Always reading stereo info from 3D conformations.

choderalab · Mar 8, 2023 · bdbc8b3 · bdbc8b3
1 parent 379ea55
commit bdbc8b3
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/perses/rjmc/atom_mapping.py b/perses/rjmc/atom_mapping.py
@@ -786,7 +786,7 @@ def copy_molecule(mol):
                     atom.name = oeatom.GetName()
             elif hasattr(mol, 'GetAtoms'):
                 # OpenEye OEMol
-                offmol = Molecule(mol, allow_undefined_stereo=True)
+                offmol = Molecule(mol)
                 oemol = oechem.OEMol(mol)
             else:
                 raise ValueError(f'Not sure how to copy {mol}; should be openff.toolkit.topology.Molecule or openeye.oechem.OEMol')

diff --git a/perses/utils/openeye.py b/perses/utils/openeye.py
@@ -362,10 +362,10 @@ def createOEMolFromSDF(sdf_filename, index=0, add_hydrogens=True, allow_undefine
     if add_hydrogens:
         oechem.OEAddExplicitHydrogens(molecule)
     oechem.OEPerceiveChiral(molecule)
+    oechem.OE3DToInternalStereo(molecule)
 
     # perceive chirality
     if not allow_undefined_stereo:
-        assert oechem.OE3DToInternalStereo(molecule), f"the stereochemistry perception from 3D coordinates failed"
         assert not has_undefined_stereocenters(molecule), f"there is an atom with an undefined stereochemistry"
 
     return molecule