From ce48c704cf34c0ed45da04ec468bfc23c1ae6f9e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 13 Sep 2022 14:46:38 +0200
Subject: [PATCH] lDDT: filter out hydrogens/deuterium in CustomCompound
---
modules/mol/alg/pymod/lddt.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index f905cf416..77ce6690d 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -22,14 +22,15 @@ class CustomCompound:
def FromResidue(res):
""" Construct custom compound from residue
- :param res: Residue from which reference atom names are extracted
+ :param res: Residue from which reference atom names are extracted,
+ hydrogen/deuterium atoms are filtered out
:type res: :class:`ost.mol.ResidueView`/:class:`ost.mol.ResidueHandle`
:returns: :class:`CustomCompound`
"""
- atom_names = [a.GetName() for a in res.atoms]
- if len(atom_names) != len(set(atom_names)):
+ at_names = [a.name for a in res.atoms if a.element not in ["H", "D"]]
+ if len(at_names) != len(set(at_names)):
raise RuntimeError("Duplicate atoms detected in CustomCompound")
- compound = CustomCompound(atom_names)
+ compound = CustomCompound(at_names)
return compound
class SymmetrySettings:
--
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