From f6e39f35f150499fa13db5aaa2e99c9e9f814bb2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 28 Jun 2023 14:31:10 +0200
Subject: [PATCH] fix: residue may be invalid if an EntityView was given as
input
---
modules/mol/alg/pymod/ligand_scoring.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 895c0875a..34308410a 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -417,9 +417,13 @@ class LigandScorer:
def _process_ligand_residue(res, rename_chain):
"""Copy or fetch the residue. Return the residue handle."""
+ new_res = None
if res.entity.handle == old_entity.handle:
- # Residue is already in copied entity. We only need to grab it
+ # Residue is part of the old_entity handle.
+ # However it may not be in the copied one, for instance it may have been a view
+ # We try to grab it grab it first, othewise we copyp it
new_res = new_entity.FindResidue(res.chain.name, res.number)
+ if new_res and new_res.valid:
LogVerbose("Ligand residue %s already in entity" % res.handle.qualified_name)
else:
# Residue is not part of the entity, need to copy it first
--
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