Refactored code to support both old/new versions of OpenMM

pdbfixer/pdbfixer.py

@@ -35,11 +35,19 @@ __version__ = "1.5"
 import simtk.openmm as mm
 import simtk.openmm as mm
 import simtk.openmm.app as app
 import simtk.openmm.app as app
 import simtk.unit as unit
 import simtk.unit as unit
-from simtk.openmm.app.internal import compiled
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
 from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
 from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
 from simtk.openmm.app.element import hydrogen, oxygen
 from simtk.openmm.app.element import hydrogen, oxygen
 from simtk.openmm.app.forcefield import NonbondedGenerator
 from simtk.openmm.app.forcefield import NonbondedGenerator
+
+# Support Cythonized functions in OpenMM 7.3
+# and also implementations in older versions.
+try:
+    from simtk.openmm.app.internal import compiled
+    matchResidue = compiled.matchResidueToTemplate
+except ImportError:
+    matchResidue = app.forcefield._matchResidue
+
 import numpy as np
 import numpy as np
 import numpy.linalg as lin
 import numpy.linalg as lin
 import sys
 import sys
@@ -1132,7 +1140,7 @@ class PDBFixer(object):
 
 
             signature = app.forcefield._createResidueSignature([atom.element for atom in residue.atoms()])
             signature = app.forcefield._createResidueSignature([atom.element for atom in residue.atoms()])
             if signature in forcefield._templateSignatures:
             if signature in forcefield._templateSignatures:
-                if any(compiled.matchResidueToTemplate(residue, t, bondedToAtom, False) is not None for t in forcefield._templateSignatures[signature]):
+                if any(matchResidue(residue, t, bondedToAtom) is not None for t in forcefield._templateSignatures[signature]):
                     continue
                     continue
 
 
             # Create a new template.
             # Create a new template.