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Commit 722d60ec authored by Studer Gabriel's avatar Studer Gabriel
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Merge branch 'master' into develop

parents 08225362 831d7bfe
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examples/scoring/compare-ligand-structures_example_out.json
+ 112
− 84
View file @ 722d60ec
...@@ -18,34 +18,6 @@ ...@@ -18,34 +18,6 @@
"model_ligand": "model_ligand-1.sdf", "model_ligand": "model_ligand-1.sdf",
"reference_ligand": "D.1.", "reference_ligand": "D.1.",
"bs_ref_res": [ "bs_ref_res": [
"A.233.",
"A.95.",
"A.38.",
"A.113.",
"A.248.",
"A.229.",
"A.57.",
"A.126.",
"A.122.",
"A.244.",
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"A.137.",
"A.118.",
"A.98.",
"A.127.",
"A.94.",
"A.133.",
"A.226.",
"A.246.",
"A.54.",
"A.60.",
"A.52.",
"A.91.",
"A.111.",
"A.45.",
"A.33.",
"A.228.",
"A.132.",
"A.225.", "A.225.",
"A.96.", "A.96.",
"A.116.", "A.116.",
...@@ -60,10 +32,10 @@ ...@@ -60,10 +32,10 @@
"A.110.", "A.110.",
"A.109.", "A.109.",
"A.245.", "A.245.",
"A.232.",
"A.235.",
"A.119.", "A.119.",
"A.251.", "A.251.",
"A.232.",
"A.235.",
"A.153.", "A.153.",
"A.50.", "A.50.",
"A.103.", "A.103.",
...@@ -72,8 +44,8 @@ ...@@ -72,8 +44,8 @@
"A.66.", "A.66.",
"A.92.", "A.92.",
"A.61.", "A.61.",
"A.63.",
"A.55.", "A.55.",
"A.63.",
"A.131.", "A.131.",
"A.230.", "A.230.",
"A.247.", "A.247.",
...@@ -105,7 +77,35 @@ ...@@ -105,7 +77,35 @@
"A.88.", "A.88.",
"A.114.", "A.114.",
"A.227.", "A.227.",
"A.157." "A.157.",
"A.233.",
"A.95.",
"A.38.",
"A.113.",
"A.248.",
"A.229.",
"A.57.",
"A.126.",
"A.122.",
"A.244.",
"A.118.",
"A.98.",
"A.127.",
"A.36.",
"A.137.",
"A.94.",
"A.133.",
"A.226.",
"A.246.",
"A.54.",
"A.60.",
"A.52.",
"A.91.",
"A.111.",
"A.45.",
"A.33.",
"A.228.",
"A.132."
], ],
"bs_mdl_res": [ "bs_mdl_res": [
"B.54.", "B.54.",
...@@ -128,8 +128,8 @@ ...@@ -128,8 +128,8 @@
"B.61.", "B.61.",
"B.118.", "B.118.",
"B.96.", "B.96.",
"B.55.",
"B.229.", "B.229.",
"B.55.",
"B.59.", "B.59.",
"B.98.", "B.98.",
"B.51.", "B.51.",
...@@ -152,6 +152,46 @@ ...@@ -152,6 +152,46 @@
"model_ligand": "model_ligand-3.sdf", "model_ligand": "model_ligand-3.sdf",
"reference_ligand": "E.1.", "reference_ligand": "E.1.",
"bs_ref_res": [ "bs_ref_res": [
"B.118.",
"B.55.",
"B.63.",
"B.56.",
"B.64.",
"B.153.",
"B.99.",
"B.102.",
"B.226.",
"B.65.",
"B.134.",
"B.109.",
"B.251.",
"B.97.",
"B.35.",
"B.126.",
"B.62.",
"B.37.",
"B.245.",
"B.49.",
"B.32.",
"B.111.",
"B.127.",
"B.129.",
"B.228.",
"B.116.",
"B.53.",
"B.225.",
"B.59.",
"B.124.",
"B.51.",
"B.247.",
"B.47.",
"B.136.",
"B.88.",
"B.125.",
"B.119.",
"B.132.",
"B.232.",
"B.95.",
"B.250.", "B.250.",
"B.57.", "B.57.",
"B.98.", "B.98.",
...@@ -188,8 +228,8 @@ ...@@ -188,8 +228,8 @@
"B.101.", "B.101.",
"B.114.", "B.114.",
"B.227.", "B.227.",
"B.130.",
"B.233.", "B.233.",
"B.130.",
"B.50.", "B.50.",
"B.103.", "B.103.",
"B.113.", "B.113.",
...@@ -200,47 +240,7 @@ ...@@ -200,47 +240,7 @@
"B.135.", "B.135.",
"B.66.", "B.66.",
"B.61.", "B.61.",
"B.92.", "B.92."
"B.63.",
"B.118.",
"B.55.",
"B.56.",
"B.64.",
"B.153.",
"B.99.",
"B.102.",
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"B.134.",
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"B.97.",
"B.35.",
"B.126.",
"B.62.",
"B.37.",
"B.245.",
"B.49.",
"B.32.",
"B.111.",
"B.127.",
"B.129.",
"B.228.",
"B.116.",
"B.53.",
"B.225.",
"B.59.",
"B.124.",
"B.51.",
"B.247.",
"B.47.",
"B.136.",
"B.88.",
"B.119.",
"B.125.",
"B.232.",
"B.132.",
"B.95."
], ],
"bs_mdl_res": [ "bs_mdl_res": [
"B.70.", "B.70.",
...@@ -250,7 +250,6 @@ ...@@ -250,7 +250,6 @@
"B.79.", "B.79.",
"B.179.", "B.179.",
"B.74.", "B.74.",
"B.249.",
"B.252.", "B.252.",
"B.76.", "B.76.",
"B.83.", "B.83.",
...@@ -260,7 +259,8 @@ ...@@ -260,7 +259,8 @@
"B.175.", "B.175.",
"B.182.", "B.182.",
"B.255.", "B.255.",
"B.254." "B.254.",
"B.249."
] ]
} }
], ],
...@@ -504,8 +504,19 @@ ...@@ -504,8 +504,19 @@
] ]
} }
}, },
"model": "model.pdb", "chem_groups": [
"reference": "reference.cif.gz", [
"A",
"B"
]
],
"chem_mapping": [
[
"A",
"B"
]
],
"mdl_chains_without_chem_mapping": [],
"model_cleanup_log": { "model_cleanup_log": {
"cleaned_residues": { "cleaned_residues": {
"no_clib": [], "no_clib": [],
...@@ -524,10 +535,27 @@ ...@@ -524,10 +535,27 @@
"unknown_atoms": [] "unknown_atoms": []
} }
}, },
"resnum_alignments": false, "model": "model.pdb",
"substructure_match": false, "reference": "reference.cif.gz",
"coverage_delta": 0.2, "model-biounit": null,
"max_symmetries": 10000.0, "reference-biounit": null,
"ost_version": "2.9.2", "fault-tolerant": false,
"residue-number-alignment": true,
"substructure-match": false,
"coverage-delta": 0.2,
"max-symmetries": 10000.0,
"min-pep-length": 6,
"min-nuc-length": 4,
"chem-group-seqid-thresh": 95.0,
"chem-map-seqid-thresh": 70.0,
"seqres": null,
"trg_seqres_mapping": null,
"allow_heuristic_conn": false,
"lddt-pli-radius": 6.0,
"lddt-pli-add-mdl-contacts": true,
"radius": 4.0,
"lddt-lp-radius": 15.0,
"full-bs-search": false,
"ost_version": "2.10.0",
"status": "SUCCESS" "status": "SUCCESS"
} }
\ No newline at end of file
examples/scoring/compare-structures_example_out.json
+ 22
− 20
View file @ 722d60ec
{ {
"reference_chains": [ "reference_chains": [
"A", "A",
"B", "B"
"C"
], ],
"model_chains": [ "model_chains": [
"A", "A",
...@@ -20,6 +19,7 @@ ...@@ -20,6 +19,7 @@
"B" "B"
] ]
], ],
"mdl_chains_without_chem_mapping": [],
"chain_mapping": { "chain_mapping": {
"A": "B", "A": "B",
"B": "A" "B": "A"
...@@ -29,7 +29,7 @@ ...@@ -29,7 +29,7 @@
">reference:B\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY---------LEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS-----VVPLSDLLLEMLDA-\n>model:A\n-----TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAH" ">reference:B\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY---------LEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS-----VVPLSDLLLEMLDA-\n>model:A\n-----TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAH"
], ],
"inconsistent_residues": [], "inconsistent_residues": [],
"lddt": 0.874, "lddt": 0.875,
"local_lddt": { "local_lddt": {
"A.19.": 0.797, "A.19.": 0.797,
"A.20.": 0.868, "A.20.": 0.868,
...@@ -313,15 +313,15 @@ ...@@ -313,15 +313,15 @@
"B.60.": 0.928, "B.60.": 0.928,
"B.61.": 0.968, "B.61.": 0.968,
"B.62.": 0.936, "B.62.": 0.936,
"B.63.": 0.905, "B.63.": 0.915,
"B.64.": 0.945, "B.64.": 0.947,
"B.65.": 0.961, "B.65.": 0.961,
"B.66.": 0.908, "B.66.": 0.915,
"B.67.": 0.895, "B.67.": 0.915,
"B.68.": 0.964, "B.68.": 0.964,
"B.69.": 0.942, "B.69.": 0.942,
"B.70.": 0.875, "B.70.": 0.887,
"B.71.": 0.773, "B.71.": 0.777,
"B.72.": 0.909, "B.72.": 0.909,
"B.73.": 0.884, "B.73.": 0.884,
"B.74.": 0.854, "B.74.": 0.854,
...@@ -330,7 +330,7 @@ ...@@ -330,7 +330,7 @@
"B.77.": 0.8, "B.77.": 0.8,
"B.78.": 0.812, "B.78.": 0.812,
"B.79.": 0.81, "B.79.": 0.81,
"B.80.": 0.809, "B.80.": 0.81,
"B.81.": 0.755, "B.81.": 0.755,
"B.82.": 0.822, "B.82.": 0.822,
"B.83.": 0.895, "B.83.": 0.895,
...@@ -497,16 +497,16 @@ ...@@ -497,16 +497,16 @@
"B.244.": 0.429, "B.244.": 0.429,
"B.245.": 0.76, "B.245.": 0.76,
"B.246.": 0.881, "B.246.": 0.881,
"B.247.": 0.885, "B.247.": 0.887,
"B.248.": 0.889, "B.248.": 0.889,
"B.249.": 0.874, "B.249.": 0.878,
"B.250.": 0.792, "B.250.": 0.819,
"B.251.": 0.84, "B.251.": 0.861,
"B.252.": 0.819, "B.252.": 0.831,
"B.253.": 0.649, "B.253.": 0.674,
"B.254.": 0.581, "B.254.": 0.608,
"B.255.": 0.517, "B.255.": 0.565,
"B.256.": 0.34 "B.256.": 0.385
}, },
"model_clashes": [], "model_clashes": [],
"model_bad_bonds": [], "model_bad_bonds": [],
...@@ -557,6 +557,8 @@ ...@@ -557,6 +557,8 @@
"lddt_add_mdl_contacts": false, "lddt_add_mdl_contacts": false,
"lddt_inclusion_radius": 15.0, "lddt_inclusion_radius": 15.0,
"dockq_capri_peptide": false, "dockq_capri_peptide": false,
"ost_version": "2.9.2", "seqres": null,
"trg_seqres_mapping": null,
"ost_version": "2.10.0",
"status": "SUCCESS" "status": "SUCCESS"
} }
\ No newline at end of file
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