From 4fbae74e34705c881afdff3555493b57e573b942 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 28 Jun 2023 14:50:49 +0200
Subject: [PATCH] fix: only copy the view atoms if a ResidueView is given
---
modules/mol/alg/pymod/ligand_scoring.py | 28 +++++++++++++++----------
1 file changed, 17 insertions(+), 11 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 34308410a..8297772d5 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -372,8 +372,8 @@ class LigandScorer:
next_chain_num = 1
new_editor = None
- def _copy_residue(handle, rename_chain):
- """ Copy the residue handle into the new chain.
+ def _copy_residue(residue, rename_chain):
+ """ Copy the residue into the new chain.
Return the new residue handle."""
nonlocal next_chain_num, new_editor
@@ -381,17 +381,17 @@ class LigandScorer:
if new_editor is None:
new_editor = new_entity.EditXCS()
- new_chain = new_entity.FindChain(handle.chain.name)
+ new_chain = new_entity.FindChain(residue.chain.name)
if not new_chain.IsValid():
- new_chain = new_editor.InsertChain(handle.chain.name)
+ new_chain = new_editor.InsertChain(residue.chain.name)
else:
# Does a residue with the same name already exist?
- already_exists = new_chain.FindResidue(handle.number).IsValid()
+ already_exists = new_chain.FindResidue(residue.number).IsValid()
if already_exists:
if rename_chain:
chain_ext = 2 # Extend the chain name by this
while True:
- new_chain_name = handle.chain.name + "_" + str(chain_ext)
+ new_chain_name = residue.chain.name + "_" + str(chain_ext)
new_chain = new_entity.FindChain(new_chain_name)
if new_chain.IsValid():
chain_ext += 1
@@ -400,15 +400,21 @@ class LigandScorer:
new_chain = new_editor.InsertChain(new_chain_name)
break
LogScript("Moved ligand residue %s to new chain %s" % (
- handle.qualified_name, new_chain.name))
+ residue.qualified_name, new_chain.name))
else:
msg = "A residue number %s already exists in chain %s" % (
- handle.number, handle.chain.name)
+ residue.number, residue.chain.name)
raise RuntimeError(msg)
# Add the residue with its original residue number
- new_res = new_editor.AppendResidue(new_chain, handle, deep=True)
- for old_atom in handle.atoms:
+ new_res = new_editor.AppendResidue(new_chain, residue.name, residue.number)
+ # Add atoms
+ for old_atom in residue.atoms:
+ new_editor.InsertAtom(new_res, old_atom.name, old_atom.pos,
+ element=old_atom.element, occupancy=old_atom.occupancy,
+ b_factor=old_atom.b_factor, is_hetatm=old_atom.is_hetatom)
+ # Add bonds
+ for old_atom in residue.atoms:
for old_bond in old_atom.bonds:
new_first = new_res.FindAtom(old_bond.first.name)
new_second = new_res.FindAtom(old_bond.second.name)
@@ -427,7 +433,7 @@ class LigandScorer:
LogVerbose("Ligand residue %s already in entity" % res.handle.qualified_name)
else:
# Residue is not part of the entity, need to copy it first
- new_res = _copy_residue(res.handle, rename_chain)
+ new_res = _copy_residue(res, rename_chain)
LogVerbose("Copied ligand residue %s" % res.handle.qualified_name)
new_res.SetIsLigand(True)
return new_res
--
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