From de75ff1d95c7b76b4c1e6e186a3be2d7f0985f69 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 8 Dec 2023 17:05:40 +0100
Subject: [PATCH] fix: SCHWED-6070 cleanup Deuteriums too
---
actions/ost-compare-ligand-structures | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 17a16f229..e892b8633 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -23,8 +23,9 @@ structures in PDB format.
Polymer/oligomeric ligands (saccharides, peptides, nucleotides) are not
supported.
-Only minimal cleanup steps are performed (remove hydrogens, and for structures
-of polymers only, remove unknown atoms and cleanup element column).
+Only minimal cleanup steps are performed (remove hydrogens and deuteriums,
+and for structures of polymers only, remove unknown atoms and cleanup element
+column).
Ligands in mmCIF and PDB files must comply with the PDB component dictionary
definition, and have properly named residues and atoms, in order for
@@ -299,8 +300,8 @@ def _LoadStructure(structure_path, format="auto", fault_tolerant=False):
f"file {structure_path}.")
# Remove hydrogens
- cleaned_entity = ost.mol.CreateEntityFromView(entity.Select("ele != H"),
- include_exlusive_atoms=False)
+ cleaned_entity = ost.mol.CreateEntityFromView(entity.Select(
+ "ele != H and ele != D"), include_exlusive_atoms=False)
cleaned_entity.SetName(structure_path)
return cleaned_entity
--
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