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reject rdkit mols with queries #90

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reject rdkit mols with queries #90

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2 changes: 2 additions & 0 deletions meeko/molsetup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -722,6 +722,8 @@ def from_mol(cls, mol, keep_chorded_rings=False, keep_equivalent_rings=False,
raise ValueError("RDKit molecule has implicit Hs. Need explicit Hs.")
if mol.GetNumConformers() == 0:
raise ValueError("RDKit molecule does not have a conformer. Need 3D coordinates.")
if mol.HasQuery():
raise ValueError("RDKit molecules with queries are not supported. The molecule may originate from a SMARTS or a MOL/SDF with non-zero values in query fields of atoms or bonds")
rdkit_conformer = mol.GetConformer(conformer_id)
if not rdkit_conformer.Is3D():
warnings.warn("RDKit molecule not labeled as 3D. This warning won't show again.")
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