All,
I touched on this subject yesterday, but wanted to add some more information
today as I didn't receive a response yet. I am having trouble with RDKit
correctly interpreting the SMARTS character [!#1], which should be interpreted
as "any atom not hydrogen. Let me give you an example:
My SMARTS input:
[#6]-1(=[!#1]-[!#1]=[!#1]-[#7](-[#6]-1=[#16])-[#1])-[#6]#[#7]
Now when I do Chem.MolFromSmarts, my mol representation has hydrogens at those
three positions, and as such I can't do sanitization of the molecule because
since it has hydrogens in the !#1 positions, there is a valency conflict.
I confirm that it does indeed insert hydrogens in to the formula by performing
Chem.MolToSmiles of the mol_file generated previously, which returns:
[H]N1[H]=[H][H]=C(C#N)C1=S
Interestingly, augmenting the original SMARTS string to include * (wild card
any atom) in those three !#1 positions returns NONE.
Has anyone else encountered this problem with !#n?
Thank you
Christopher R. Bodle
PhD Candidate, University of Iowa
College of Pharmacy
Division of Medicinal and Natural Products Chemistry
115 S. Grand Avenue-Rm. S338
Iowa City, Iowa 52242
(319) 335-7845
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