add support for sanitize=false in MolFromSmiles
sarmbruster opened this issue · 0 comments
sarmbruster commented
For example, a 5 coordinate neutral carbon will generate errors if you attempt to sanitize it normally, but can be handled if you turn off the appropriate pieces. For example:
In [2]: m = Chem.MolFromSmiles('ClC(C)(C)Br')
[04:56:25] Explicit valence for atom # 1 C, 5, is greater than permitted
In [3]: m = Chem.MolFromSmiles('ClC(C)(C)Br',sanitize=False)
In [4]: Chem.SanitizeMol(m,Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_PROPERTIES)
Out[4]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [5]: m.HasSubstructMatch(Chem.MolFromSmarts('ClCBr'))
Out[5]: True