I have a strange behavior on trasformation smirks node , i try to trasform benzamide . I use this smirks
but in the resuts i find a breaks in to the NH2* and my results...
Is it my error in smirks line?
Thank you for your question and sorry for delay.
The problem hides in [*;C,c:1] atom, that doesn't match to the hydrogen in benzamide.
In Indigo '*' means any atom but not hydrogen, it was made to avoid many unexpected results. You can read our discussion about it here: http://blueobelisk.shapado.com/questions/smarts-queries-and-implicit-explicit-hydrogens
If you want to describe any atom which includes hydrogen you should write [H,*].
To answer your question I should know what did you mean by [*;C,c:1]?
And another problem is that benzamide has aromatic ring, but in your SMIRKS atoms of the ring are set as aliphatic, so they can't be matched to the reactant atoms.
I think that your reaction should look like:
If you will have "Incorrect AAM" error on this transformation, take nightly Indigo builds. This bug was fixed.
Best regards, Andrey
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