/Sources/ClustalW.h +++ b/Phylo/Sources/ClustalW.h @@ -137,7 +137,7 @@ class ClustalW: public MultipleAlignmentAlgorithm { * @param[in] weights Weights * @return Multiple sequence alignment */ - MultipleAlignment &align( + MultipleAlignment *align( Sequences &sequences, const RootedTree &node, Weights &weights) const; diff --git a/Phylo/Sources/FengDoolittle.cc b/Phylo/Sources/FengDoolittle.cc index 2324bd9..2386240 100644 --- a/Phylo/Sources/FengDoolittle.cc +++ b/Phylo/Sources/FengDoolittle.cc @@ -75,12 +75,12 @@ namespace Phylo { RootedTree guide_tree = build_tree(d).asRootedTree(); // Progressive alignments - return align(sequences, guide_tree); + return *align(sequences, guide_tree); } - MultipleAlignment & + MultipleAlignment * FengDoolittle::align( Sequences &sequences, const RootedTree &node) const { @@ -89,7 +89,7 @@ namespace Phylo { if (node.isLeaf()) { const string identifier = node.getLabel(), residues = sequences[identifier]; - return *(new MultipleAlignment(Sequence(identifier, residues))); + return new MultipleAlignment(Sequence(identifier, residues)); } @@ -102,30 +102,30 @@ namespace Phylo { //////////////////////////////////////////////////////////////// // Two MSAs: performs alignment - const MultipleAlignment A = align(sequences, node[0]), - B = align(sequences, node[1]); + const MultipleAlignment *A = align(sequences, node[0]), + *B = align(sequences, node[1]); double max_score = -999999.0; string horizontal, vertical; #if VERBOSE==1 cout << "Now aligning:" << endl; - for (size_t i = 0; i < A.getSize(); i++) { - cout << A.getSequence(i).getIdentifier() << endl; + for (size_t i = 0; i < A->getSize(); i++) { + cout << A->getSequence(i).getIdentifier() << endl; } cout << "---------- against ----------" << endl; - for (size_t j = 0; j < B.getSize(); j++) { - cout << B.getSequence(j).getIdentifier() << endl; + for (size_t j = 0; j < B->getSize(); j++) { + cout << B->getSequence(j).getIdentifier() << endl; } cout << endl << endl; #endif // Finds best alignment - for (size_t i = 0; i < A.getSize(); i++) { - const string seqA = replace_gaps(A.getSequence(i).getResidues()); - for (size_t j = 0; j < B.getSize(); j++) { - const string seqB = replace_gaps(B.getSequence(j).getResidues()); + for (size_t i = 0; i < A->getSize(); i++) { + const string seqA = replace_gaps(A->getSequence(i).getResidues()); + for (size_t j = 0; j < B->getSize(); j++) { + const string seqB = replace_gaps(B->getSequence(j).getResidues()); AlignmentData *data = new SequenceData(2, seqA, seqB, "", ""); ScoringS2S scoring_scheme(&matrix, data, nullptr, 1.0); @@ -143,9 +143,9 @@ namespace Phylo { // Builds a new MSA using best alignment vector new_sequences; - for (size_t i = 0; i < A.getSize(); i++) { - const string identifier = A.getSequence(i).getIdentifier(), - sequence = A.getSequence(i).getResidues(); + for (size_t i = 0; i < A->getSize(); i++) { + const string identifier = A->getSequence(i).getIdentifier(), + sequence = A->getSequence(i).getResidues(); size_t cursor = 0; string residues = ""; for (char residue : horizontal) { @@ -154,9 +154,9 @@ namespace Phylo { new_sequences.push_back(Sequence(identifier, residues)); } - for (size_t i = 0; i < B.getSize(); i++) { - const string identifier = B.getSequence(i).getIdentifier(), - sequence = B.getSequence(i).getResidues(); + for (size_t i = 0; i < B->getSize(); i++) { + const string identifier = B->getSequence(i).getIdentifier(), + sequence = B->getSequence(i).getResidues(); size_t cursor = 0; string residues = ""; for (char residue : vertical) { @@ -167,7 +167,7 @@ namespace Phylo { // Returns multiple alignmnet - return *(new MultipleAlignment(new_sequences)); + return new MultipleAlignment(new_sequences); } } // namespace Phylo diff --git a/Phylo/Sources/FengDoolittle.h b/Phylo/Sources/FengDoolittle.h index 41cb499..ca0534c 100644 --- a/Phylo/Sources/FengDoolittle.h +++ b/Phylo/Sources/FengDoolittle.h @@ -94,7 +94,7 @@ class FengDoolittle: public MultipleAlignmentAlgorithm { * @param[in] node Next node of the guide tree * @return Multiple sequence alignment */ - MultipleAlignment &align( + MultipleAlignment *align( Sequences &sequences, const RootedTree &node) const; }; diff --git a/Phylo/Sources/MultipleAlignment.cc b/Phylo/Sources/MultipleAlignment.cc index ba2e358..a3ffa61 100644 --- a/Phylo/Sources/MultipleAlignment.cc +++ b/Phylo/Sources/MultipleAlignment.cc @@ -173,7 +173,7 @@ namespace Phylo { - string & + string MultipleAlignment::getResidues(const size_t position) const { char *s = new char[getSize()]; size_t idx = 0; @@ -184,7 +184,9 @@ namespace Phylo { } } - return *(new string(s)); + string result(s); + delete [] s; + return result; } diff --git a/Phylo/Sources/MultipleAlignment.h b/Phylo/Sources/MultipleAlignment.h index bac8253..ad6538e 100644 --- a/Phylo/Sources/MultipleAlignment.h +++ b/Phylo/Sources/MultipleAlignment.h @@ -130,7 +130,7 @@ class MultipleAlignment { * @param[in] position Index of the columng. * @return Residues at given position */ - string &getResidues(const size_t position) const; + string getResidues(const size_t position) const; /** @brief Returns number of residues (or gaps) at given position. * From 1e482c2567c6d3af44769dd1b3737662b780e3a1 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Wed, 22 Jul 2015 18:19:27 +0200 Subject: [PATCH 21/25] Fixed memory leaks --- Phylo/Sources/ClustalW.cc | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index 0366d72..a68e332 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -171,7 +171,7 @@ namespace Phylo { if (node.isLeaf()) { const string identifier = node.getLabel(); const string residues = sequences[identifier]; - return (new MultipleAlignment(Sequence(identifier, residues))); + return new MultipleAlignment(Sequence(identifier, residues)); } @@ -193,12 +193,12 @@ namespace Phylo { #if VERBOSE==1 cout << "Now aligning:" << endl; - for (size_t i = 0; i < A.getSize(); i++) { - cout << A.getSequence(i).getIdentifier() << endl; + for (size_t i = 0; i < A->getSize(); i++) { + cout << A->getSequence(i).getIdentifier() << endl; } cout << "---------- against ----------" << endl; - for (size_t j = 0; j < B.getSize(); j++) { - cout << B.getSequence(j).getIdentifier() << endl; + for (size_t j = 0; j < B->getSize(); j++) { + cout << B->getSequence(j).getIdentifier() << endl; } cout << endl << endl; #endif @@ -281,7 +281,7 @@ namespace Phylo { // Returns multiple alignment delete A; delete B; - return (new MultipleAlignment(joint)); + return new MultipleAlignment(joint); } From 7ef9270cdadd34f434f6f5cd5342781305e3ee2a Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Thu, 23 Jul 2015 16:44:44 +0200 Subject: [PATCH 22/25] Improved quality of alignment algorithm --- Phylo/Sources/ClustalW.cc | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index a68e332..26c76aa 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -207,9 +207,14 @@ namespace Phylo { // Allocates score and traceback matrices vector> score(N + 1); vector> direction(N + 1); + vector> hgapT(N + 1); + vector> vgapT(N + 1); for (size_t i = 0; i <= N; i++) { score[i] = vector(M + 1); direction[i] = vector(M + 1); + + hgapT[i] = vector(M + 1); + vgapT[i] = vector(M + 1); } @@ -221,6 +226,9 @@ namespace Phylo { const double GEP = getPositionSpecificGEP(*A, *B, j - 1); score[0][j] = -(GOP + GEP * (j - 1)); direction[0][j] = LEFT; + + hgapT[0][j] = 1; + vgapT[0][j] = 1; } @@ -230,6 +238,9 @@ namespace Phylo { GEP = getPositionSpecificGEP(*B, *A, i - 1); score[i][0] = -(GOP + GEP * (i - 1)); direction[i][0] = UP; + + hgapT[i][0] = 1; + vgapT[i][0] = 1; } @@ -250,10 +261,10 @@ namespace Phylo { hgap = (direction[i][j - 1] != LEFT) ? getPositionSpecificGOP(*A, *B, ss, j - 1) - : getPositionSpecificGEP(*A, *B, j - 1); + : getPositionSpecificGEP(*A, *B, j - 1) * hgapT[i][j - 1]; vgap = (direction[i - 1][j] != UP) ? getPositionSpecificGOP(*B, *A, ss, i - 1) - : getPositionSpecificGEP(*B, *A, i - 1); + : getPositionSpecificGEP(*B, *A, i - 1) * vgapT[i - 1][j]; const double d = score[i-1][j-1] + S(*A, *B, i, j, ss, weights), u = score[i - 1][j] - vgap, @@ -263,9 +274,22 @@ namespace Phylo { score[i][j] = max(d, max(u, l)); direction[i][j] = dir; + if (dir == UP) { + vgapT[i][j] = vgapT[i - 1][j] + 1; + hgapT[i][j] = 1; + } + else if (dir == LEFT) { + vgapT[i][j] = 1; + hgapT[i][j] = hgapT[i][j - 1] + 1; + } + else { + vgapT[i][j] = 1; + hgapT[i][j] = 1; + } + // Written in a LP-fashion way for performance reasons - vgaps = (dir == UP) * (vgaps + 1); - hgaps = (dir == LEFT) * (hgaps + 1); + //vgaps = (dir == UP) * (vgaps + 1); + //hgaps = (dir == LEFT) * (hgaps + 1); } } From 67e465f181dda199039e47f94fc2d7ba7680c9d7 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Thu, 23 Jul 2015 16:46:04 +0200 Subject: [PATCH 23/25] Improved quality of alignment algorithm --- Phylo/Sources/ClustalW.cc | 45 ++++++++++++++------------------------- 1 file changed, 16 insertions(+), 29 deletions(-) diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index 26c76aa..4d1c3f9 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -207,14 +207,14 @@ namespace Phylo { // Allocates score and traceback matrices vector> score(N + 1); vector> direction(N + 1); - vector> hgapT(N + 1); - vector> vgapT(N + 1); + vector> hgaps(N + 1); + vector> vgaps(N + 1); for (size_t i = 0; i <= N; i++) { score[i] = vector(M + 1); direction[i] = vector(M + 1); - hgapT[i] = vector(M + 1); - vgapT[i] = vector(M + 1); + hgaps[i] = vector(M + 1); + vgaps[i] = vector(M + 1); } @@ -227,8 +227,8 @@ namespace Phylo { score[0][j] = -(GOP + GEP * (j - 1)); direction[0][j] = LEFT; - hgapT[0][j] = 1; - vgapT[0][j] = 1; + hgaps[0][j] = 1; + vgaps[0][j] = 1; } @@ -239,32 +239,23 @@ namespace Phylo { score[i][0] = -(GOP + GEP * (i - 1)); direction[i][0] = UP; - hgapT[i][0] = 1; - vgapT[i][0] = 1; + hgaps[i][0] = 1; + vgaps[i][0] = 1; } // Calculates score matrix - size_t hgaps = 1, vgaps = 1; for (size_t i = 1; i <= N; i++) { for (size_t j = 1; j <= M; j++) { double vgap = 0.0; double hgap = 0.0; - /* Documentation is unclear about gaps values. - hgap = getPositionSpecificGOP(A, B, ss, j - 1) - + hgaps * getPositionSpecificGEP(A, B, j - 1); - - vgap = getPositionSpecificGOP(B, A, ss, i - 1) - + vgaps * getPositionSpecificGEP(B, A, i - 1); - */ - hgap = (direction[i][j - 1] != LEFT) ? getPositionSpecificGOP(*A, *B, ss, j - 1) - : getPositionSpecificGEP(*A, *B, j - 1) * hgapT[i][j - 1]; + : getPositionSpecificGEP(*A, *B, j - 1) * hgaps[i][j - 1]; vgap = (direction[i - 1][j] != UP) ? getPositionSpecificGOP(*B, *A, ss, i - 1) - : getPositionSpecificGEP(*B, *A, i - 1) * vgapT[i - 1][j]; + : getPositionSpecificGEP(*B, *A, i - 1) * vgaps[i - 1][j]; const double d = score[i-1][j-1] + S(*A, *B, i, j, ss, weights), u = score[i - 1][j] - vgap, @@ -275,21 +266,17 @@ namespace Phylo { direction[i][j] = dir; if (dir == UP) { - vgapT[i][j] = vgapT[i - 1][j] + 1; - hgapT[i][j] = 1; + vgaps[i][j] = vgaps[i - 1][j] + 1; + hgaps[i][j] = 1; } else if (dir == LEFT) { - vgapT[i][j] = 1; - hgapT[i][j] = hgapT[i][j - 1] + 1; + vgaps[i][j] = 1; + hgaps[i][j] = hgaps[i][j - 1] + 1; } else { - vgapT[i][j] = 1; - hgapT[i][j] = 1; + vgaps[i][j] = 1; + hgaps[i][j] = 1; } - - // Written in a LP-fashion way for performance reasons - //vgaps = (dir == UP) * (vgaps + 1); - //hgaps = (dir == LEFT) * (hgaps + 1); } } From dd625c9fc9a40271a82ee79778a340dc4895fc0a Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Thu, 23 Jul 2015 17:09:29 +0200 Subject: [PATCH 24/25] Improved quality of alignment algorithm --- Phylo/Sources/ClustalW.cc | 21 +++++---------------- 1 file changed, 5 insertions(+), 16 deletions(-) diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index 4d1c3f9..9bb1e20 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -226,8 +226,7 @@ namespace Phylo { const double GEP = getPositionSpecificGEP(*A, *B, j - 1); score[0][j] = -(GOP + GEP * (j - 1)); direction[0][j] = LEFT; - - hgaps[0][j] = 1; + hgaps[0][j] = 0; vgaps[0][j] = 1; } @@ -238,9 +237,8 @@ namespace Phylo { GEP = getPositionSpecificGEP(*B, *A, i - 1); score[i][0] = -(GOP + GEP * (i - 1)); direction[i][0] = UP; - hgaps[i][0] = 1; - vgaps[i][0] = 1; + vgaps[i][0] = 0; } @@ -265,18 +263,9 @@ namespace Phylo { score[i][j] = max(d, max(u, l)); direction[i][j] = dir; - if (dir == UP) { - vgaps[i][j] = vgaps[i - 1][j] + 1; - hgaps[i][j] = 1; - } - else if (dir == LEFT) { - vgaps[i][j] = 1; - hgaps[i][j] = hgaps[i][j - 1] + 1; - } - else { - vgaps[i][j] = 1; - hgaps[i][j] = 1; - } + // Written in term of Linear programming for performance + hgaps[i][j] = 1 + (dir == LEFT) * hgaps[i][j - 1]; + vgaps[i][j] = 1 + (dir == UP) * vgaps[i - 1][j]; } } From f8f2f0135b42a96d1337ab9542151bbe0d223ba7 Mon Sep 17 00:00:00 2001 From: Marco Zanella Date: Thu, 23 Jul 2015 17:27:01 +0200 Subject: [PATCH 25/25] Changed base of logarithm --- .gitignore | 8 +++++++- Phylo/Sources/ClustalW.cc | 4 ++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 691e5f6..0d72f4c 100644 --- a/.gitignore +++ b/.gitignore @@ -40,4 +40,10 @@ Lobo/Tests/*.a Lobo/Tests/*.o tools/*.o tools/*.a -tools/Depend \ No newline at end of file +tools/Depend +Phylo/Sources/*.o +Phylo/Sources/*.a +Phylo/APPS/*.o +Phylo/APPS/*.a +Phylo/Tests/*.o +Phylo/Test/*.a diff --git a/Phylo/Sources/ClustalW.cc b/Phylo/Sources/ClustalW.cc index 9bb1e20..4244189 100644 --- a/Phylo/Sources/ClustalW.cc +++ b/Phylo/Sources/ClustalW.cc @@ -295,7 +295,7 @@ namespace Phylo { N = B.getLength(), avg = matrix.getAvgMismatchScore(), identity = A.getPercentIdentity(); - return gap_open + log(min(M, N)) * avg * identity; + return gap_open + log10(min(M, N)) * avg * identity; } @@ -306,7 +306,7 @@ namespace Phylo { const MultipleAlignment &B) const { const double N = A.getLength(), M = B.getLength(); - return gap_extension * (1.0 + abs(log(N / M))); + return gap_extension * (1.0 + abs(log10(N / M))); }