From abb82d884d3520c332e522a2b39bc461392f7dc9 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 10 Mar 2023 13:35:10 +0100
Subject: [PATCH] refactor: SCHWED-5481 expose residues
This should clarify what the binding site.
---
actions/ost-compare-ligand-structures | 12 +++++++++
modules/mol/alg/pymod/ligand_scoring.py | 34 +++++++++++++++++--------
2 files changed, 36 insertions(+), 10 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 616821413..b04f1be17 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -354,6 +354,12 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
lddt_pli["transform"] = [transform_data[i:i + 4]
for i in range(0, len(transform_data),
4)]
+ lddt_pli["bs_ref_res"] = [r.qualified_name for r in
+ lddt_pli["bs_ref_res"]]
+ lddt_pli["bs_ref_res_mapped"] = [r.qualified_name for r in
+ lddt_pli["bs_ref_res_mapped"]]
+ lddt_pli["bs_mdl_res_mapped"] = [r.qualified_name for r in
+ lddt_pli["bs_mdl_res_mapped"]]
out["lddt_pli"][model_key] = lddt_pli
if args.rmsd:
@@ -367,6 +373,12 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
transform_data = rmsd["transform"].data
rmsd["transform"] = [transform_data[i:i + 4]
for i in range(0, len(transform_data), 4)]
+ rmsd["bs_ref_res"] = [r.qualified_name for r in
+ rmsd["bs_ref_res"]]
+ rmsd["bs_ref_res_mapped"] = [r.qualified_name for r in
+ rmsd["bs_ref_res_mapped"]]
+ rmsd["bs_mdl_res_mapped"] = [r.qualified_name for r in
+ rmsd["bs_mdl_res_mapped"]]
out["rmsd"][model_key] = rmsd
return out
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 330b13683..ac7dc060d 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -479,8 +479,9 @@ class LigandScorer:
rmsd_full_matrix[target_i, model_i] = {
"rmsd": rmsd,
"lddt_bs": binding_site.lDDT,
- "bs_num_res": len(binding_site.substructure.residues),
- "bs_num_overlap_res": len(binding_site.ref_residues),
+ "bs_ref_res": binding_site.substructure.residues,
+ "bs_ref_res_mapped": binding_site.ref_residues,
+ "bs_mdl_res_mapped": binding_site.mdl_residues,
"bb_rmsd": binding_site.bb_rmsd,
"target_ligand": target_ligand,
"model_ligand": model_ligand,
@@ -538,8 +539,9 @@ class LigandScorer:
"rmsd": rmsd,
"lddt_bs": binding_site.lDDT,
"lddt_pli_n_contacts": lddt_tot,
- "bs_num_res": len(binding_site.substructure.residues),
- "bs_num_overlap_res": len(binding_site.ref_residues),
+ "bs_ref_res": binding_site.substructure.residues,
+ "bs_ref_res_mapped": binding_site.ref_residues,
+ "bs_mdl_res_mapped": binding_site.mdl_residues,
"bb_rmsd": binding_site.bb_rmsd,
"target_ligand": target_ligand,
"model_ligand": model_ligand,
@@ -744,9 +746,15 @@ class LigandScorer:
* `rmsd`: the RMSD score value.
* `lddt_bs`: the lDDT-BS score of the binding site.
- * `bs_num_res`: number of residues in the target binding site.
- * `bs_num_overlap_res`: number of residues in the model overlapping
- with the target binding site.
+ * `bs_ref_res`: a list of residues (:class:`~ost.mol.ResidueHandle`)
+ that define the binding site in the reference.
+ * `bs_ref_res_mapped`: a list of residues
+ (:class:`~ost.mol.ResidueHandle`) in the reference binding site
+ that could be mapped to the model.
+ * `bs_mdl_res_mapped`: a list of residues
+ (:class:`~ost.mol.ResidueHandle`) in the model that were mapped to
+ the reference binding site. The residues are in the same order as
+ `bs_ref_res_mapped`.
* `bb_rmsd`: the RMSD of the binding site backbone after superposition
* `target_ligand`: residue handle of the target ligand.
* `model_ligand`: residue handle of the model ligand.
@@ -791,9 +799,15 @@ class LigandScorer:
* `lddt_pli_n_contacts`: number of total contacts used in lDDT-PLI,
summed over all thresholds. Can be divided by 8 to obtain the number
of atomic contacts.
- * `bs_num_res`: number of residues in the target binding site.
- * `bs_num_overlap_res`: number of residues in the model overlapping
- with the target binding site.
+ * `bs_ref_res`: a list of residues (:class:`~ost.mol.ResidueHandle`)
+ that define the binding site in the reference.
+ * `bs_ref_res_mapped`: a list of residues
+ (:class:`~ost.mol.ResidueHandle`) in the reference binding site
+ that could be mapped to the model.
+ * `bs_mdl_res_mapped`: a list of residues
+ (:class:`~ost.mol.ResidueHandle`) in the model that were mapped to
+ the reference binding site. The residues are in the same order as
+ `bs_ref_res_mapped`.
* `bb_rmsd`: the RMSD of the binding site backbone after superposition.
Note: not used for lDDT-PLI computation.
* `target_ligand`: residue handle of the target ligand.
--
GitLab