Dear colleagues, I have a molecule "FC12C3CCCC1C32F". I stripped it of the F's, and tried to do a GetSubstructMatch. It worked. But if I reconstruct the stripped molecule from a smiles string, it does not. Please see attached.
I suppose some info is lost when you reconstruct the stripped core from a smiles string. But still, I would think it should match anyway. Another issue is that the 2D depiction has the left most carbons lying exactly on top of each other, creating a false impression. A better depiction would be like the second attached image. (Not sure if this is easy to fix though.) Thank you for you attention. Ling
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