Merge pull request #62 from KULL-Centre/v0.2.1-testing

KULL-Centre · May 17, 2022 · 224ebc0 · 224ebc0
2 parents 8b38320 + aeefa50
commit 224ebc0
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diff --git a/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/ddG/input/parse_ddgs.sbatch b/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/ddG/input/parse_ddgs.sbatch
@@ -6,4 +6,4 @@
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3 /parser_ddg_v2.py homodimer-1afo_renum_uniquechain A VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKVQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKK /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True 55ed3262f36d5b9b70a2a62f59530c23f72722edtagv0.1.1-25-g55ed326 /prepare/cleaning True 1
+python3 /parser_ddg_v2.py homodimer-1afo_renum_uniquechain A VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKVQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKK /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...eline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/input/args.info b/...eline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/input/args.info
@@ -11,6 +11,8 @@
     "SLURM_PARTITION": "sbinlab",
     "GAPS_OUTPUT": false,
     "DUMP_PDB": 0,
+    "DO_CHECKING": true,
+    "NO_ZIP": false,
     "ZIP_FILES": true,
     "VERBOSE": false,
     "IS_MP": true,

diff --git a/...put/MPpipelineCreateGlpGTestCase_homodimer/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb b/...put/MPpipelineCreateGlpGTestCase_homodimer/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb
@@ -1,12 +1,4 @@
-HEADER                                            14-MAR-22   XXXX              
 EXPDTA    THEORETICAL MODEL                                                     
-REMARK 220                                                                      
-REMARK 220 EXPERIMENTAL DETAILS                                                 
-REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
-REMARK 220  DATE OF DATA COLLECTION        : 14-MAR-22                          
-REMARK 220                                                                      
-REMARK 220 REMARK: MODEL GENERATED BY ROSETTA                                   
-REMARK 220  VERSION 2021.31+HEAD.c7009b3115c                                    
 ATOM      1  N   VAL A   1       1.977 -20.146   7.910  1.00 50.00           N  
 ATOM      2  CA  VAL A   1       2.007 -18.799   8.547  1.00 50.00           C  
 ATOM      3  C   VAL A   1       2.086 -18.955  10.069  1.00 50.00           C  

diff --git a/.../mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/relax/input/parse_relax.sbatch b/.../mp-pipeline/output/MPpipelineCreateGlpGTestCase_homodimer/relax/input/parse_relax.sbatch
@@ -5,4 +5,4 @@
 #SBATCH --partition=sbinlab
 
 # launching parsing script 
-python /relax_parse_results.py True 1AFO_A /input /relax/run /relax/output /ddG/input relax_scores
+python /relax_parse_results.py True True 1AFO_A /relax/input /relax/run /relax/output /ddG/input relax_scores
diff --git a/...a/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/ddG/input/parse_ddgs.sbatch b/...a/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/ddG/input/parse_ddgs.sbatch
@@ -6,4 +6,4 @@
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True 55ed3262f36d5b9b70a2a62f59530c23f72722edtagv0.1.1-25-g55ed326 /prepare/cleaning True 1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/input/args.info b/...pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/input/args.info
@@ -11,6 +11,8 @@
     "SLURM_PARTITION": "sbinlab",
     "GAPS_OUTPUT": false,
     "DUMP_PDB": 0,
+    "DO_CHECKING": true,
+    "NO_ZIP": false,
     "ZIP_FILES": true,
     "VERBOSE": false,
     "IS_MP": true,

diff --git a/...output/MPpipelineCreateGlpGTestCase_mutdir/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb b/...output/MPpipelineCreateGlpGTestCase_mutdir/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb
@@ -1,12 +1,4 @@
-HEADER                                            14-MAR-22   XXXX              
 EXPDTA    THEORETICAL MODEL                                                     
-REMARK 220                                                                      
-REMARK 220 EXPERIMENTAL DETAILS                                                 
-REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
-REMARK 220  DATE OF DATA COLLECTION        : 14-MAR-22                          
-REMARK 220                                                                      
-REMARK 220 REMARK: MODEL GENERATED BY ROSETTA                                   
-REMARK 220  VERSION 2021.31+HEAD.c7009b3115c                                    
 ATOM      1  N   GLU A   1       1.307 -15.219 -19.353  1.00  0.00           N  
 ATOM      2  CA  GLU A   1       1.604 -14.601 -18.029  1.00  0.00           C  
 ATOM      3  C   GLU A   1       0.854 -13.279 -17.825  1.00  0.00           C  

diff --git a/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/relax/input/parse_relax.sbatch b/...est/mp-pipeline/output/MPpipelineCreateGlpGTestCase_mutdir/relax/input/parse_relax.sbatch
@@ -5,4 +5,4 @@
 #SBATCH --partition=sbinlab
 
 # launching parsing script 
-python /relax_parse_results.py True 6xro_A /input /relax/run /relax/output /ddG/input relax_scores
+python /relax_parse_results.py True True 6xro_A /relax/input /relax/run /relax/output /ddG/input relax_scores
diff --git a/...t/mp-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/ddG/input/parse_ddgs.sbatch b/...t/mp-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/ddG/input/parse_ddgs.sbatch
@@ -6,4 +6,4 @@
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True 55ed3262f36d5b9b70a2a62f59530c23f72722edtagv0.1.1-25-g55ed326 /prepare/cleaning True 1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/...ine/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/input/args.info b/...ine/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/input/args.info
@@ -11,6 +11,8 @@
     "SLURM_PARTITION": "sbinlab",
     "GAPS_OUTPUT": false,
     "DUMP_PDB": 0,
+    "DO_CHECKING": true,
+    "NO_ZIP": false,
     "ZIP_FILES": true,
     "VERBOSE": false,
     "IS_MP": true,

diff --git a/...t/MPpipelineCreateGlpGTestCase_pipemutfile/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb b/...t/MPpipelineCreateGlpGTestCase_pipemutfile/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb
@@ -1,9 +1,9 @@
-HEADER                                            14-MAR-22   XXXX              
+HEADER                                            16-MAY-22   XXXX              
 EXPDTA    THEORETICAL MODEL                                                     
 REMARK 220                                                                      
 REMARK 220 EXPERIMENTAL DETAILS                                                 
 REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
-REMARK 220  DATE OF DATA COLLECTION        : 14-MAR-22                          
+REMARK 220  DATE OF DATA COLLECTION        : 16-MAY-22                          
 REMARK 220                                                                      
 REMARK 220 REMARK: MODEL GENERATED BY ROSETTA                                   
 REMARK 220  VERSION 2021.31+HEAD.c7009b3115c                                    

diff --git a/...p-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/relax/input/parse_relax.sbatch b/...p-pipeline/output/MPpipelineCreateGlpGTestCase_pipemutfile/relax/input/parse_relax.sbatch
@@ -5,4 +5,4 @@
 #SBATCH --partition=sbinlab
 
 # launching parsing script 
-python /relax_parse_results.py True 6xro_A /input /relax/run /relax/output /ddG/input relax_scores
+python /relax_parse_results.py True True 6xro_A /relax/input /relax/run /relax/output /ddG/input relax_scores
diff --git a/...p-pipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/ddG/input/parse_ddgs.sbatch b/...p-pipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/ddG/input/parse_ddgs.sbatch
@@ -6,4 +6,4 @@
 #SBATCH --partition=sbinlab 
 
 #This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
-python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True 55ed3262f36d5b9b70a2a62f59530c23f72722edtagv0.1.1-25-g55ed326 /prepare/cleaning True 1
+python3 /parser_ddg_v2.py 6xro_final_renum A ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA /ddG/run /ddG/output /prepare/checking/structure_input.json /ddG/input /output /prepare/checking False True XXXtagvXXX /prepare/cleaning True 1
diff --git a/.../data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/input/args.info b/.../data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/input/args.info
@@ -11,6 +11,8 @@
     "SLURM_PARTITION": "sbinlab",
     "GAPS_OUTPUT": false,
     "DUMP_PDB": 0,
+    "DO_CHECKING": true,
+    "NO_ZIP": false,
     "ZIP_FILES": true,
     "VERBOSE": false,
     "IS_MP": true,

diff --git a/...PpipelineCreateGlpGTestCase_rosettamutfile/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb b/...PpipelineCreateGlpGTestCase_rosettamutfile/prepare/mp_files/mp_lipid_acc/input_A_0001.pdb
@@ -1,12 +1,4 @@
-HEADER                                            14-MAR-22   XXXX              
 EXPDTA    THEORETICAL MODEL                                                     
-REMARK 220                                                                      
-REMARK 220 EXPERIMENTAL DETAILS                                                 
-REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
-REMARK 220  DATE OF DATA COLLECTION        : 14-MAR-22                          
-REMARK 220                                                                      
-REMARK 220 REMARK: MODEL GENERATED BY ROSETTA                                   
-REMARK 220  VERSION 2021.31+HEAD.c7009b3115c                                    
 ATOM      1  N   GLU A   1       1.307 -15.219 -19.353  1.00  0.00           N  
 ATOM      2  CA  GLU A   1       1.604 -14.601 -18.029  1.00  0.00           C  
 ATOM      3  C   GLU A   1       0.854 -13.279 -17.825  1.00  0.00           C  

diff --git a/...ipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/relax/input/parse_relax.sbatch b/...ipeline/output/MPpipelineCreateGlpGTestCase_rosettamutfile/relax/input/parse_relax.sbatch
@@ -5,4 +5,4 @@
 #SBATCH --partition=sbinlab
 
 # launching parsing script 
-python /relax_parse_results.py True 6xro_A /input /relax/run /relax/output /ddG/input relax_scores
+python /relax_parse_results.py True True 6xro_A /relax/input /relax/run /relax/output /ddG/input relax_scores
diff --git a/...ata/test/mp-pipeline/output/MPpipelineFullrunGlpGTestCase_rosettamutfile/GlpG_cutoffs.txt b/...ata/test/mp-pipeline/output/MPpipelineFullrunGlpGTestCase_rosettamutfile/GlpG_cutoffs.txt
@@ -39,3 +39,13 @@ date,exp,corr,slope,intercept,count
 2022-03-15-09-41,ddG_sds_07_01,0.221,0.181,0.354,8
 2022-03-15-09-41,ddG_unf_08_01,-1.0,-3.943,3.269,2
 2022-03-15-09-41,all,0.158,0.529,4.074,161
+2022-05-17-07-18,ddG_unf_00_01,-0.257,-0.729,-3.998,6
+2022-05-17-07-18,ddG_unf_01_01,-0.952,-0.866,-3.001,3
+2022-05-17-07-18,ddG_kin_02_01,0.316,2.17,3.492,67
+2022-05-17-07-18,ddG_03_01,0.363,4.531,1.274,27
+2022-05-17-07-18,ddG_unf_04_01,0.63,3.028,-1.63,20
+2022-05-17-07-18,ddG_unf_05_01,0.764,5.419,-2.881,20
+2022-05-17-07-18,ddG_sds_06_01,0.132,0.115,-0.092,8
+2022-05-17-07-18,ddG_sds_07_01,0.222,0.169,-0.191,8
+2022-05-17-07-18,ddG_unf_08_01,-1.0,-3.763,3.396,2
+2022-05-17-07-18,all,0.156,0.515,3.873,161