From 7dca8ec55f5eadd01c7177b29a8e1ebf64d6e303 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Thu, 16 Feb 2023 10:38:19 +0100
Subject: [PATCH] feat: SCHWED-5783 report substructure matches
---
modules/mol/alg/pymod/ligand_scoring.py | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index d4b5c7bd7..fdc61c75f 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -434,6 +434,8 @@ class LigandScorer:
LogVerbose("No symmetry between %s and %s" % (
str(model_ligand), str(target_ligand)))
continue
+ substructure_match = len(symmetries[0][0]) != len(
+ model_ligand.atoms)
rmsd = SCRMSD(model_ligand, target_ligand,
transformation=binding_site.transform,
@@ -452,7 +454,8 @@ class LigandScorer:
"bs_num_res": len(binding_site.substructure.residues),
"bs_num_overlap_res": len(binding_site.ref_residues),
"target_ligand": target_ligand,
- "model_ligand": model_ligand
+ "model_ligand": model_ligand,
+ "substructure_match": substructure_match,
}
LogDebug("Saved RMSD")
@@ -512,7 +515,8 @@ class LigandScorer:
"bs_num_res": len(binding_site.substructure.residues),
"bs_num_overlap_res": len(binding_site.ref_residues),
"target_ligand": target_ligand,
- "model_ligand": model_ligand
+ "model_ligand": model_ligand,
+ "substructure_match": substructure_match,
}
LogDebug("Saved lDDT-PLI")
@@ -720,6 +724,10 @@ class LigandScorer:
* `model_ligand`: residue handle of the model ligand
* `chain_mapping`: local chain mapping as a dictionary, with target
chain name as key and model chain name as value.
+ * `substructure_match`: whether the score is the result of a partial
+ (substructure) match. A value of `True` indicates that the target
+ ligand covers only part of the model, while `False` indicates a
+ perfect match.
:rtype: :class:`dict`
"""
@@ -762,6 +770,10 @@ class LigandScorer:
* `model_ligand`: residue handle of the model ligand
* `chain_mapping`: local chain mapping as a dictionary, with target
chain name as key and model chain name as value.
+ * `substructure_match`: whether the score is the result of a partial
+ (substructure) match. A value of `True` indicates that the target
+ ligand covers only part of the model, while `False` indicates a
+ perfect match.
:rtype: :class:`dict`
"""
--
GitLab