From 391c267f27870b23464b567777a8f0ecc6f19358 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Tue, 23 Apr 2024 16:29:54 +0200
Subject: [PATCH] doc: reflect changes to model_representation with new
full_bs_search=False
---
modules/mol/alg/pymod/ligand_scoring.py | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index c630598ae..009b72a39 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -1384,9 +1384,9 @@ class LigandScorer:
* `disconnected`: the ligand graph was disconnected.
* `binding_site`: no residues were in proximity of the ligand.
* `model_representation`: no representation of the reference binding
- site was found in the model. (I.e. the binding site was not modeled.
- Remember: the binding site is defined in the target structure,
- the position of the model ligand itself is ignored at this point.)
+ site was found in the model. (I.e. the binding site was not modeled,
+ or the model ligand was positioned too far in combination with
+ `full_bs_search=False`)
* `identity`: the ligand was not found in the model (by graph
isomorphism). Check your ligand connectivity, and enable the
`substructure_match` option if the target ligand is incomplete.
@@ -1449,9 +1449,8 @@ class LigandScorer:
target.
* `model_representation`: a potential assignment was found in the target,
but no representation of the binding site was found in the model.
- (I.e. the binding site was not modeled. Remember: the binding site
- is defined in the target structure, the position of the model ligand
- itself is ignored at this point.)
+ (I.e. the binding site was not modeled, or the model ligand was
+ positioned too far in combination with `full_bs_search=False`)
* `identity`: the ligand was not found in the target (by graph
isomorphism). Check your ligand connectivity, and enable the
`substructure_match` option if the target ligand is incomplete.
--
GitLab