diff --git a/.cproject b/.cproject new file mode 100644 index 0000000..63da05e --- /dev/null +++ b/.cproject @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.project b/.project new file mode 100644 index 0000000..9ac00be --- /dev/null +++ b/.project @@ -0,0 +1,27 @@ + + + Mobi + + + + + + org.eclipse.cdt.managedbuilder.core.genmakebuilder + clean,full,incremental, + + + + + org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder + full,incremental, + + + + + + org.eclipse.cdt.core.cnature + org.eclipse.cdt.core.ccnature + org.eclipse.cdt.managedbuilder.core.managedBuildNature + org.eclipse.cdt.managedbuilder.core.ScannerConfigNature + + diff --git a/.settings/language.settings.xml b/.settings/language.settings.xml new file mode 100644 index 0000000..7596dc4 --- /dev/null +++ b/.settings/language.settings.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + diff --git a/Biopool/APPS/pdb2secondary.cc b/Biopool/APPS/pdb2secondary.cc index f05e856..decfec5 100644 --- a/Biopool/APPS/pdb2secondary.cc +++ b/Biopool/APPS/pdb2secondary.cc @@ -14,8 +14,11 @@ along with Victor. If not, see . */ /** + + @Description */ +// Includes: #include #include #include diff --git a/Biopool/Sources/Atom.h b/Biopool/Sources/Atom.h index 3df6f47..6f20f05 100644 --- a/Biopool/Sources/Atom.h +++ b/Biopool/Sources/Atom.h @@ -45,6 +45,8 @@ namespace Victor { namespace Biopool { virtual ~Atom(); // PREDICATES: + + AtomCode getCode() const; unsigned long getNumber() const; @@ -130,17 +132,30 @@ namespace Victor { namespace Biopool { // -----------------x-------------------x-------------------x----------------- // PREDICATES: - + /** + * Return the code of the Atom + * @param none + * @return AtomCode + */ inline AtomCode Atom::getCode() const { return type; } - + /** + * Return the number of the Atom in the model + * @param none + * @return id, id of atom + */ inline unsigned long Atom::getNumber() const { return id; } + /** + * Return 3D vector with coordinate 3D of the Atom + * @param none + * @return vgVector3 + */ inline vgVector3 Atom::getCoords() { if (!inSync()) diff --git a/Biopool/Sources/PdbLoader.h b/Biopool/Sources/PdbLoader.h index f4c1bc9..f41505f 100644 --- a/Biopool/Sources/PdbLoader.h +++ b/Biopool/Sources/PdbLoader.h @@ -92,19 +92,35 @@ namespace Victor { namespace Biopool { void setNonPermissive() { permissive = false; } - + /** + You can chose if you want verbose output from this class + @param none + @return void + */ void setVerbose() { verbose = true; } - + /** + You can chose if you want not verbose output from this class + @param none + @return void + */ void setNoVerbose() { verbose = false; } - + /** + Set the chain that do you want load + @param char + @return void + */ void setChain(char _ch) { chain = _ch; } - + /** + set the Model that do you want load + @param unsigned int + @return void + */ void setModel(unsigned int _mod) { model = _mod; } diff --git a/Biopool/Sources/PdbSaver.h b/Biopool/Sources/PdbSaver.h index c20220e..dc059a6 100644 --- a/Biopool/Sources/PdbSaver.h +++ b/Biopool/Sources/PdbSaver.h @@ -56,6 +56,11 @@ namespace Victor { namespace Biopool { // PREDICATES: + /** + close the output file + @param none + @return void + */ void endFile() { output << "END\n"; } @@ -103,8 +108,6 @@ namespace Victor { namespace Biopool { protected: - private: - // HELPERS: void writeSeqRes(Spacer& sp); // writes SEQRES entry void writeSecondary(Spacer& sp); diff --git a/Biopool/Sources/Protein.cc b/Biopool/Sources/Protein.cc index 6c9dbfe..b424590 100644 --- a/Biopool/Sources/Protein.cc +++ b/Biopool/Sources/Protein.cc @@ -18,9 +18,9 @@ // Includes: #include #include -using namespace std; -using namespace Victor; using namespace Victor::Biopool; +using namespace std; +using namespace Victor; using namespace Victor::Biopool; // CONSTRUCTORS/DESTRUCTOR: diff --git a/Biopool/Sources/Protein.h b/Biopool/Sources/Protein.h index 79bcb74..d058591 100644 --- a/Biopool/Sources/Protein.h +++ b/Biopool/Sources/Protein.h @@ -68,7 +68,18 @@ namespace Victor { namespace Biopool { void deleteComponent(Component* c); void copy(const Protein& orig); - void load(Loader& l); // data loader + + /** + * load one model by Loader object. Use after command PdbLoader.setModel(i) , PdbLoader.checkModel(); + * @code + * Loader.setModel(i); + Loader.checkModel(); + this->load(Loader); + * @endcode + * @param Loader& , loader object + * @return void + */ + virtual void load(Loader& l); // data loader virtual Protein* clone(); diff --git a/Biopool/Sources/Spacer.cc b/Biopool/Sources/Spacer.cc index 6c43431..4a76026 100644 --- a/Biopool/Sources/Spacer.cc +++ b/Biopool/Sources/Spacer.cc @@ -1664,25 +1664,29 @@ void Spacer::setDSSP(bool verbose) { set ::iterator it = ss[i].find(turns[l]); if (it != ss[i].end()) { // found a n-turn char pos_s = *it; - int pos = atoi(&(pos_s)); - set ::iterator it1 = ss[i + pos - 1].find(turns[l]); - if (it1 != ss[i + pos - 1].end()) { // found the same n-turn after n-1 positions - bool helixBreak = false; - for (unsigned int m = i; m < (i + pos); m++) { - set ::iterator it2 = ss[m].find(turns[l]); - if (it2 == ss[m].end()) { - helixBreak = true; - } - } - if (!helixBreak) { - for (unsigned int m = i; m < (i + pos); m++) { - ss[m].insert(helices[l]); - } - } - break; - } - } - } + int pos = atoi(&(pos_s)); + if(i+pos-1 >= ss.size()) + break; + set::iterator it1 = ss[i + pos - 1].find( + turns[l]); + if (it1 != ss[i + pos - 1].end()) { // found the same n-turn after n-1 positions + bool helixBreak = false; + for (unsigned int m = i; m < (i + pos); m++) { + set::iterator it2 = ss[m].find(turns[l]); + if (it2 == ss[m].end()) { + helixBreak = true; + } + } + if (!helixBreak) { + for (unsigned int m = i; m < (i + pos); m++) { + ss[m].insert(helices[l]); + } + } + break; + } + + } + } // Set sheets (E) set ::iterator it = ss[i].find('B'); if (it != ss[i].end()) { diff --git a/Biopool/Sources/Spacer.h b/Biopool/Sources/Spacer.h index 9217341..64ca3aa 100644 --- a/Biopool/Sources/Spacer.h +++ b/Biopool/Sources/Spacer.h @@ -160,6 +160,21 @@ namespace Victor { namespace Biopool { void setStateFromTorsionAngles(); void setDSSP(bool verbose); + + /** + * + * Return a vector of set, each set correspond whit one amino acid. + * Use this command after setDSSP(boool verbose) command. + * Each set contain many information about secondary structure of one amino acid. + * The first letter of the set is the secondary structure. + * @code + * Spacer.setDSSP(false); + * vector > = Spacer.getDSSP(); + * @endcode + * + * @param none + * @return vector > , a vector of set + */ vector< set > getDSSP() { return ss; }; diff --git a/Makefile b/Makefile index c0f7aa4..657c031 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ # 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 Mobi/Sources Mobi/APPS # # Libraries and paths (which are not defined globally). @@ -27,8 +27,8 @@ BINPATH = bin SOURCES = OBJECTS = -EXECS = -TARGET = +EXECS = +TARGET = LIBRARY = # diff --git a/Makefile.global b/Makefile.global index 1f78a89..781398e 100644 --- a/Makefile.global +++ b/Makefile.global @@ -77,7 +77,7 @@ ifeq ($(verbose), 3) USERFLAGS += -DVERBOSE=3 endif -CFLAGS = $(USERFLAGS) +CFLAGS = $(USERFLAGS) # # Tools @@ -106,11 +106,13 @@ SUBDIRS += _dummy_ LIB_PATH += -L$(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 +### MODIFIED BY MOBI - ***LUCA DEMO*** +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$(UPDIR)/Mobi/Sources -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS -I$(UPDIR)/Lobo/APPS -I$(UPDIR)/Mobi/APPS +### MODIFIED BY MOBI - ***LUCA DEMO*** 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)/Mobi/Tests + SUBDIRS = Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests Mobi/Tests endif ####### Implicit rules @@ -175,6 +177,8 @@ subclean: $(RM) -fr ./Energy/data $(RM) -fr ./Lobo/data $(RM) -fr ./Biopool/data + $(RM) -fr ./Mobi/data + $(RM) -fr ./Mobi/data/* diff --git a/Mobi/APPS/Makefile b/Mobi/APPS/Makefile new file mode 100644 index 0000000..fcd6e6d --- /dev/null +++ b/Mobi/APPS/Makefile @@ -0,0 +1,54 @@ +#--*- makefile -*-------------------------------------------------------------- +# +# Standard makefile +# +#------------------------------------------------------------------------------ + +# Path to project directory. +UPDIR = ../.. +# Path to subdirectories. +SUBDIR= +# Path to directory for binaries: +BINPATH = ../../bin + + +# +# Libraries and paths (which are not defined globally). +# + +LIBS = -lMobi -lBiopool -ltools + +LIB_PATH = -L. + +INC_PATH = -I. -I../../tools/ -I../../Biopool/Sources -I../../Mobi/Sources + +# +# Objects and headers +# + +SOURCES = mobi.cc + +OBJECTS = mobi.o + +TARGETS = mobi + +EXECS = mobi + +LIBRARY = APPSlibMobi.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 diff --git a/Mobi/APPS/mobi.cc b/Mobi/APPS/mobi.cc new file mode 100644 index 0000000..3380b93 --- /dev/null +++ b/Mobi/APPS/mobi.cc @@ -0,0 +1,314 @@ +/* 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 . + */ + +/* + @file Mobi.cc + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* --*- C++ -*------x----------------------------------------------------------- + * + * + * Description: Mobi is a software that take in input .pdb file created + * Whit NMR technology. + * this file contained more models of the same protein, + * he take it, then he imposed all models whit all models + * and return mobility part of the protein in a .pdb file + * + * + * -----------------x----------------------------------------------------------- + */ + +// Includes: +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor; +using namespace Victor::Biopool; +using namespace Victor::Mobi; + +const string OUTPDB = "ResultMobi.pdb"; + +void sShowHelp() { + + cout << "NAME" << endl; + cout << "\t mobi" << endl; + + cout << "SYNOPSIS" << endl; + cout << "\t mobi [FILE]... [OPTION]..." << endl; + + cout << "DESCRIPTION \n" << endl; + cout + << "\t Mobi is a software that take in input a .pdb file created by NMR tecnology." + << endl; + cout + << "\t this file contained more models of the same protein, then Mobi imposed models and return " + << endl; + cout << "\t aminoacid's mobility." << endl; + + cout << "\n" << endl; + + cout << "\t -v verbose output. \n" << endl; + cout << "\t -o [FILE OUTPUT] Output to file (default stdout)\n" << endl; + cout << "\t -m load any models \n" << endl; + + cout << "\t -c arg Chain identifier to read (default is first chain)\n" << endl; + cout << "\t -s arg Set bound everage scale distance mobility (default is 0.85)\n" << endl; + cout << "\t -d arg Set bound standard deviation mobility (default is 0.09)\n" << endl; + cout << "\t -y arg Set bound angle Phi mobility (default is 20)\n" << endl; + cout << "\t -x arg Set bound angle Psi mobility (default is 20)\n" << endl; + + cout << "\t -h help" << endl; + + exit(EXIT_SUCCESS); + +} + +int main(int argc, char* argv[]) { + + bool v, models; + double ScalD, StandD, anglePHI, anglePSI; + string inputFile, outputFile, input, chainID; + + //guide with -h option + if (getArg("h", argc, argv)) { + sShowHelp(); + return 1; + } + if (argc == 1) { + sShowHelp(); + return 1; + } + + getArg("o", outputFile, argc, argv, "!"); + getArg("c", chainID, argc, argv, "!"); + getArg("s", ScalD ,argc, argv, 0.85); + getArg("d", StandD ,argc, argv, 0.09); + getArg("y", anglePHI ,argc, argv, 20); + getArg("x", anglePSI ,argc, argv, 20); + + models = getArg("m",argc, argv); + v = getArg("v", argc, argv); + + + cout << "Welcome to Mobi!" << endl; + + //loan pdb file from input + inputFile = argv[1]; + + ifstream inFile(inputFile.c_str()); + + if (!inFile) + ERROR("Error opening input .pdb file.", exception); + + PdbLoader pl(inFile); // creates the PdbLoader object + + ProteinModels prot; + + if (v) { + pl.setVerbose(); + prot.setVerbose(); + } else + pl.setNoVerbose(); + + // -------------------------------------------------- + // 1. ask how much models load in protein + // -------------------------------------------------- + +// do { +// cout << "This file include: "; +// cout << pl.getMaxModels() << endl; +// +// cout << "Do you want load all models? [y/n]" << endl; +// getline(cin, input); +// // cin >> input; +// +// } while ((strcmp(input.c_str(), "y")) != 0 +// && (strcmp(input.c_str(), "n")) != 0); + + + // User selected chain + if (chainID != "!") { + if (chainID.size() > 1) + ERROR("You can choose only 1 chain", error); + pl.setChain(chainID[0]); + pl.checkAndSetChain(); + if (v) + cout << "Selected chain: " << chainID[0] << endl; + } // First chain + else { + if (pl.getAllChains().size() > 0) { + pl.setChain(pl.getAllChains()[0]); + if (v) + cout << "Selected chain: " << pl.getAllChains()[0] << endl; + chainID = pl.getAllChains()[0]; + } else if (v) + ERROR("No chains found. Quit...", exception); + } + + if (!v) + cout << "\nLOAD..." << endl; + + if (!models) { + prot.load(pl); + } else { + prot.loadSameModels(pl); + } + + // -------------------------------------------------- + // 2. set path to output file + // -------------------------------------------------- + + if (outputFile != "!") { + outputFile = "../Mobi/data/" + outputFile; + } else + outputFile = "../Mobi/data/stdout"; + + // -------------------------------------------------- + // 3. method that save in separated file each models + // -------------------------------------------------- + + prot.save(outputFile); + + ///////////////////////////////////////////////////////////////////// + + //SUPER IMPOSITION + unsigned int d = 0; + + // ------------------------------------------------------ + // 4. TmScore object make super imposition of each models + // ------------------------------------------------------ + + TmScore tm("../Mobi/data/TMscore", outputFile, v); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < prot.size() - 1; i++) + for (unsigned int j = i + 1; j < prot.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + prot.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", + exeption); + + prot.addModels(*(prot.getSpacer(j))); + + } + + // ---------------------------------------------------------------------------------------- + // 5. Standard Deviation object calculate metrics (everage ScalD, StanDevScalD ,phi, psi) + // ---------------------------------------------------------------------------------------- + + StandardDeviation std(prot, v); + + vector ever; + + ever = std.get_everage_distance(); + + //print vector +// cout << "AVERAGE" << endl; +// for (vector::iterator everage = ever.begin(); everage != ever.end(); +// everage++) { +// cout << *everage << endl; +// +// } + + vector SD; + SD = std.get_standard_deviation(); + + //print vector +// cout << "STANDARD DEVIATION" << endl; +// for (vector::iterator walk = SD.begin(); walk != SD.end(); +// walk++) { +// cout << *walk << endl; +// } + +/////////////////////////////////////////////////// + + //ANGLE + + vector ANGLE_PHI; + ANGLE_PHI = std.get_StandarDev_angle_PHI(); + +// cout << "ANGLE PHI" << endl; +// for (vector::iterator walk = ANGLE_PHI.begin(); walk != ANGLE_PHI.end(); +// walk++) { +// cout << *walk << endl; +// +// } + + vector ANGLE_PSI; + ANGLE_PSI = std.get_StandarDev_angle_PSI(); + +// cout << "ANGLE PSI" << endl; +// for (vector::iterator walk = ANGLE_PSI.begin(); walk != ANGLE_PSI.end(); +// walk++) { +// cout << *walk << endl; +// +// } + +/////////////////////////////////////////////////////////////////////////////////// + + //SECONDARY STRUCTURE + + SecondaryStructure sstr(prot, v); + + vector MOB; + MOB = sstr.getMobilitySecondaryStructure(); + + //print vector +// cout << "\nSECONDARY STRUCTURE" << endl; +// for (vector::iterator walk = MOB.begin(); walk != MOB.end(); walk++) { +// cout << *walk << " "; +// +// } +// +// cout << endl; + +///////////////////////////////////////////////////////////////////////////////////// + + // -------------------------------------------------- + // 6. MobiSaver object save mobility in output file + // -------------------------------------------------- + + string out_pdb = outputFile + OUTPDB; + ofstream ofstream(out_pdb.c_str(), ofstream::app); + + MobiSaver* saver = new MobiSaver(prot, outputFile, ofstream, v, ScalD, StandD , anglePHI, anglePSI); + saver->allMobility(ever, SD, ANGLE_PHI, ANGLE_PSI, MOB); + + + prot.remove(outputFile); + //remove trash file + outputFile = outputFile + "TMScore.pdb_atm"; + remove(outputFile.c_str()); + + saver-> saveProtein(prot, ever, SD); + + delete saver; + + return 0; +} diff --git a/Mobi/Sources/Makefile b/Mobi/Sources/Makefile new file mode 100644 index 0000000..f18271c --- /dev/null +++ b/Mobi/Sources/Makefile @@ -0,0 +1,62 @@ +#--*- makefile -*-------------------------------------------------------------- +# +# Standard makefile +# +#------------------------------------------------------------------------------ + +# Path to project directory. +UPDIR = ../.. +# Path to subdirectories. +SUBDIR = ../../tools +# Path to directory for binaries: +BINPATH = ../../bin + + +# +# Libraries and paths (which are not defined globally). +# + +LIBS = -lBiopool -ltools + +LIB_PATH = -L. + +INC_PATH = -I. -I../../tools -I../../Biopool/Sources + +# +# Objects and headers +# + + +SOURCES = ProteinModels.cc TmScore.cc StandardDeviation.cc SecondaryStructure.cc MobiSaver.cc + + +OBJECTS = ProteinModels.o TmScore.o StandardDeviation.o SecondaryStructure.o MobiSaver.o + + +TARGETS = + +EXECS = + +LIBRARY = libMobi.a + +# +# Install rule +# + +#start: subdirs + +compile: all + +allinstall: $(LIBRARY) $(TARGETS) + mv $(LIBRARY) $(UPDIR)/lib/ + + +install: subinstall allinstall + +all: install +# +# Call global Makefile to do the job. +# + +include ../../Makefile.global + diff --git a/Mobi/Sources/MobiSaver.cc b/Mobi/Sources/MobiSaver.cc new file mode 100644 index 0000000..79a23b7 --- /dev/null +++ b/Mobi/Sources/MobiSaver.cc @@ -0,0 +1,643 @@ +/* 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 . + */ + +/** + * @file MobiSaver.h + * @author Riccardo Zanella + * @date 21 lug 2015 + * @version 0.1 + */ + +//Includes: +#include "MobiSaver.h" + +using namespace Victor; +using namespace Victor::Biopool; +using namespace Victor::Mobi; + +const string OUT = "ResultMobi.fasta"; + +/** + * Default Constructor + * @param ProteinModels& , object PreteinModels + * @param string output, path file output + * @param bool verbose , verbose + * @param double boundSD, default = 0.85 + * @param double boundStandD, default = 0.09 + * @param double anglePHI, default = 20 + * @param double anglePSI, default = 20 + */ +MobiSaver::MobiSaver(ProteinModels prot, string output, ofstream& stream, + bool verbose, double boundSD, double boundStandD, double anglePHI, + double anglePSI) : + PdbSaver(stream), verbose(verbose), ScalD(boundSD), StandD(boundStandD), angPHI( + anglePHI), angPSI(anglePSI) { + // TODO Auto-generated constructor stub + + //if file does not exist then create and insert aminoacid sequence in head otherwise don't create file + out = output + OUT; + + if (access(out.c_str(), F_OK) != 0) { + + if (verbose) + cout << "\n ### Create fasta file in output ###" << endl; + + ofstream fout; //stream in output + vector::iterator walk = prot.sequence.begin(); + + fout.open(out.c_str()); + if (!fout) { + ERROR("Error to create file!", error); + } else { + fout << "> sequence" << endl; + while (walk != prot.sequence.end()) { + fout << *(walk); + walk++; + } + + fout.close(); + + if (verbose) + cout << "file success created!" << endl; + } + + } + +} + +/** + * Default Deconstructor + * + */ +MobiSaver::~MobiSaver() { + // TODO Auto-generated destructor stub +} + +// PREDICATES: + +/** + * save mobility from average scale distance vector + * @param vector , vector of average scale distance + * @return void + */ +void MobiSaver::mob_eveScalD(vector everageDistance) { + + if (everageDistance.size() == 0) + ERROR("Vector everage distance empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout << "\n ### Save mobility from average distance ###" << endl; + + fout << endl; + fout << "> Average scale distance 0" << endl; + + for (vector::iterator walk = everageDistance.begin(); + walk != everageDistance.end(); walk++) { + if (*(walk) < ScalD) + fout << "M"; + else + fout << "."; + } + + fout.close(); + + if (verbose) + cout << "Mobility from average scaled distance saved!" << endl; + +} + +/** + * save mobility from standard deviation distance vector + * @param vector , vector of scale distance + * @return void + */ +void MobiSaver::mob_stanD(vector Scale_distance) { + + if (Scale_distance.size() == 0) + ERROR("Vector standard deviation empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout << "\n ### Mobility from standard deviation saved on file ###" + << endl; + + fout << endl; + fout << "> Standard deviation distance 1" << endl; + + for (vector::iterator walk = Scale_distance.begin(); + walk != Scale_distance.end(); walk++) { + if (*(walk) > StandD) + fout << "M"; + else + fout << "."; + } + + fout.close(); + + if (verbose) + cout << "Mobility from standard deviation saved!" << endl; + +} + +/** + * save mobility from vector of phi angle + * @param vector , vector of scale distance + * @return void + */ +void MobiSaver::mob_aPHI(vector angle_PHI) { + + if (angle_PHI.size() == 0) + ERROR("Vector angle PHI empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout << "\n ### Mobility from angle phi saved on file ###" << endl; + + fout << endl; + fout << "> Phi angle 2" << endl; + + for (vector::iterator walk = angle_PHI.begin(); + walk != angle_PHI.end(); walk++) { + if (*(walk) > angPHI) + fout << "M"; + else + fout << "."; + } + + fout.close(); + + if (verbose) + cout << "Mobility from angle_PHI saved!" << endl; + +} + +/** + * save mobility from vector of psi angle + * @param vector , from vector of psi angle + * @return void + */ +void MobiSaver::mob_aPSI(vector angle_PSI) { + + if (angle_PSI.size() == 0) + ERROR("Vector angle PSI empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout << "\n ### Mobility from angle phi saved on file ###" << endl; + + fout << endl; + fout << "> Psi angle 3" << endl; + + for (vector::iterator walk = angle_PSI.begin(); + walk != angle_PSI.end(); walk++) { + if (*(walk) > angPSI) + fout << "M"; + else + fout << "."; + } + + fout.close(); + + if (verbose) + cout << "Mobility from angle_PSI saved!" << endl; + +} + +/** + * save mobility structure + * @param vector, from vector of mobility structure + * @return void + */ +void MobiSaver::mob_SecS(vector Mob_SecStructure) { + + if (Mob_SecStructure.size() == 0) + ERROR("Vector Mob_SecStructure empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout << "\n ### Mobility from secondary structures saved on file ###" + << endl; + + fout << endl; + fout << "> Secondary structure 4" << endl; + + for (vector::iterator walk = Mob_SecStructure.begin(); + walk != Mob_SecStructure.end(); walk++) + fout << *(walk); + + fout.close(); + + if (verbose) + cout << "Mobility from secondary structure saved!" << endl; + +} + +/** + * save mobility from average scale distance filtered by secondary structures + * @param vector , vector average scaled distance + * @param vector , vector secondary structures + * @return void + */ +void MobiSaver::mob_eveScalD_filtSecS(vector everageDistance, + vector mobSecS) { + + if (everageDistance.size() == 0 || mobSecS.size() == 0) + ERROR("Exception: Vectors must be full.", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout + << "\n ### Save mobility from average Scale distance filtered by Secondary Structure... ###" + << endl; + + fout << endl; + fout << "> Average scale distance filtered with SecStr 0" << endl; + + vector::iterator everage = everageDistance.begin(); + vector::iterator secStruct = mobSecS.begin(); + + //If average is fix stay fix, if average is mobile and DSSP is mobile then change + //to fix + while (everage != everageDistance.end() || secStruct != mobSecS.end()) { + + if (*(everage) < ScalD && *(secStruct) != '.') + fout << "M"; + else + fout << "."; + + everage++; + secStruct++; + } + + fout.close(); + + if (verbose) + cout + << "Mobility from average scaled distance filtered by Secondary Structure saved!" + << endl; + +} + +/** + * save mobility from average scale distance filtered by angles and scaled distance + * @param vector , vector average scaled distance + * @param vector , angle phi + * @param vector , angle psi + * @param vector , Scaled Distance + * @return void + */ +void MobiSaver::mob_eveScalD_filteredByPHI_PSI_standD( + vector everageDistance, vector angle_PHI, + vector angle_PSI, vector Scale_distance) { + + vector vettoreSupporto; + + if (everageDistance.size() == 0 || angle_PHI.size() == 0 + || angle_PSI.size() == 0 || Scale_distance.size() == 0) + ERROR("One vectors is empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout + << "\n ### Save mobility from average Scale distance filtered by PHI PSI Standard deviation... ###" + << endl; + + fout << endl; + fout << "> Average scale distance filtered with PHI PSI StdD 0" << endl; + + const string filter1 = "MM."; + const string filter2 = ".MM"; + + for (vector::iterator walk = everageDistance.begin(); + walk != everageDistance.end(); walk++) { + if (*(walk) < ScalD) + vettoreSupporto.push_back("M"); + else + vettoreSupporto.push_back("."); + } + + string test; + + vector::iterator mob = vettoreSupporto.begin(); + vector::iterator phi = angle_PHI.begin(); + vector::iterator psi = angle_PSI.begin(); + vector::iterator stdD = Scale_distance.begin(); + + int i; + bool flag; + vector::iterator j; + vector::iterator h, s, d; + + while (mob != vettoreSupporto.end()) { + + i = 0; + flag = true; + test.clear(); + j = mob; + h = phi; + s = psi; + d = stdD; + + while (j != vettoreSupporto.end() && i < 3 && flag) { + + test = test + (*(j)); + + if (test.compare(filter1) == 0) { + if (*(h) > angPHI && *(s) > angPSI && *(d) > StandD + && (*(s - 1) > angPSI)) + flag = false; + + } else if (test.compare(filter2) == 0) { + + if (*(h - 2) > angPHI && *(s - 2) > angPSI && *(d - 2) > StandD + && (*(h - 1) > angPHI)) + flag = false; + + } + + j++; + h++; + s++; + d++; + i++; + } + + if (!flag) { + + fout << "MMM"; + mob = j; + phi = h; + psi = s; + stdD = d; + + } else { + fout << *(mob); + mob++; + } + + } + + fout.close(); + + if (verbose) + cout + << "Mobility from average Scale distance filtered by PHI PSI Standard deviation whith mask saved!" + << endl; + +} + +/** + * save mobility from standard deviation with mask + * @param vector , vector scaled distance + * @return void + */ +void MobiSaver::mob_stanD_withMask(vector Scale_distance) { + + vector vettoreSupporto; + map map; + + if (Scale_distance.size() == 0) + ERROR("Vector standard deviation empty!", exception); + + ofstream fout(out.c_str(), ofstream::app); + + if (!fout) + ERROR("Could not open file for writing.", error); + + if (verbose) + cout << "\n ### Save on file standard deviation with Mask ###" << endl; + + fout << endl; + fout << "> Standard deviation distance with mask 1" << endl; + + const pair product1("M.MM", "MMMM"); + const pair product2("MM.M", "MMMM"); + const pair product3("M..MM", "MMMMM"); + const pair product4("MM..M", "MMMMM"); + const pair product5(".M.M.", "....."); + const pair product6("..M..", "....."); + const pair product7("..MM..", "......"); + + map.insert(product1); + map.insert(product2); + map.insert(product3); + map.insert(product4); + map.insert(product5); + map.insert(product6); + map.insert(product7); + + for (vector::iterator walk = Scale_distance.begin(); + walk != Scale_distance.end(); walk++) { + if (*(walk) > StandD) + vettoreSupporto.push_back("M"); + else + vettoreSupporto.push_back("."); + } + + string test; + + vector::iterator mob = vettoreSupporto.begin(); + std::map::iterator iter = map.begin(); + + int i; + bool flag; + vector::iterator j; + + while (mob != vettoreSupporto.end()) { + + i = 0; + flag = true; + test.clear(); + j = mob; + + while (j != vettoreSupporto.end() && i < 6 && flag) { + + test = test + (*(j)); + iter = map.find(test); + if (iter != map.end()) { + test = iter->second; + flag = false; + } + + j++; + i++; + } + + if (!flag) { + fout << test; + mob = j; + } else { + fout << *(mob); + mob++; + } + + } + + fout.close(); + + if (verbose) + cout << "Mobility from standard deviation whith mask saved!" << endl; + +} + +/** + * save all type of mobility + * @param vector , vector average scaled distance + * @param vector , vector Scaled Distance + * @param vector , angle phi + * @param vector , angle psi + * @param vector , secondary structures + * + * @return void + */ +void MobiSaver::allMobility(vector everageDistance, + vector Scale_distance, vector angle_PHI, + vector angle_PSI, vector Mob_SecStructure) { + + mob_eveScalD(everageDistance); + mob_eveScalD_filtSecS(everageDistance, Mob_SecStructure); + mob_eveScalD_filteredByPHI_PSI_standD(everageDistance, angle_PHI, angle_PSI, + Scale_distance); + mob_stanD(Scale_distance); + mob_stanD_withMask(Scale_distance); + mob_aPHI(angle_PHI); + mob_aPSI(angle_PSI); + mob_SecS(Mob_SecStructure); + +} + +/** + * Method that shadow save Protein of PdbSaver, this method save in .pdb format + * all original models in ProteinModels with column standard deviation modified + * and column B factor modified with average scaled distance. + * @param ProteinModels , object ProteinModels + * @param vector , vector average scaled distance + * @param vector , vector standard deviation + * @return void + */ + +void MobiSaver::saveProtein(ProteinModels prot, + vector everageDistance, vector Scale_distance) { + + if (everageDistance.size() == 0 || Scale_distance.size() == 0) + ERROR("One vector is empty!", exception); + + vector::iterator walk; + vector::iterator walk2; + + if (verbose) + cout << "\n ### Save Pdb file with column b factor modify ###" << endl; + + output << "REMARK 1 template_A_NMRMOV.pdb" << "\n" + << "REMARK 2 B-factors changed to averaged Scaled Distance x 100 \n" + << "REMARK 3 after TMScore super imposition with d0 = 4.0; Occupancy changed to SD \n"; + + int g; + for (unsigned int i = 0; i < prot.original_models.size(); i++) { + if (prot.original_models[i].size() > 0) { + + aminoOffset = 1; + g = i + 1; + output << "MODEL " << g << endl; + //method of class Component. It checks how deep is the spacer + + walk = everageDistance.begin(); + walk2 = Scale_distance.begin(); + //saving is one ammino at a time + for (unsigned int j = 0; j < prot.original_models[i].sizeAmino(); + j++) { + AminoAcid gr = prot.original_models[i].getAmino(j); + gr.sync(); + + for (unsigned int y = 0; y < gr.size(); y++) { + string atName = gr[y].getType(); + + if (atName == "OXT") // cosmetics: OXT has to be output after + continue; // the sidechain and therefore goes in saveSpacer + + // Added variable for correcting atom type H (last column in PDBs) + char atomOneLetter; + if (!isdigit(atName[0])) { + atomOneLetter = atName[0]; + } else { + atomOneLetter = atName[1]; + } + + // Added control for size by Damiano Piovesan + // example HG12 + if (!isdigit(atName[0]) && (atName.size() < 4)) + atName = ' ' + atName; + while (atName.size() < 4) + atName += ' '; + + output << "ATOM" << setw(7) << gr[y].getNumber() << " " + << atName << " " << gr.getType() << " " << chain + << setw(4) << aminoOffset << " " << setw(8) + << setprecision(3) << gr[y].getCoords().x << setw(8) + << setprecision(3) << gr[y].getCoords().y << setw(8) + << setprecision(3) << gr[y].getCoords().z << " " + << fixed << setprecision(2)<< *(walk2) + << setw(6) << fixed << setprecision(2) + << (*(walk) * 100) << " " << atomOneLetter << "\n"; + + atomOffset = gr[y].getNumber() + 1; + + } + walk++; + walk2++; + aminoOffset++; + } + + output << "ENDMODL\n"; + } + + } + + endFile(); + + if (verbose) + cout << "Pdb file saved!" << endl; + +} diff --git a/Mobi/Sources/MobiSaver.h b/Mobi/Sources/MobiSaver.h new file mode 100644 index 0000000..5a872e3 --- /dev/null +++ b/Mobi/Sources/MobiSaver.h @@ -0,0 +1,78 @@ +/* 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 . + */ + +/** + * @file MobiSaver.h + * @author Riccardo Zanella + * @date 21 lug 2015 + * @version 0.1 + */ + + +#ifndef MOBI_SOURCES_MOBISAVER_H_ +#define MOBI_SOURCES_MOBISAVER_H_ + +//Includes: +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor::Biopool; + +namespace Victor { +namespace Mobi { + +/**@brief Implements a MobiSaver. + * This class inherit PdbSaver class. This class allow to Saver in output file all type of vector generated from + * Standard Deviation and SecondaryStructure classes to have the mobility. + * You can save Mobility also filtered by same type of mask. + */ + +class MobiSaver : public PdbSaver{ +public: + + // CONSTRUCTORS/DESTRUCTOR: + MobiSaver(ProteinModels __protein,string __output, ofstream& __stream, bool __verbose = false, double __boundSD = 0.85, double __boundStandD = 0.09, double __anglePHI = 20, double __anglePSI = 20); + virtual ~MobiSaver(); + + // PREDICATES: + + void mob_eveScalD(vector __everageDistance); + void mob_eveScalD_filtSecS(vector __everageDistance, vector __mobSecS); + void mob_eveScalD_filteredByPHI_PSI_standD(vector __everageDistance, vector __angle_PHI, vector __angle_PSI, vector __Scale_distance); + void mob_stanD(vector __Scale_distance); + void mob_stanD_withMask(vector __Scale_distance); + void mob_aPHI(vector __angle_PHI); + void mob_aPSI(vector __angle_PSI); + void mob_SecS(vector __Mob_SecStructure); + void allMobility(vector __everageDistance, + vector __Scale_distance, vector __angle_PHI, + vector __angle_PSI, vector __Mob_SecStructure); + virtual void saveProtein(ProteinModels __protein, vector __everageDistance, vector __StandardDeviation); + +private: + bool verbose; + string out; + double ScalD, StandD, angPHI, angPSI; +}; +} +} + +#endif /* MOBI_SOURCES_MOBISAVER_H_ */ diff --git a/Mobi/Sources/ProteinModels.cc b/Mobi/Sources/ProteinModels.cc new file mode 100644 index 0000000..e261dfc --- /dev/null +++ b/Mobi/Sources/ProteinModels.cc @@ -0,0 +1,277 @@ +/* + @file ProteinModels.cc + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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 . + */ + +// Includes: +#include +#include +#include +#include + +using namespace Victor; +using namespace Victor::Mobi; +using namespace Victor::Biopool; + +const string PDB = ".pdb"; + +// CONSTRUCTORS/DESTRUCTOR: + +/** + * Default Constructor + * @param nothing. + */ +ProteinModels::ProteinModels() : + Protein(), verbose(false) { +} + +/** + * Constructor. Copy another Protein object. + *@param Protein + */ +ProteinModels::ProteinModels(const Protein& _orig) : + Protein(_orig), verbose(false) { +} + +/** + * DESTRUCTOR + *@param none + */ +ProteinModels::~ProteinModels() { +} + +// PREDICATES: + +/** + Overloading method load, this method load all models in Protein Models Object + @param (PdbLoader&) , object PdbLoader + @return void + */ +void ProteinModels::load(PdbLoader& pl) { + + unsigned int d = 0; + + if (!verbose) + pl.setNoVerbose(); +//Load Models + for (unsigned int i = 1; i <= pl.getMaxModels(); i++) { + if (verbose) + cout << ">>>model#" << i << endl; + pl.setModel(i); + pl.checkModel(); + this->Protein::load(pl); + } + + if (this->size() != 0) { + for (unsigned int i = 0; i < this->size(); i++) + original_models.push_back(*(this->getSpacer(i))); + + for (unsigned int i = 0; i < this->getSpacer(d)->sizeAmino(); i++) + sequence.push_back(this->getSpacer(d)->getAmino(i).getType1L()); + + if (verbose) + cout << "\n" << "Models load in protein" << endl; + } +} + +/** + Internal method + Chose how much models do you want loa + @param (PdbLoader&) , object PdbLoader + @return unsigned int + */ +unsigned int ProteinModels::selectModels(PdbLoader& pl) { + + unsigned int modelNum; + string input; + + cout << "How much do you want load? Insert a value between 2 and "; + cout << pl.getMaxModels() << endl; + + getline(cin, input); + + modelNum = stouiDEF(input); + + while (modelNum > pl.getMaxModels() || modelNum < 2) { + cerr << "Number of models selected out of bounds! Reinput please..." + << endl; + getline(cin, input); + modelNum = stouiDEF(input); + + } + + return modelNum; + +} + +/** + Load same models + @param (PdbLoader&) , object PdbLoader + @return void + */ +void ProteinModels::loadSameModels(PdbLoader& pl) { + + unsigned int d=0; + unsigned int modelNum = selectModels(pl); + + for (unsigned int i = 1; i <= modelNum; i++) { + if (verbose) + cout << "\t>>>model#" << i << endl; + pl.setModel(i); //from pdb loader choose model to load in the protein + pl.checkModel(); + this->Protein::load(pl); // creates the Protein object + } + + if (this->size() != 0) { + for (unsigned int i = 0; i < this->size(); i++) + original_models.push_back(*(this->getSpacer(i))); + + for (unsigned int i = 0; i < this->getSpacer(d)->sizeAmino(); i++) + sequence.push_back(this->getSpacer(d)->getAmino(i).getType1L()); + + if (verbose) + cout << "\n" << "Models load in protein" << endl; + } +} + +/** + Save vector of models in output file + @param (string output) , name of output file + @return void + */ +void ProteinModels::printModels(string outputFile) { + + /**stream in output*/ + ofstream fout; + string outputFile_1; + PdbSaver ps(fout); + const string VECTOR = "Vector"; + + unsigned int i = 0; + + if (verbose) + cout << "\n ###Save models on file ###" << endl; + vector::iterator walk = models.begin(); + while (walk != models.end()) { + + outputFile_1 = outputFile + VECTOR + (itosDEF(i)) + PDB; + if (verbose) + cout << outputFile_1 << endl; + + fout.open(outputFile_1.c_str()); + if (!fout) { + ERROR("Could not open file for writing.", exception); + } else { + + ps.saveSpacer(*walk); + walk++; + i++; + ps.endFile(); + fout.close(); + + if (verbose) + cout << "file cloased" << endl; + } + } + +} + +/** + Overloading method save, save models in output file + @param (string output) , name of output file + @return void + */ +void ProteinModels::save(string outputFile) { + + /**stream in output*/ + ofstream fout; + string outputFile_1; + PdbSaver ps(fout); + + if (verbose) + cout << "Save models on file..." << endl; + // Open the proper output stream (file or stdout) + for (unsigned int i = 0; i < this->size(); i++) { + + outputFile_1 = outputFile + (itosDEF(i)) + PDB; + + if (verbose) + cout << outputFile_1 << endl; + + fout.open(outputFile_1.c_str()); + + if (!fout) { + ERROR("Could not open file for writing.", exception); + } else + ps.saveSpacer(*(this->getSpacer(i))); + + ps.endFile(); + fout.close(); + + if (verbose) + cout << "file closed." << endl; + } + if (verbose) + cout << " " << endl; + +} + +/** + Remove file created by save method + @param (string output) , name of output file + @return void + */ +void ProteinModels::remove(string outputFile) { + + string outputFile_1; + + if (verbose) + cout << "Deleting file..." << endl; + // Open the proper output stream (file or stdout) + for (unsigned int i = 0; i < this->size(); i++) { + + outputFile_1 = outputFile + (itosDEF(i)) + PDB; + if (std::remove(outputFile_1.c_str()) != 0) + ERROR("File don't deleted! ", exception); + + } + if (verbose) + cout << " " << endl; + +} + +/** + Add Spacer in object ProteinModels + @param (Spacer&) , object Spacer + @return void + */ +void ProteinModels::addModels(Spacer& sp) { + this->models.push_back(sp); + +} + +/** + Get Spacer from Protein Models + @param (unsigned int) , number of Spacer (range 0/number Spacer) + @return Spacer + */ +Spacer ProteinModels::getModel(unsigned int u) { + return this->models[u]; +} diff --git a/Mobi/Sources/ProteinModels.h b/Mobi/Sources/ProteinModels.h new file mode 100644 index 0000000..05664d0 --- /dev/null +++ b/Mobi/Sources/ProteinModels.h @@ -0,0 +1,92 @@ +/* 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 . + */ + +/** + * @file PreteinModel.h + * @author Riccardo Zanella + * @date Lug 2015 + * @version 0.1 + */ + +#ifndef MOBI_SOURCES_PROTEINMODEL_ +#define MOBI_SOURCES_PROTEINMODEL_ + +//Includes: +#include +#include + +using namespace Victor::Biopool; + +namespace Victor { +namespace Mobi { +/** + * @brief Extends Protein class with functionalities related to manipulation of NMR model and models comparations. + * Scale Distance metric is provided. + */ +class ProteinModels: public Protein { + +public: + + // CONSTRUCTORS/DESTRUCTOR: + ProteinModels(); + + ProteinModels(const Protein& _orig); + + virtual ~ProteinModels(); + + // PREDICATES: + + virtual void load(PdbLoader& pl); + + + void loadSameModels(PdbLoader& pl); + + +private: + unsigned int selectModels(PdbLoader& pl); + +public: + // MODIFIERS: + + /** + You can chose if you want verbose output from this class + @param none + @return void + */ + void setVerbose() { + verbose = true; + } + + void save(string outputFile); + void remove(string outputFile); + + Spacer getModel(unsigned u); + void addModels(Spacer& sp); + + void printModels(string outputFile); + + + // MODIFIERS: +private: + + bool verbose; + +public: + vector original_models; + vector models; + vector sequence; + +}; +} +} +#endif /* MOBI_SOURCES_PROTEINMODEL_ */ diff --git a/Mobi/Sources/SecondaryStructure.cc b/Mobi/Sources/SecondaryStructure.cc new file mode 100644 index 0000000..97149b4 --- /dev/null +++ b/Mobi/Sources/SecondaryStructure.cc @@ -0,0 +1,171 @@ +/* + @file ProteinModels.cc + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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 . + */ + +// Includes: +#include "SecondaryStructure.h" + +using namespace Victor; +using namespace Victor::Mobi; +using namespace Victor::Biopool; + +// CONSTRUCTORS/DESTRUCTOR: + +/** + * Default Constructor + * @param ( ProteinModels& ), object PreteinModels . + */ +SecondaryStructure::SecondaryStructure(const ProteinModels& modelli, + bool verbose) : + verbose(verbose), models(modelli.original_models) { +} + +/** + * Default Deconstructor + * @param ( ProteinModels& ), object PreteinModels . + */ +SecondaryStructure::~SecondaryStructure() { +} + +/** + * get the secondary structure. Return is a vector of vector of char where vector[i][j] + * 'i' is a specific amino acid + * 'j' is a specific model + * and char is a letter of secondary structure of amino acid 'i' and models 'j' + * @return vector< vector > , return vector of vector of char. + */ +vector< vector > SecondaryStructure::getSecStructFromModels(){ + + unsigned int num_amino = 0; + if (models.size() != 0) + num_amino = models[0].sizeAmino(); + else + ERROR("Nothing models in the protein, remember load models.", exception); + + //create a support vector to get secondary structure + vector > vettore_di_supporto(num_amino, set()); + + //create a vector for manipulated all amiocid's structure + vector< vector > sec_Structures(num_amino, + vector(models.size())); + + if (verbose) { + cout << "\nStart procedure select secondary structure... " << endl; + cout << "Model size: " << models.size() << endl; + } + //for each models + for (unsigned int i = 0; i < models.size(); i++) { + + models[i].setDSSP(false); + vettore_di_supporto = models[i].getDSSP(); + //cout << "support vector size: " << vettore_di_supporto.size() << endl; + + //iteration on vector of set + for (unsigned int j = 0; j < num_amino; j++) { + //extract first char value and push it in vector char + sec_Structures[j][i] = (*(vettore_di_supporto[j].begin())); + + } + + } + +return sec_Structures; + +} + +/** + * get the mobility analyzing secondary structures + * @return vector , return vector of mobility from Secondary Structure + */ +vector SecondaryStructure::getMobilitySecondaryStructure() { + + mobility.clear(); + vector< vector > sec_Structures; + + unsigned int num_amino = 0; + if (models.size() != 0) + num_amino = models[0].sizeAmino(); + else + ERROR("Nothing models in the protein, remember load models.", exception); + + + sec_Structures = getSecStructFromModels(); + + char test; + bool flag; + + for (unsigned int i = 0; i < num_amino; i++) { + + test = sec_Structures[i][0]; + flag = true; + + //if the first letter is empty or is a S + if ((test != 'G') && (test != 'H') && (test != 'I') && (test != 'T') + && (test != 'E') && (test != 'B')) { + //verifing that is all S and/or empty space. + + for (unsigned int j = 0; j < models.size(); j++) { + + if ((sec_Structures[i][j] != 'G') + && (sec_Structures[i][j] != 'H') + && (sec_Structures[i][j] != 'I') + && (sec_Structures[i][j] != 'T') + && (sec_Structures[i][j] != 'E') + && (sec_Structures[i][j] != 'B')) { + } else { + + mobility.push_back('M'); + flag = false; + break; + + } + + } + if (flag) { + mobility.push_back('c'); + } + //the first letter is the letter of Secondary Structure + } else { + + //verifing that all letter is the same + for (unsigned int j = 0; j < models.size(); j++) { + + if ((sec_Structures[i][j] == test)) { + } else { + + mobility.push_back('M'); + flag = false; + break; + + } + + } + if (flag) { + mobility.push_back('.'); + } + + } + + } + + return mobility; +} + diff --git a/Mobi/Sources/SecondaryStructure.h b/Mobi/Sources/SecondaryStructure.h new file mode 100644 index 0000000..813c082 --- /dev/null +++ b/Mobi/Sources/SecondaryStructure.h @@ -0,0 +1,56 @@ +/* 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 . + */ + +/** + * @file SecondaryStructure.h + * @author Riccardo Zanella + * @date 21 lug 2015 + * @version 0.1 + */ + +// Includes: +#ifndef MOBI_SOURCES_SECONDARYSTRUCTURE_H_ +#define MOBI_SOURCES_SECONDARYSTRUCTURE_H_ + +#include + +using namespace Victor::Biopool; + +namespace Victor { +namespace Mobi { + +/**@brief Implements a Secondary Structure. + * Includes methods to obtain mobility from the analyze of Secondary Structure. + */ + +class SecondaryStructure { +public: + + // CONSTRUCTORS/DESTRUCTOR: + + SecondaryStructure(const ProteinModels& _orig, bool _verbose = false); + virtual ~SecondaryStructure(); + + // PREDICATES: + vector< vector >getSecStructFromModels(); + vector getMobilitySecondaryStructure(); + +private: + bool verbose; + vector models; + vector mobility; + +}; +} +} +#endif /* MOBI_SOURCES_SECONDARYSTRUCTURE_H_ */ diff --git a/Mobi/Sources/StandardDeviation.cc b/Mobi/Sources/StandardDeviation.cc new file mode 100644 index 0000000..942cfbc --- /dev/null +++ b/Mobi/Sources/StandardDeviation.cc @@ -0,0 +1,373 @@ +/* + @file StandardDeviation.cc + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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 . + */ + +// Includes: +#include "StandardDeviation.h" + +using namespace Victor; +using namespace Victor::Mobi; +using namespace Victor::Biopool; + +// CONSTRUCTORS/DESTRUCTOR: + +/** + * Default Constructor + * @param (const ProteinModels&), object ProteinModels + * @param (bool verbose), verbose + */ +StandardDeviation::StandardDeviation(const ProteinModels& modelli, bool verbose) : + verbose(verbose), original_models(modelli.original_models), models( + modelli.models) { +} + +/** + * DESTRUCTOR + *@param none + */ +StandardDeviation::~StandardDeviation() { +} + +/** + * internal method, take atom from spacer + * @param (Spacer* s), pointer to the spacer object + * @param (bool flag), internal flag + */ +void StandardDeviation::getCaAtom(Spacer* s, bool flag) { + +//per un modello fissato creo il vettore di atomi + AminoAcid* a = new AminoAcid; + + for (unsigned int u = 0; u < s->sizeAmino(); u++) { + a = &(s->getAmino(u)); + + unsigned int i = 1; + + if (flag) + this->CaVector1.push_back(a->getAtom(i)); + else + this->CaVector2.push_back(a->getAtom(i)); + + if (a->getAtom(i).getCode() != CA) + ERROR("Atom find is not CA atom.", exception); + + } + +} + +/** + * Get average distance Scale Distance + * @return vector + * + */ +vector StandardDeviation::get_everage_distance() { + + if (verbose) + cout << "### Start average distance scale distance ###" << endl; + /** vector average Scale Distance*/ + dist_everage.clear(); + + Spacer* primo_modello = new Spacer; + Spacer* secondo_modello = new Spacer; + + unsigned int num_atomi = 0; + double ScalD, distance = -1.0; + + if (models.size() != 0) + num_atomi = models[0].sizeAmino(); + else + ERROR("ProteinModels empty, remember execute TmImpose.", exception); + + vector > dist_from_Ca_atoms(num_atomi, vector(0.0)); + + if (verbose) { + cout << "Number of models: " << models.size() << endl; + cout << "Number of CA atoms in each models: " << num_atomi << endl; + } + + //for any models create atom's vector + unsigned int u = 0; + + while (u < (models.size())) { + + primo_modello = &models[u]; + getCaAtom(primo_modello, true); + u++; + + secondo_modello = &models[u]; + getCaAtom(secondo_modello, false); + u++; + + for (unsigned int i = 0; i < num_atomi; i++) { + distance = CaVector1[i].distance(CaVector2[i]); + ScalD = 1.0 / (1.0 + (pow((distance / 4.0), 2.0))); + dist_from_Ca_atoms[i].push_back(ScalD); + } + + CaVector1.clear(); + CaVector2.clear(); + + } + + int count; + double sum; + for (unsigned int i = 0; i < num_atomi; i++) { + count = 0; + sum = 0; + vector::iterator atom = dist_from_Ca_atoms[i].begin(); + while (atom != dist_from_Ca_atoms[i].end()) { + + sum = sum + (*atom); + + atom++; + count++; + } + dist_everage.push_back((sum / count)); + + } + + return dist_everage; + +} + +/** + * Get standard deviation from Scale Distance + * @return vector + */ +vector StandardDeviation::get_standard_deviation() { + + if (verbose) + cout << "### Start calculate standard deviation ###" << endl; + + dist_everage.clear(); + ScD.clear(); + + Spacer* primo_modello = new Spacer; + Spacer* secondo_modello = new Spacer; + + unsigned int num_atomi = 0; + double ScalD, distance = -1.0; + + if (models.size() != 0) + num_atomi = models[0].sizeAmino(); + else + ERROR("ProteinModels empty, remember execute TmImpose.", exception); + + vector > dist_from_Ca_atoms(num_atomi, vector(0.0)); + + if (verbose) { + cout << "Number of models: " << models.size() << endl; + cout << "Number of CA atoms in each models: " << num_atomi << endl; + } + //scorro i modelli e per ognuno creo il vettore di atomi + unsigned int u = 0; + + while (u < (models.size())) { + + primo_modello = &models[u]; + getCaAtom(primo_modello, true); + u++; + + secondo_modello = &models[u]; + getCaAtom(secondo_modello, false); + u++; + + for (unsigned int i = 0; i < num_atomi; i++) { + distance = CaVector1[i].distance(CaVector2[i]); + ScalD = 1.0 / (1.0 + (pow((distance / 4.0), 2.0))); + dist_from_Ca_atoms[i].push_back(ScalD); + } + + CaVector1.clear(); + CaVector2.clear(); + + } + + int count; + double sum; + for (unsigned int i = 0; i < num_atomi; i++) { + count = 0; + sum = 0; + vector::iterator atom = dist_from_Ca_atoms[i].begin(); + while (atom != dist_from_Ca_atoms[i].end()) { + + sum = sum + (*atom); + + atom++; + count++; + } + dist_everage.push_back((sum / count)); + + } + + double standDev = -1; + + vector::iterator everage = dist_everage.begin(); + + for (unsigned int i = 0; i < num_atomi; i++) { + sum = 0; + count = 0; + vector::iterator atom = dist_from_Ca_atoms[i].begin(); + + while (atom != dist_from_Ca_atoms[i].end()) { + sum += (pow(((*atom) - (*everage)), 2.0)); + atom++; + count++; + + } + + standDev = sqrt(sum / count); + + ScD.push_back(standDev); + + everage++; + + } + + return ScD; +} + +/** + * Get standard deviation from angle_PHI + * @return vector + */ +vector StandardDeviation::get_StandarDev_angle_PHI() { + + if (verbose) + cout << "### Start calculate standard deviation from angle PHI ###" << endl; + + double num_amino = 0; + double sum = 0; + + if (original_models.size() < 2) + ERROR("Number of models insufficient", exception) + else + num_amino = original_models[0].sizeAmino(); + + if (verbose) { + cout << "Number of models: " << original_models.size() << endl; + cout << "Number of amino in each models: " << num_amino << endl; + } + + + + angle_PHI.clear(); + vector > misure_PHI(num_amino, + vector(original_models.size())); + vector everage(num_amino); + +//calculate angle + for (unsigned int i = 0; i < original_models.size(); i++) + for (unsigned int j = 0; j < num_amino; j++) + misure_PHI[j][i] = original_models[i].getAmino(j).getPhi(); + +//calculate average angle + for (unsigned int j = 0; j < num_amino; j++) { + sum = 0; + + for (unsigned int i = 0; i < original_models.size(); i++) { + sum = sum + misure_PHI[j][i]; + } + + everage[j] = (sum / (original_models.size())); + + } + + //calculate stadDev + double standDev = -1; + + for (unsigned int j = 0; j < num_amino; j++) { + sum = 0; + for (unsigned int i = 0; i < original_models.size(); i++) { + + sum += (pow((misure_PHI[j][i] - everage[j]), 2.0)); + } + + standDev = sqrt(sum / original_models.size()); + angle_PHI.push_back(standDev); + } + + return angle_PHI; + +} + +/** + * Get standard deviation from angle_PSI + * @return vector + */ +vector StandardDeviation::get_StandarDev_angle_PSI() { + + if (verbose) + cout << "### Start calculate standard deviation from angle PSI ###" << endl; + + double num_amino = 0; + double sum = 0; + + if (original_models.size() < 2) + ERROR("Number of models insufficient", exception) + else + num_amino = original_models[0].sizeAmino(); + + if (verbose) { + cout << "Number of models: " << original_models.size() << endl; + cout << "Number of amino in each models: " << num_amino << endl; + } + + + angle_PSI.clear(); + vector > misure_PSI(num_amino, + vector(original_models.size())); + vector everage(num_amino); + +//calcolo angoli + for (unsigned int i = 0; i < original_models.size(); i++) + for (unsigned int j = 0; j < num_amino; j++) + misure_PSI[j][i] = original_models[i].getAmino(j).getPsi(); + +//calcolo media angoli + for (unsigned int j = 0; j < num_amino; j++) { + sum = 0; + + for (unsigned int i = 0; i < original_models.size(); i++) { + sum = sum + misure_PSI[j][i]; + } + + everage[j] = (sum / (original_models.size())); + + } + + //calcolo stadDev + double standDev = -1; + + for (unsigned int j = 0; j < num_amino; j++) { + sum = 0; + for (unsigned int i = 0; i < original_models.size(); i++) { + + sum += (pow((misure_PSI[j][i] - everage[j]), 2.0)); + } + + standDev = sqrt(sum / original_models.size()); + angle_PSI.push_back(standDev); + } + + return angle_PSI; + +} diff --git a/Mobi/Sources/StandardDeviation.h b/Mobi/Sources/StandardDeviation.h new file mode 100644 index 0000000..f39318b --- /dev/null +++ b/Mobi/Sources/StandardDeviation.h @@ -0,0 +1,71 @@ +/* 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 . + */ + +/** + * @file ScaleDistance.h + * @author Riccardo Zanella + * @date 11 lug 2015 + * @version 0.1 + */ + +#ifndef MOBI_SOURCES_STANDARDDEVIATION_H_ +#define MOBI_SOURCES_STANDARDDEVIATION_H_ + +#include +#include +#include +#include + +using namespace Victor::Biopool; + +namespace Victor { +namespace Mobi { + +class StandardDeviation { + + /** + * @brief Extends Protein class with functionalities related to manipulation of NMR model and models comparations. + * Scale Distance metric is provided. + */ + +public: + + // CONSTRUCTORS/DESTRUCTOR: + StandardDeviation(const ProteinModels& _orig, bool _verbose = false); + + virtual ~StandardDeviation(); + + vector get_everage_distance(); + vector get_standard_deviation(); + vector get_StandarDev_angle_PHI(); + vector get_StandarDev_angle_PSI(); + +private: + void getCaAtom(Spacer* s, bool flag); + +private: + bool verbose; + vector original_models; + vector models; + vector CaVector1, CaVector2; + vector > dist_from_Ca_atoms; + vector dist_everage; + vector ScD; + vector angle_PHI; + vector angle_PSI; + +}; +} +} + +#endif /* MOBI_SOURCES_STANDARDDEVIATION_H_ */ diff --git a/Mobi/Sources/TmScore.cc b/Mobi/Sources/TmScore.cc new file mode 100644 index 0000000..ed5875d --- /dev/null +++ b/Mobi/Sources/TmScore.cc @@ -0,0 +1,148 @@ +/* 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 . + */ + +/** + * @file TmScore.cc + * @author Riccardo Zanella + * @date Lug 2015 + * @version 0.1 + */ + +//Includes: +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace Victor::Mobi; +using namespace Victor::Biopool; +using namespace std; + +const string TMTMP_OUT = "TMScore.pdb"; + +/** + * @brief Default Constructor + * @param _binary (string) full path to binary TMScore file, must have execution permission + * @param _tmp (string) full path to temp dir, must have write permission + * @param _tmp bool verbose + */ +TmScore::TmScore(string _binary, string output, bool verbose) : + binary(_binary), outputTmScore(output + TMTMP_OUT), verbose(verbose) { +} + +//TmScore::TmScore(string _binary, string output, bool verbose) : +// binary(_binary), tmp(output.substr(output.length() - 1, 1) == "/" ? +// output : output + "/"), verbose(verbose) { +//} + +TmScore::~TmScore() { +} + +/** + * + * @param _binary (string) full path to binary TMScore file, must have execution permission + * @param _tmp string, path of model file, must have read permission + * @param _tmp string, path of native file, must have read permission + * @return (Protein*), return pointer to rototraslated protein + */ +Protein* TmScore::TmImpose(string modelFile, string nativeFile) { + + Protein* prot = NULL; + //if have read permission + if (access(modelFile.c_str(), R_OK) == 0 + && access(nativeFile.c_str(), R_OK) == 0) { + + //if binary have execute permission + if (access(binary.c_str(), X_OK) == 0) { + pid_t pid; + //Pipeing TMS output + int pipefd[2]; + pipe(pipefd); + //Forking child for TMS + pid = fork(); + if (pid < 0) { + ERROR("Unable to fork child process", error); + } else { + if (pid == 0) { + close(pipefd[0]); //close input pipe + if (dup2(pipefd[1], 1) < 0) + ERROR("Unable to redirect output TMScore", error);//stdout + if (dup2(pipefd[1], 2) < 0) + ERROR("Unable to redirect error output TMScore", error);//stderr + close(pipefd[1]); //close output pipe + if (execl(binary.c_str(), binary.c_str(), modelFile.c_str(), + nativeFile.c_str(), "-o", outputTmScore.c_str(), + NULL)) + ERROR("Unable to exec", error); + } else { + //Read output from child pipe + + ////////////////////////////////////////////////////////////////////////// + int status; + + wait(&status); + + remove(outputTmScore.c_str()); + + if (access((outputTmScore + "_atm").c_str(), R_OK) != 0) + ERROR("Cannot read pdb file to fix", exception); + + ifstream inFile((outputTmScore + "_atm").c_str()); + stringstream buffer; + string line; + + while (inFile) { + line = readLine(inFile); + if (line.substr(0, 16) == "REMARK TM-score") { + buffer << line << endl; + buffer << "MODEL 1" << endl; + + } else if (line.substr(0, 6) == "ATOM ") { + buffer << line << endl; + } else if (line.substr(0, 3) == "TER") { + buffer << line << endl; + buffer << "ENDMDL" << endl; + break; + } + } + + buffer.clear(); + + //Load from memory buffer + PdbLoader pl(buffer); + + pl.setNoVerbose(); + + pl.setModel(1); + pl.checkModel(); + + prot = new Protein(); + + pl.loadProtein(*prot); + + } + } + } else + ERROR("No access to " + binary + " binary!", exception); + } else + ERROR("No access to pdb files " + modelFile + " or " + nativeFile, + exception); + return prot; +} diff --git a/Mobi/Sources/TmScore.h b/Mobi/Sources/TmScore.h new file mode 100644 index 0000000..e3e0277 --- /dev/null +++ b/Mobi/Sources/TmScore.h @@ -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 . + */ +/** + * @file TmScore.h + * @author Riccardo Zanella + * @date Lug 2015 + * @version 0.1 + */ + +#ifndef MOBI_SOURCES_TMSCOREBIN_H_ +#define MOBI_SOURCES_TMSCOREBIN_H_ + +//Include: +#include +#include +#include + +using namespace Victor::Biopool; +using namespace Victor::Mobi; +using namespace std; + +extern const string TMTMP_OUT; + +namespace Victor { + +namespace Mobi { + +/** + * @brief TMScore functionalities through external binary. + */ + +class TmScore { + + // CONSTRUCTORS/DESTRUCTOR: +public: + + TmScore(string _binary = "TMScore", string output = ".", bool _verbose = + false); + + // PREDICATES: + Protein* TmImpose(string modelFile, string nativeFile); + + // MODIFIERS: + /** + You can chose if you want verbose output from this class + @param none + @return void + */ + void setVerbose(bool v) { + verbose = v; + } + /** + * Default deconstructor + */ + ~TmScore(); + +private: + string binary; + const string outputTmScore; + bool verbose; +}; +} +} +#endif /* MOBI_SOURCES_TMSCOREBIN_H_ */ diff --git a/Mobi/Tests/Makefile b/Mobi/Tests/Makefile new file mode 100644 index 0000000..52cf192 --- /dev/null +++ b/Mobi/Tests/Makefile @@ -0,0 +1,57 @@ +#--*- makefile -*-------------------------------------------------------------- +# +# Standard makefile +# +#------------------------------------------------------------------------------ + +# Path to project directory. +UPDIR = ../.. +# Path to subdirectories. +SUBDIR= +# Path to directory for binaries: +BINPATH = ../../bin + + +# +# Libraries and paths (which are not defined globally). +# + +LIBS = -lMobi -lBiopool -ltools -L/usr/lib/ -lm -ldl -lcppunit + +LIB_PATH = -L. + +INC_PATH = -I. -I../../tools/ -I../../Biopool/Sources -I../../Mobi/Sources + +# +# Objects and headers +# + +SOURCES = TestMobi.cc TestProteinModels.h TestStandardDeviation.h TestSaver.h + +OBJECTS = $(SOURCES:.cpp=.o) + +TARGETS = TestMobi + +EXECS = TestMobi + +LIBRARY = TESTlibMobi.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 \ No newline at end of file diff --git a/Mobi/Tests/TestMobi.cc b/Mobi/Tests/TestMobi.cc new file mode 100644 index 0000000..408bad7 --- /dev/null +++ b/Mobi/Tests/TestMobi.cc @@ -0,0 +1,46 @@ +/* + @file TestMobi.cc + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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::Mobi; +using namespace Victor::Biopool; +using namespace std; + +int main() { + CppUnit::TextUi::TestRunner runner; + + cout << "Creating Test Suites:" << endl; + runner.addTest(TestProteinModels::suite()); + runner.addTest(TestStandardDeviation::suite()); + runner.addTest(TestSecondaryStructure::suite()); + runner.addTest(TestSaver::suite()); + + cout << "Running the unit tests. " << endl; + runner.run(); + return 0; +} diff --git a/Mobi/Tests/TestProteinModels.h b/Mobi/Tests/TestProteinModels.h new file mode 100644 index 0000000..4b3ae74 --- /dev/null +++ b/Mobi/Tests/TestProteinModels.h @@ -0,0 +1,249 @@ +/* + @file TestProteinModels.h + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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 MOBI_TESTS_TESTPROTEINMODELS_H_ +#define MOBI_TESTS_TESTPROTEINMODELS_H_ + +#include +#include +#include +#include +#include +#include + +#include "ProteinModels.h" +#include + +using namespace std; +using namespace Victor::Mobi; + + +class TestProteinModels : public CppUnit::TestFixture { + +public: + TestProteinModels() {} + virtual ~TestProteinModels(){} + + + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite( + "TestProteinModels"); + + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test1 - Populate the ProteinModels", + &TestProteinModels::testPopulation)); + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test2 - Correct aminoacid sequence", + &TestProteinModels::aminoSequence)); + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test3 - Correct load protein rototralated", + &TestProteinModels::rototraslated)); + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test4 - Save protein models rototraslated", + &TestProteinModels::printModels)); + + return suiteOfTests; + } + + /** @brief Setup method. */ + void setUp() { + } + /** @brief Teardown method. */ + void tearDown() { + } + +protected: + /** @brief Test load */ + void testPopulation() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.load(pl); + + // -------------------------------------------------- + // 3. Test + // -------------------------------------------------- + cout << endl << "Models in pdb file is: " << pl.getMaxModels() << "\n" + << "Models load is" << test.original_models.size() << endl; + CPPUNIT_ASSERT(pl.getMaxModels() == test.original_models.size()); + + } + /** @brief Test aminoSequence */ + void aminoSequence() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned d = 0; + string aminoaced_sequence = + "GSGNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRGIHRD"; + string amino; + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels* test = new ProteinModels; + test->setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + pl.setModel(1); + pl.checkModel(); + test->Protein::load(pl); + + for (unsigned int i = 0; i < test->getSpacer(d)->sizeAmino(); i++) + amino += (test->getSpacer(d)->getAmino(i).getType1L()); + + // -------------------------------------------------- + // 3. Test + // -------------------------------------------------- + cout << endl << "Sequence in pdb file is: " << aminoaced_sequence + << "\n" << "Sequence load is" << amino << endl; + CPPUNIT_ASSERT(aminoaced_sequence == amino); + + } + /** @brief Test function of TmScore */ + void rototraslated() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned int d = 0; + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + + // -------------------------------------------------- + // 2. Save + // -------------------------------------------------- + + test.save(outputFile); + + // -------------------------------------------------- + // 2. Rototranslation + // -------------------------------------------------- + TmScore tm("../Mobi/data/TMscore", outputFile, true); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < test.size() - 1; i++) + for (unsigned int j = i + 1; j < test.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + test.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", exeption); + + test.addModels(*(test.getSpacer(j))); + + } + // -------------------------------------------------------- + // 2. Test save model vector that contain couple of models, + // the first rototranslate, the second is the model + // -------------------------------------------------------- + cout << endl << "Models load is: " << test.original_models.size() + << "\n" + << "Models load whit models rototranslated (all models imposed on all models) " + << test.models.size() << endl; + unsigned int test_model_size = (test.original_models.size() + * (test.original_models.size() - 1)); + CPPUNIT_ASSERT(test_model_size == test.models.size()); + + } + /** @brief Test function printmodels */ + void printModels() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned int d = 0; + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + // -------------------------------------------------- + // 2. Save + // -------------------------------------------------- + test.save(outputFile); + // -------------------------------------------------- + // 2. Rototraslation + // -------------------------------------------------- + TmScore tm("../Mobi/data/TMscore", outputFile, true); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < test.size() - 1; i++) + for (unsigned int j = i + 1; j < test.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + test.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", exeption); + + test.addModels(*(test.getSpacer(j))); + + } + // ------------------------------------------------------ + // 5. save model vector that contain couple of models, + // the first rototranslate, the second is the model + // ------------------------------------------------------ + + test.printModels(outputFile); + cout << endl << "File saved in folder data: " << endl; + + } + +}; + +#endif /* MOBI_TESTS_TESTPROTEINMODELS_H_ */ diff --git a/Mobi/Tests/TestSaver.h b/Mobi/Tests/TestSaver.h new file mode 100644 index 0000000..8b5324d --- /dev/null +++ b/Mobi/Tests/TestSaver.h @@ -0,0 +1,253 @@ +/* + @file TestSaver.h + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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 MOBI_TESTS_TESTSAVER_H_ +#define MOBI_TESTS_TESTSAVER_H_ + +#include +#include +#include +#include +#include +#include + +#include "ProteinModels.h" +#include "StandardDeviation.h" +#include "MobiSaver.h" + +using namespace std; +using namespace Victor::Mobi; + + +class TestSaver : public CppUnit::TestFixture { + +public: + TestSaver() {} + virtual ~TestSaver(){} + + + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite( + "TestSaver"); + + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test1 - Test mask average filtered with DSSP", + &TestSaver::testFilterDSSP)); + + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test2 - Test mask scaled distance filtered by logic mask", + &TestSaver::testFilterMask)); + return suiteOfTests; + } + + /** @brief Setup method. */ + void setUp() { + } + /** @brief Teardown method. */ + void tearDown() { + } + +protected: + /** @brief Test save mobility from average filtered by DSSP */ + void testFilterDSSP() { + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned int d = 0; + const string OUTPDB = "ResultMobi.pdb"; + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + string out_pdb = outputFile + OUTPDB; + ofstream ofstream(out_pdb.c_str(), ofstream::app); + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + // -------------------------------------------------- + // 3. Save + // -------------------------------------------------- + test.save(outputFile); + // -------------------------------------------------- + // 4. Rototraslation + // -------------------------------------------------- + TmScore tm("../Mobi/data/TMscore", outputFile, true); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < test.size() - 1; i++) + for (unsigned int j = i + 1; j < test.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + test.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", exeption); + + test.addModels(*(test.getSpacer(j))); + + } + + // -------------------------------------------------- + // 5. Calculate average + // -------------------------------------------------- + MobiSaver saver(test, outputFile, ofstream, true); + + StandardDeviation std(test, true); + vector ever; + ever = std.get_everage_distance(); + + // -------------------------------------------------- + // 6. save everage + // -------------------------------------------------- + saver.mob_eveScalD(ever); + + // -------------------------------------------------- + // 7. Calculate secondary structure + // -------------------------------------------------- + SecondaryStructure sstr(test, true); + + vector MOB; + MOB = sstr.getMobilitySecondaryStructure(); + + // -------------------------------------------------- + // 8. save secondary structure + // -------------------------------------------------- + + saver.mob_SecS(MOB); + + // -------------------------------------------------- + // 9. save mobility filtered + // -------------------------------------------------- + + saver.mob_eveScalD_filtSecS(ever, MOB); + + // -------------------------------------------------- + // 9. remove trash + // -------------------------------------------------- + + test.remove(outputFile); + remove(out_pdb.c_str()); + string trash = outputFile + "TMScore.pdb_atm"; + remove(trash.c_str()); + + } + + + /** @brief Test save mobility from standard deviation filtered whith logic mask */ + void testFilterMask() { + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned int d = 0; + const string OUTPDB = "ResultMobi.pdb"; + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + string out_pdb = outputFile + OUTPDB; + ofstream ofstream(out_pdb.c_str(), ofstream::app); + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + // -------------------------------------------------- + // 3. Save + // -------------------------------------------------- + test.save(outputFile); + // -------------------------------------------------- + // 4. Rototraslation + // -------------------------------------------------- + TmScore tm("../Mobi/data/TMscore", outputFile, true); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < test.size() - 1; i++) + for (unsigned int j = i + 1; j < test.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + test.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", exeption); + + test.addModels(*(test.getSpacer(j))); + + } + + // -------------------------------------------------- + // 5. Calculate average + // -------------------------------------------------- + MobiSaver saver(test, outputFile, ofstream, true); + + StandardDeviation std(test, true); + + vector SD; + SD = std.get_standard_deviation(); + + + // -------------------------------------------------- + // 6. save standard deviation + // -------------------------------------------------- + saver.mob_stanD(SD); + + // -------------------------------------------------- + // 7. save mobility filtered with logic mask + // 0 = fixed + // 1 = mobile + // + // 1011 » 1111 + // 1101 » 1111 + // 10011 » 11111 + // 11001 » 11111 + // 01010 » 00000 + // 00100 » 00000 + // 001100 » 000000 + // + // --------------------------------------------------- + + saver.mob_stanD_withMask(SD); + + // -------------------------------------------------- + // 9. remove trash + // -------------------------------------------------- + + test.remove(outputFile); + remove(out_pdb.c_str()); + string trash = outputFile + "TMScore.pdb_atm"; + remove(trash.c_str()); + + } + + + +}; + + + +#endif /* MOBI_TESTS_TESTSAVER_H_ */ diff --git a/Mobi/Tests/TestSecondaryStructure.h b/Mobi/Tests/TestSecondaryStructure.h new file mode 100644 index 0000000..e4e824b --- /dev/null +++ b/Mobi/Tests/TestSecondaryStructure.h @@ -0,0 +1,112 @@ +/* + @file TestSecondaryStructure.h + @author Riccardo Zanella, riccardozanella89@gmail.com + @version 1.0 + */ + +/* 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 MOBI_TESTS_TESTSECONDARYSTRUCTURE_H_ +#define MOBI_TESTS_TESTSECONDARYSTRUCTURE_H_ + + +#include +#include +#include +#include +#include +#include + +#include "ProteinModels.h" +#include "SecondaryStructure.h" + +using namespace std; +using namespace Victor::Mobi; + + +class TestSecondaryStructure : public CppUnit::TestFixture { + +public: + TestSecondaryStructure() {} + virtual ~TestSecondaryStructure(){} + + + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite( + "TestSecondaryStructure"); + + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test1 - Test Secondary Structure", + &TestSecondaryStructure::testStructure)); + + return suiteOfTests; + } + + /** @brief Setup method. */ + void setUp() { + } + /** @brief Teardown method. */ + void tearDown() { + } + +protected: + /** @brief Test Secondary Structure */ + void testStructure() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + + // -------------------------------------------------- + // 3. Secondary Structure + // -------------------------------------------------- + + SecondaryStructure sstr(test, true); + + vector< vector > sec_structures; + sec_structures = sstr.getSecStructFromModels(); + + vector MOB; + MOB = sstr.getMobilitySecondaryStructure(); + + + // ---------------------------------------------------- + // 4. Print vector o secondary structure for amino acid + // ---------------------------------------------------- + cout << "\nSECONDARY STRUCTURE" << endl; + for (unsigned int i=0; i<109 ; i++){ + cout << "Print secondary structure amino acid number #" << i << endl; + for (unsigned int j = 0; j < test.original_models.size(); j++) + cout << sec_structures[i][j] << endl; + + cout << "Final valutation of amino acid #" << i << " is " << MOB[i] <. + */ + + +#ifndef MOBI_TESTS_TESTSTANDARDDEVIATION_H_ +#define MOBI_TESTS_TESTSTANDARDDEVIATION_H_ + + +#include +#include +#include +#include +#include +#include + +#include "StandardDeviation.h" + +using namespace std; +using namespace Victor::Mobi; + + +class TestStandardDeviation : public CppUnit::TestFixture { + +public: + TestStandardDeviation() {} + virtual ~TestStandardDeviation(){} + + + static CppUnit::Test *suite() { + CppUnit::TestSuite *suiteOfTests = new CppUnit::TestSuite( + "TestProteinModels"); + + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test1 - test everage scaled distance", + &TestStandardDeviation::getEverage)); + + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test2 - test standard deviation", + &TestStandardDeviation::getSD)); + suiteOfTests->addTest( + new CppUnit::TestCaller( + "Test3 - test standard deviation angle PHI", + &TestStandardDeviation::getanglePHI)); + return suiteOfTests; + } + + /** @brief Setup method. */ + void setUp() { + } + /** @brief Teardown method. */ + void tearDown() { + } + +protected: + /** @brief Test for parse/write. */ + void getEverage() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned int d = 0; + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + + // -------------------------------------------------- + // 2. Save + // -------------------------------------------------- + + test.save(outputFile); + + // -------------------------------------------------- + // 2. Rototranslation + // -------------------------------------------------- + TmScore tm("../Mobi/data/TMscore", outputFile, true); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < test.size() - 1; i++) + for (unsigned int j = i + 1; j < test.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + test.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", exeption); + + test.addModels(*(test.getSpacer(j))); + + } + + // -------------------------------------------------- + // 3. everage scaled distance Test + // -------------------------------------------------- + + StandardDeviation st(test, true); + + vector everage = st.get_everage_distance(); + cout << endl << "Test first 5: " << everage[0] << " " << everage[1] + << " " << everage[2] << " " << everage[3] << " " << everage[4] + << " " << endl; + + } + + void getSD() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + unsigned int d = 0; + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + + // -------------------------------------------------- + // 2. Save + // -------------------------------------------------- + + test.save(outputFile); + + // -------------------------------------------------- + // 2. Rototranslation + // -------------------------------------------------- + TmScore tm("../Mobi/data/TMscore", outputFile, true); + + Protein* traslata = new Protein(); + + for (unsigned int i = 0; i < test.size() - 1; i++) + for (unsigned int j = i + 1; j < test.size(); j++) { + traslata = tm.TmImpose(outputFile + (itosDEF(i)), + outputFile + (itosDEF(j))); + if (traslata != NULL) { + + test.addModels(*(traslata->getSpacer(d))); + } else + ERROR("Error in the creation of shift models.", exeption); + + test.addModels(*(test.getSpacer(j))); + + } + // -------------------------------------------------- + // 3. StandardDeviation Test + // -------------------------------------------------- + StandardDeviation st(test, true); + + vector SD = st.get_standard_deviation(); + cout << endl << "Test first 5: " << SD[0] << " " << SD[1] << " " + << SD[2] << " " << SD[3] << " " << SD[4] << " " << endl; + + } + + void getanglePHI() { + + // -------------------------------------------------- + // 1. Initialization + // -------------------------------------------------- + + ifstream inputFile("/home/riccardo/mobi/1AB2_input.pdb"); + string outputFile = "../Mobi/data/stdout"; + PdbLoader pl(inputFile); + pl.setVerbose(); + ProteinModels test; + test.setVerbose(); + + // -------------------------------------------------- + // 2. Load + // -------------------------------------------------- + test.loadSameModels(pl); + + // -------------------------------------------------- + // 3. StandardDeviation Test + // -------------------------------------------------- + StandardDeviation st(test, true); + + vector SD = st.get_StandarDev_angle_PHI(); + cout << endl << "Test first 5: " << SD[0] << " " << SD[1] << " " + << SD[2] << " " << SD[3] << " " << SD[4] << " " << endl; + + } + +}; + +#endif /* MOBI_TESTS_TESTSTANDARDDEVIATION_H_ */ diff --git a/Mobi/data/TMscore b/Mobi/data/TMscore new file mode 100755 index 0000000..e77791c Binary files /dev/null and b/Mobi/data/TMscore differ diff --git a/Mobi/readme b/Mobi/readme new file mode 100644 index 0000000..ada832e --- /dev/null +++ b/Mobi/readme @@ -0,0 +1,40 @@ + + MOBI + + +Mobi software allows to load pdb file. Pdb file must be created with NMR technology. Mobi can calculate +amino acid's residue mobility inside protein. +The software can load the pdb file entirely (all models of protein), or just partly (only selected models). +The user can choose the chain to load, the default is first chain of pdb file. +Different metrics evaluate mobility part of the protein for example the everage scale distance, +standard deviation, scale distance, the evaluation of angle phi, psi, and various logic mask. + +Mobi is a Victor folder, inside are located subfolder APP which includes mobi.cc file that +includes main. +After compiling project the executable files are located in /Victor/bin/ with mobi's name. +For execute Mobi launch with no option or with option -h. +A help menu will appear showing how to use the program. +The output file will locate in directory /Victor/Mobi/data. +Remind that the output file must be deleted if you want rerun the program, +if this were not the case, the output file could be added in append to the file. + +==Usage== +Requirement: +Input: NMR pdb file. + +Execution: ./mobi pathpdbfile (options in addition) + +Option: + -o namefile for output to personalize the name of the output file, default is “stdout” + -v set verbosity of all object + -c set chain of protein to read (default is first chain) + -m to load a restricted numbers of models and not all present models in the file + -s modify value of mobility of average scaled distance + -d modify value of mobility of standard deviation of scaled distance + -y modify value of mobility of angle PHI + -x modify value of mobility of angle PSI + -h help + +Output: Output is two files, the first will be a fasta file with different mobility metrics, the second will be + a pdb file with save models and the last columns changed with standard deviation and average scaled + distance x 100. diff --git a/documentation.Doxyfile b/documentation.Doxyfile new file mode 100644 index 0000000..589cb5c --- /dev/null +++ b/documentation.Doxyfile @@ -0,0 +1,2303 @@ +# Doxyfile 1.8.6 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the config file +# that follow. The default is UTF-8 which is also the encoding used for all text +# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv +# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv +# for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = documentation Mobi + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify an logo or icon that is included in +# the documentation. The maximum height of the logo should not exceed 55 pixels +# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo +# to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a +# new page for each member. If set to NO, the documentation of a member will be +# part of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines. + +ALIASES = + +# This tag can be used to specify a number of word-keyword mappings (TCL only). +# A mapping has the form "name=value". For example adding "class=itcl::class" +# will allow you to use the command class in the itcl::class meaning. + +TCL_SUBST = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, Javascript, +# C#, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL. For instance to make +# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C +# (default is Fortran), use: inc=Fortran f=C. +# +# Note For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See http://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by by putting a % sign in front of the word +# or globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES, then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. When set to YES local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO these classes will be included in the various overviews. This option has +# no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# (class|struct|union) declarations. If set to NO these declarations will be +# included in the documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the +# todo list. This list is created by putting \todo commands in the +# documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the +# test list. This list is created by putting \test commands in the +# documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST = YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES the list +# will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. Do not use file names with spaces, bibtex cannot handle them. See +# also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error ( stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO doxygen will only warn about wrong or incomplete parameter +# documentation, but not about the absence of documentation. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. +# Note: If this tag is empty the current directory is searched. + +INPUT = . + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank the +# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, +# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, +# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, +# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, +# *.qsf, *.as and *.js. + +FILE_PATTERNS = + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER ) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# function all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES, then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see http://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user- +# defined cascading style sheet that is included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefor more robust against future updates. +# Doxygen will copy the style sheet file to the output directory. For an example +# see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the stylesheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to NO can help when comparing the output of multiple runs. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: http://developer.apple.com/tools/xcode/), introduced with +# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html +# for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler ( hhc.exe). If non-empty +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated ( +# YES) or that it should be included in the master .chm file ( NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated ( +# YES) or a normal table of contents ( NO) in the .chm file. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# http://www.mathjax.org) which uses client side Javascript for the rendering +# instead of using prerendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from http://www.mathjax.org before deployment. +# The default value is: http://cdn.mathjax.org/mathjax/latest. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /