Merge pull request OpenBioSim#235 from OpenBioSim/feature_atomcoordma…

…tcher Update makeCompatibleWith to use the new AtomCoordMatcher
fjclark · Jan 26, 2024 · dff31eb · dff31eb
2 parents 15e37d9 + 90b6e9d
commit dff31eb
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Showing 2 changed files with 6 additions and 20 deletions.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py
@@ -787,9 +787,8 @@ def makeCompatibleWith(
 
             # Have we matched all of the atoms?
             if len(matches) < num_atoms0:
-                # Atom names might have changed. Try to match by residue index
-                # and coordinates.
-                matcher = _SireMol.ResIdxAtomCoordMatcher()
+                # Atom names or order might have changed. Try to match by coordinates.
+                matcher = _SireMol.AtomCoordMatcher()
                 matches = matcher.match(mol0, mol1)
 
                 # We need to rename the atoms.
@@ -989,9 +988,6 @@ def makeCompatibleWith(
             # Tally counter for the total number of matches.
             num_matches = 0
 
-            # Initialise the offset.
-            offset = 0
-
             # Get the molecule numbers in the system.
             mol_nums = mol1.molNums()
 
@@ -1001,16 +997,13 @@ def makeCompatibleWith(
                 mol = mol1[num]
 
                 # Initialise the matcher.
-                matcher = _SireMol.ResIdxAtomCoordMatcher(_SireMol.ResIdx(offset))
+                matcher = _SireMol.AtomCoordMatcher()
 
                 # Get the matches for this molecule and append to the list.
                 match = matcher.match(mol0, mol)
                 matches.append(match)
                 num_matches += len(match)
 
-                # Increment the offset.
-                offset += mol.nResidues()
-
             # Have we matched all of the atoms?
             if num_matches < num_atoms0:
                 raise _IncompatibleError("Failed to match all atoms!")

diff --git a/python/BioSimSpace/_SireWrappers/_molecule.py b/python/BioSimSpace/_SireWrappers/_molecule.py
@@ -743,9 +743,8 @@ def makeCompatibleWith(
 
             # Have we matched all of the atoms?
             if len(matches) < num_atoms0:
-                # Atom names might have changed. Try to match by residue index
-                # and coordinates.
-                matcher = _SireMol.ResIdxAtomCoordMatcher()
+                # Atom names or order might have changed. Try to match by coordinates.
+                matcher = _SireMol.AtomCoordMatcher()
                 matches = matcher.match(mol0, mol1)
 
                 # We need to rename the atoms.
@@ -945,9 +944,6 @@ def makeCompatibleWith(
             # Tally counter for the total number of matches.
             num_matches = 0
 
-            # Initialise the offset.
-            offset = 0
-
             # Get the molecule numbers in the system.
             mol_nums = mol1.molNums()
 
@@ -957,16 +953,13 @@ def makeCompatibleWith(
                 mol = mol1[num]
 
                 # Initialise the matcher.
-                matcher = _SireMol.ResIdxAtomCoordMatcher(_SireMol.ResIdx(offset))
+                matcher = _SireMol.AtomCoordMatcher()
 
                 # Get the matches for this molecule and append to the list.
                 match = matcher.match(mol0, mol)
                 matches.append(match)
                 num_matches += len(match)
 
-                # Increment the offset.
-                offset += mol.nResidues()
-
             # Have we matched all of the atoms?
             if num_matches < num_atoms0:
                 raise _IncompatibleError("Failed to match all atoms!")