smirks problem

[fab]

 

dear ,

I have a strange behavior on trasformation smirks node , i try to trasform benzamide . I use this smirks

O=C(C1=[C:2][C:3]=[C:4][C:5]=C1[H])N[*;C,c:1]>>[*;C,c:1]NC1=NOc2c1[c:2][c:3][c:4][c:5]2

but in the resuts i find a breaks in to the NH2* and my results...

Is it my error in smirks line?

thanks

 

[achurinov]

Hello,

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:

O=C(c1=[c:2][c:3]=[c:4][c:5]=c1[H])N[H,*:1]>>[H,*:1]NC1=NOc2c1[c:2][c:3][c:4][c:5]2

If you will have "Incorrect AAM" error on this transformation, take nightly Indigo builds. This bug was fixed.

Best regards, Andrey