Acedrg atom name fixes (#123)

Author: stuartjamesmcnicholas

CHANGELOG.md

@@ -1,5 +1,9 @@
 # CCP4i2 Changelog
 
+## [2.5.1] - 2026-02-05
+
+- Fix to spaces/quoting in AceDRG atom name matching
+
 ## [2.5.0] - 2026-01-06
 
 - New task to check a model against AU contents

VERSION

@@ -1 +1 @@
-v2.5.0
+v2.5.1

core/version.params.xml

@@ -5,8 +5,8 @@
     <function>PARAMS</function>
     <pluginName>ccp4i2</pluginName>
     <userId></userId>
-    <creationTime>06/Jan/2026</creationTime>
-    <ccp4iVersion>2.5.0</ccp4iVersion>
+    <creationTime>05/Feb/2026</creationTime>
+    <ccp4iVersion>2.5.1</ccp4iVersion>
     <pluginVersion></pluginVersion>
   </ccp4i2_header>
 </ccp4i2>

wrappers/acedrgNew/script/atomMatching.py

@@ -1,18 +1,11 @@
-from __future__ import print_function
-
 import sys
 import os
 import argparse
-import re
 
 import ccp4mg
 import mmdb2
 import ccp4srs
 
-from rdkit import Chem
-from rdkit.Chem import AllChem
-import rdkit
-
 from gemmi import cif
 
 from .dictFileToMonomer import dictFileToMonomer
@@ -27,11 +20,15 @@ def changeDictionaryAtomNames(doc, changes):
                     col = block.find_values(tag)
                     for i, atomId in enumerate(col):
                         if atomId in changes:
-                            col[i] = cif.quote(changes[atomId])
+                            newId = changes[atomId]
+                            if "'" in newId or '"' in newId:
+                                col[i] = cif.quote(newId)
+                            else:
+                                col[i] = newId
 
 def replaceMatchesInDict(matches,theDict,outfile):
     #Gemmi returns the vaules in the cif document with no leading/trailing whitespace.
-    matches = {k.strip(): v for k, v in matches.items()}
+    matches = {k.strip(): v.strip() for k, v in matches.items()}
     try:
         doc = cif.read_file(theDict)
         changeDictionaryAtomNames(doc,matches)
@@ -369,10 +366,3 @@ def matchAtoms(ifname,ofname=None,dictMatchName=None,selection="",dictFileName=N
     dictFileName = args.f
     retMatches = matchAtoms(ifname,ofname,dictMatchName,selection,dictFileName)
     print(retMatches)
-
-"""
-mol = Chem.rdmolfiles.MolFromPDBFile(sys.argv[1],removeHs=False)
-print mol
-This is how we'd get to PDB file from RDKit.
-print Chem.rdmolfiles.MolToPDBBlock(mol)
-"""