diff --git a/examples/scoring/compare-ligand-structures_example_out.json b/examples/scoring/compare-ligand-structures_example_out.json
index 0553ba5a91f751692c59a5cefa24c9abe33f7a79..c2444d5b68f807e889610ab8a477556dc1e8dc52 100644
--- a/examples/scoring/compare-ligand-structures_example_out.json
+++ b/examples/scoring/compare-ligand-structures_example_out.json
@@ -18,34 +18,6 @@
"model_ligand": "model_ligand-1.sdf",
"reference_ligand": "D.1.",
"bs_ref_res": [
- "A.233.",
- "A.95.",
- "A.38.",
- "A.113.",
- "A.248.",
- "A.229.",
- "A.57.",
- "A.126.",
- "A.122.",
- "A.244.",
- "A.36.",
- "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.96.",
"A.116.",
@@ -60,10 +32,10 @@
"A.110.",
"A.109.",
"A.245.",
- "A.232.",
- "A.235.",
"A.119.",
"A.251.",
+ "A.232.",
+ "A.235.",
"A.153.",
"A.50.",
"A.103.",
@@ -72,8 +44,8 @@
"A.66.",
"A.92.",
"A.61.",
- "A.63.",
"A.55.",
+ "A.63.",
"A.131.",
"A.230.",
"A.247.",
@@ -105,7 +77,35 @@
"A.88.",
"A.114.",
"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": [
"B.54.",
@@ -128,8 +128,8 @@
"B.61.",
"B.118.",
"B.96.",
- "B.55.",
"B.229.",
+ "B.55.",
"B.59.",
"B.98.",
"B.51.",
@@ -152,6 +152,46 @@
"model_ligand": "model_ligand-3.sdf",
"reference_ligand": "E.1.",
"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.57.",
"B.98.",
@@ -188,8 +228,8 @@
"B.101.",
"B.114.",
"B.227.",
- "B.130.",
"B.233.",
+ "B.130.",
"B.50.",
"B.103.",
"B.113.",
@@ -200,47 +240,7 @@
"B.135.",
"B.66.",
"B.61.",
- "B.92.",
- "B.63.",
- "B.118.",
- "B.55.",
- "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.119.",
- "B.125.",
- "B.232.",
- "B.132.",
- "B.95."
+ "B.92."
],
"bs_mdl_res": [
"B.70.",
@@ -250,7 +250,6 @@
"B.79.",
"B.179.",
"B.74.",
- "B.249.",
"B.252.",
"B.76.",
"B.83.",
@@ -260,7 +259,8 @@
"B.175.",
"B.182.",
"B.255.",
- "B.254."
+ "B.254.",
+ "B.249."
]
}
],
@@ -504,8 +504,19 @@
]
}
},
- "model": "model.pdb",
- "reference": "reference.cif.gz",
+ "chem_groups": [
+ [
+ "A",
+ "B"
+ ]
+ ],
+ "chem_mapping": [
+ [
+ "A",
+ "B"
+ ]
+ ],
+ "mdl_chains_without_chem_mapping": [],
"model_cleanup_log": {
"cleaned_residues": {
"no_clib": [],
@@ -524,10 +535,27 @@
"unknown_atoms": []
}
},
- "resnum_alignments": false,
- "substructure_match": false,
- "coverage_delta": 0.2,
- "max_symmetries": 10000.0,
- "ost_version": "2.9.2",
+ "model": "model.pdb",
+ "reference": "reference.cif.gz",
+ "model-biounit": null,
+ "reference-biounit": null,
+ "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"
}
\ No newline at end of file
diff --git a/examples/scoring/compare-structures_example_out.json b/examples/scoring/compare-structures_example_out.json
index 716f9229571292e850993aa3027ab804b06b21c4..9746c579210655935b64a8551e008643f8643d38 100644
--- a/examples/scoring/compare-structures_example_out.json
+++ b/examples/scoring/compare-structures_example_out.json
@@ -1,8 +1,7 @@
{
"reference_chains": [
"A",
- "B",
- "C"
+ "B"
],
"model_chains": [
"A",
@@ -20,6 +19,7 @@
"B"
]
],
+ "mdl_chains_without_chem_mapping": [],
"chain_mapping": {
"A": "B",
"B": "A"
@@ -29,7 +29,7 @@
">reference:B\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY---------LEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS-----VVPLSDLLLEMLDA-\n>model:A\n-----TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAH"
],
"inconsistent_residues": [],
- "lddt": 0.874,
+ "lddt": 0.875,
"local_lddt": {
"A.19.": 0.797,
"A.20.": 0.868,
@@ -313,15 +313,15 @@
"B.60.": 0.928,
"B.61.": 0.968,
"B.62.": 0.936,
- "B.63.": 0.905,
- "B.64.": 0.945,
+ "B.63.": 0.915,
+ "B.64.": 0.947,
"B.65.": 0.961,
- "B.66.": 0.908,
- "B.67.": 0.895,
+ "B.66.": 0.915,
+ "B.67.": 0.915,
"B.68.": 0.964,
"B.69.": 0.942,
- "B.70.": 0.875,
- "B.71.": 0.773,
+ "B.70.": 0.887,
+ "B.71.": 0.777,
"B.72.": 0.909,
"B.73.": 0.884,
"B.74.": 0.854,
@@ -330,7 +330,7 @@
"B.77.": 0.8,
"B.78.": 0.812,
"B.79.": 0.81,
- "B.80.": 0.809,
+ "B.80.": 0.81,
"B.81.": 0.755,
"B.82.": 0.822,
"B.83.": 0.895,
@@ -497,16 +497,16 @@
"B.244.": 0.429,
"B.245.": 0.76,
"B.246.": 0.881,
- "B.247.": 0.885,
+ "B.247.": 0.887,
"B.248.": 0.889,
- "B.249.": 0.874,
- "B.250.": 0.792,
- "B.251.": 0.84,
- "B.252.": 0.819,
- "B.253.": 0.649,
- "B.254.": 0.581,
- "B.255.": 0.517,
- "B.256.": 0.34
+ "B.249.": 0.878,
+ "B.250.": 0.819,
+ "B.251.": 0.861,
+ "B.252.": 0.831,
+ "B.253.": 0.674,
+ "B.254.": 0.608,
+ "B.255.": 0.565,
+ "B.256.": 0.385
},
"model_clashes": [],
"model_bad_bonds": [],
@@ -557,6 +557,8 @@
"lddt_add_mdl_contacts": false,
"lddt_inclusion_radius": 15.0,
"dockq_capri_peptide": false,
- "ost_version": "2.9.2",
+ "seqres": null,
+ "trg_seqres_mapping": null,
+ "ost_version": "2.10.0",
"status": "SUCCESS"
}
\ No newline at end of file