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Commit 627f06c7 authored by Studer Gabriel's avatar Studer Gabriel
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scoring: add examples for compare-structures and compare-ligand-structures actions

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examples/scoring/README.md 0 → 100644
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Structure comparison examples
=============================
OpenStructure provides "actions" for general benchmarking use cases.
* compare-structures: Focuses on comparisons involving polymer entities, i.e.
protein, DNA and RNA chains
* compare-ligand-structures: Focuses on comparisons of interactions between
polymer entities and non-polymer entities, i.e. small molecule ligands
The example commands here assume an OpenStructure installation
(compile instructions: https://openstructure.org/docs/dev/install/). Detailed
instructions for running equivalent computations are available for
* Docker: https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker
* Singularity https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity
The command
```
ost <ACTION> -h
```
will list all available options of the respective action. Both actions compute
scores on an “opt-in” basis and produce output in JSON format. Example to compute
global and per-residue LDDT scores, as well as as QS-scores which are written to
default output (out.json):
```
ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score
```
By default, model-reference chains are aligned using Needleman-Wunsch.
Many benchmarking efforts such as CASP and CAMEO assume residue numbers
according to target sequence(s). Both "actions" allow to derive model-reference
chain alignments according to these numbers which should be preferred in these
cases. This can be enabled by adding a `-rna` (residue number alignment) flag:
```
ost compare-structures -m model.pdb -r reference.cif.gz --lddt --local-lddt --qs-score -rna
```
The same example also contains small molecule ligands which can be scored with:
```
ost compare-ligand-structures -m model.pdb -r reference.cif.gz -ml *.sdf --rmsd --lddt-pli
```
Again, it is advised to use the `-rna` flag if applicable. In this example,
reference ligands are directly extracted from the provided mmCIF file based on
"non-polymer" entity types.
This only works in case of mmCIF input AND if the respective ligand is in the
PDB component dictionary which defines connectivity (matching based on compound
name).
Container solutions come with such a dictionary which has been created at build
time. Check the Docker/Singularity instructions linked above on how to set the
latest dictionary, i.e. "Compound Library".
You can override automatic extraction by providing SDF files with ligand
coordinates and connectivity information. If the receptor is provided in
PDB format, ligands must be provided in SDF format.
examples/scoring/compare-ligand-structures_example_out.json 0 → 100644
+ 533
− 0
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{
"model_ligands": [
"model_ligand-1.sdf",
"model_ligand-2.sdf",
"model_ligand-3.sdf"
],
"reference_ligands": [
"C.1.",
"D.1.",
"E.1."
],
"lddt_pli": {
"assigned_scores": [
{
"score": 0.791304349899292,
"coverage": 1.0,
"lddt_pli_n_contacts": 1035,
"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.",
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"A.98.",
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"A.94.",
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"A.54.",
"A.60.",
"A.52.",
"A.91.",
"A.111.",
"A.45.",
"A.33.",
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"A.225.",
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"A.116.",
"A.100.",
"A.135.",
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"A.34.",
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"A.129.",
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"A.110.",
"A.109.",
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"A.50.",
"A.103.",
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"A.37.",
"A.49.",
"A.32.",
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"A.51.",
"A.88.",
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"A.157."
],
"bs_mdl_res": [
"B.54.",
"B.136.",
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"B.243.",
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"B.112.",
"B.133.",
"B.129.",
"B.58.",
"B.56.",
"B.99.",
"B.110.",
"B.242.",
"B.102."
]
},
{
"score": 0.0,
"coverage": 1.0,
"lddt_pli_n_contacts": 1338,
"model_ligand": "model_ligand-3.sdf",
"reference_ligand": "E.1.",
"bs_ref_res": [
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"B.103.",
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"B.66.",
"B.61.",
"B.92.",
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"B.153.",
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"B.65.",
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"B.97.",
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"B.95."
],
"bs_mdl_res": [
"B.70.",
"B.80.",
"B.77.",
"B.78.",
"B.79.",
"B.179.",
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"B.249.",
"B.252.",
"B.76.",
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"B.75.",
"B.253.",
"B.178.",
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"B.182.",
"B.255.",
"B.254."
]
}
],
"model_ligand_unassigned_reason": {
"model_ligand-2.sdf": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
},
"reference_ligand_unassigned_reason": {
"C.1.": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
}
},
"rmsd": {
"assigned_scores": [
{
"score": 1.3892921209335327,
"coverage": 1.0,
"lddt_lp": 0.9220483938256153,
"bb_rmsd": 0.6037176251411438,
"model_ligand": "model_ligand-1.sdf",
"reference_ligand": "D.1.",
"chain_mapping": {
"A": "B"
},
"bs_ref_res": [
"A.51.",
"A.54.",
"A.55.",
"A.57.",
"A.58.",
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],
"bs_ref_res_mapped": [
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],
"bs_mdl_res_mapped": [
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"B.59.",
"B.61.",
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"B.132.",
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"B.136.",
"B.232.",
"B.233.",
"B.244.",
"B.247."
],
"inconsistent_residues": [],
"transform": [
[
-0.3686985373497009,
0.3980128765106201,
0.8400280475616455,
7.079176902770996
],
[
-0.8913460969924927,
-0.40779373049736023,
-0.19800609350204468,
-3.9579238891601562
],
[
0.26374921202659607,
-0.8217602968215942,
0.5051202774047852,
6.306806564331055
],
[
0.0,
0.0,
0.0,
1.0
]
]
},
{
"score": 29.482725143432617,
"coverage": 1.0,
"lddt_lp": 0.9362713153035733,
"bb_rmsd": 0.3739512264728546,
"model_ligand": "model_ligand-3.sdf",
"reference_ligand": "E.1.",
"chain_mapping": {
"B": "B"
},
"bs_ref_res": [
"B.54.",
"B.55.",
"B.58.",
"B.59.",
"B.61.",
"B.62.",
"B.91.",
"B.92.",
"B.95.",
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"B.99.",
"B.102.",
"B.112.",
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"B.133.",
"B.136.",
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"B.247."
],
"bs_ref_res_mapped": [
"B.54.",
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"B.58.",
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],
"bs_mdl_res_mapped": [
"B.54.",
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"B.129.",
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"B.133.",
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"B.233.",
"B.247."
],
"inconsistent_residues": [],
"transform": [
[
-0.5568894743919373,
-0.6022372841835022,
-0.5720000267028809,
41.09874725341797
],
[
-0.7276356816291809,
0.021647661924362183,
0.6856220960617065,
-26.01633644104004
],
[
-0.4005247950553894,
0.7980234622955322,
-0.4502646327018738,
42.01909637451172
],
[
0.0,
0.0,
0.0,
1.0
]
]
}
],
"model_ligand_unassigned_reason": {
"model_ligand-2.sdf": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
},
"reference_ligand_unassigned_reason": {
"C.1.": [
"no_iso",
"No full isomorphic match could be found - enabling substructure_match might allow a match"
]
}
},
"model": "model.pdb",
"reference": "reference.cif.gz",
"model_cleanup_log": {
"cleaned_residues": {
"no_clib": [],
"not_linking": []
},
"cleaned_atoms": {
"unknown_atoms": []
}
},
"reference_cleanup_log": {
"cleaned_residues": {
"no_clib": [],
"not_linking": []
},
"cleaned_atoms": {
"unknown_atoms": []
}
},
"resnum_alignments": false,
"substructure_match": false,
"coverage_delta": 0.2,
"max_symmetries": 10000.0,
"ost_version": "2.9.2",
"status": "SUCCESS"
}
\ No newline at end of file
examples/scoring/compare-structures_example_out.json 0 → 100644
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− 0
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{
"reference_chains": [
"A",
"B",
"C"
],
"model_chains": [
"A",
"B"
],
"chem_groups": [
[
"A",
"B"
]
],
"chem_mapping": [
[
"A",
"B"
]
],
"chain_mapping": {
"A": "B",
"B": "A"
},
"aln": [
">reference:A\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTF--STLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSM-------LSDLLLEMLDAHRL\n>model:B\n----LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAHR-",
">reference:B\nLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY---------LEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS-----VVPLSDLLLEMLDA-\n>model:A\n-----TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKSKNVVPLSDLLLEMLDAH"
],
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},
"model_clashes": [],
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"model_bad_angles": [],
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"model_biounit": null,
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"residue_number_alignment": true,
"enforce_consistency": false,
"cad_exec": null,
"usalign_exec": null,
"lddt_no_stereochecks": false,
"min_pep_length": 6,
"min_nuc_length": 4,
"lddt_add_mdl_contacts": false,
"lddt_inclusion_radius": 15.0,
"dockq_capri_peptide": false,
"ost_version": "2.9.2",
"status": "SUCCESS"
}
\ No newline at end of file
examples/scoring/model.pdb 0 → 100644
+ 3802
− 0
View file @ 627f06c7
Source diff could not be displayed: it is too large. Options to address this: view the blob.
examples/scoring/model_ligand-1.sdf 0 → 100644
+ 155
− 0
View file @ 627f06c7
LIG
OST02122508393D
72 77 0 0 0 0 999 V2000
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M END
$$$$
examples/scoring/model_ligand-2.sdf 0 → 100644
+ 46
− 0
View file @ 627f06c7
LIG
OST02122508393D
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M END
$$$$
examples/scoring/model_ligand-3.sdf 0 → 100644
+ 159
− 0
View file @ 627f06c7
LIG
OST02122508393D
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7.2637 8.9337 4.3112 H 0 0 0 0 0 0
5.8310 9.9812 4.5996 H 0 0 0 0 0 0
9.2593 10.0963 0.7020 H 0 0 0 0 0 0
7.5901 10.6984 0.6283 H 0 0 0 0 0 0
11.5644 10.9154 -3.1665 H 0 0 0 0 0 0
12.2904 9.4681 -5.0020 H 0 0 0 0 0 0
9.4195 7.4518 -5.6881 H 0 0 0 0 0 0
8.4925 7.2944 -8.0127 H 0 0 0 0 0 0
8.9380 6.0000 -10.3050 H 0 0 0 0 0 0
12.2764 5.9204 -9.5225 H 0 0 0 0 0 0
14.0194 5.4783 -7.9522 H 0 0 0 0 0 0
14.1376 6.8351 -6.8072 H 0 0 0 0 0 0
12.8631 2.7941 -5.8536 H 0 0 0 0 0 0
13.3666 3.0018 -7.3018 H 0 0 0 0 0 0
14.8697 3.9460 -4.5573 H 0 0 0 0 0 0
15.7299 4.3582 -5.7843 H 0 0 0 0 0 0
1 2 2 0 0 0
2 3 1 0 0 0
2 9 1 0 0 0
3 4 2 0 0 0
3 8 1 0 0 0
4 5 1 0 0 0
4 39 1 0 0 0
5 6 2 0 0 0
5 40 1 0 0 0
6 7 1 0 0 0
6 41 1 0 0 0
7 8 2 0 0 0
7 42 1 0 0 0
8 43 1 0 0 0
9 10 1 0 0 0
9 36 1 0 0 0
10 11 1 0 0 0
10 28 1 0 0 0
10 44 1 0 0 0
11 12 2 0 0 0
11 27 1 0 0 0
12 13 1 0 0 0
12 45 1 0 0 0
13 14 2 0 0 0
13 46 1 0 0 0
14 15 1 0 0 0
14 26 1 0 0 0
15 16 1 0 0 0
16 17 1 0 0 0
16 47 1 0 0 0
16 48 1 0 0 0
17 18 1 0 0 0
17 25 1 0 0 0
17 49 1 0 0 0
18 19 1 0 0 0
18 50 1 0 0 0
18 51 1 0 0 0
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19 53 1 0 0 0
20 21 1 0 0 0
20 25 1 0 0 0
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21 22 1 0 0 0
21 55 1 0 0 0
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22 23 1 0 0 0
22 57 1 0 0 0
22 58 1 0 0 0
23 24 1 0 0 0
23 59 1 0 0 0
23 60 1 0 0 0
25 61 1 0 0 0
25 62 1 0 0 0
26 27 2 0 0 0
26 63 1 0 0 0
27 64 1 0 0 0
28 29 2 0 0 0
28 34 1 0 0 0
29 30 1 0 0 0
29 65 1 0 0 0
30 31 2 0 0 0
30 66 1 0 0 0
31 32 1 0 0 0
31 33 1 0 0 0
32 67 1 0 0 0
33 34 2 0 0 0
33 68 1 0 0 0
34 35 1 0 0 0
35 36 1 0 0 0
35 69 1 0 0 0
35 70 1 0 0 0
36 37 1 0 0 0
36 38 1 0 0 0
37 38 1 0 0 0
37 71 1 0 0 0
37 72 1 0 0 0
38 73 1 0 0 0
38 74 1 0 0 0
M END
$$$$
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