From 91cc02300e8142792016ea5244ee5f2ef9a975dc Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Tue, 26 Sep 2023 11:09:19 -0700 Subject: [PATCH] revert openbabel.OBAlign() calls to use positional args for includeH=True, symmetry=False --- pymatgen/analysis/molecule_matcher.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pymatgen/analysis/molecule_matcher.py b/pymatgen/analysis/molecule_matcher.py index 0def6c3bee5..c84576a0ce8 100644 --- a/pymatgen/analysis/molecule_matcher.py +++ b/pymatgen/analysis/molecule_matcher.py @@ -143,7 +143,7 @@ def uniform_labels(self, mol1, mol2): label2_list = tuple(tuple(p[1] + 1 for p in x) for x in sorted_isomorph) vmol1 = ob_mol1 - aligner = openbabel.OBAlign(includeH=True, symmetry=False) + aligner = openbabel.OBAlign(True, False) # meaning includeH=True, symmetry=False # noqa: FBT003 aligner.SetRefMol(vmol1) least_rmsd = float("Inf") best_label2 = None @@ -647,7 +647,7 @@ def _calc_rms(mol1, mol2, clabel1, clabel2): a2.SetAtomicNum(oa2.GetAtomicNum()) a2.SetVector(oa2.GetVector()) - aligner = openbabel.OBAlign(includeH=True, symmetry=False) + aligner = openbabel.OBAlign(True, False) # meaning includeH=True, symmetry=False # noqa: FBT003 aligner.SetRefMol(cmol1) aligner.SetTargetMol(cmol2) aligner.Align()