(resending to list)
It's best to practice this on SMILES strings, as you may be running into
problems reading the MOL2 format. OB's MOL2 format reader needs a rewrite,
but it's a horrible format with all sorts of implicit semantics that are
not documented. (Excuses, excuses, I suppose.)
So I would create a SMILES string that you expect to match the left-hand
side. Check that it *does* match the left hand side, and then see whether
the transformation gives what you expect. Then try it on a large test set
to ensure that the observed transformations don't have weird side-effects.
- Noel
On 26 September 2017 at 23:01, Stefano Forli <fo...@scripps.edu> wrote:
> Hi,
>
> I'm trying to write a rule for the phmodel that generates the Watson-Crick
> tautomer of guanine (guanine.mol2), using OpenBabel 2.3.2.
>
> These were the most promising attempts, but none of them work:
>
> -----
> #guanine whatson & crick tautomer
> TRANSFORM *[n]1[c][n][c]2[c]1[#7D3:1][c]([N])[#7D2:2][c]2=[O] >>
> *[n]1[c][n][c]2[c]1[#7D2:1][c]([N])[#7D3:2][c]2=[O] 1E+19
>
> TRANSFORM *[c]1[c][#7D3:1][c]([N])[#7D2:2][c]1=[O] >>
> *[c]1[c][#7D2:1][c]([N])[#7D3:2][c]1=[O] 1E+19
> -----
>
> and multiple hydrogens are attached to the molecule (guanine_after).mol2:
>
> $ obabel -imol2 guanine.mol2 -p 9 -omol2 -O guanine_after.mol2
>
> Any advice would be welcome.
>
> Thanks,
>
> S
>
>
>
>
>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor
> Dept. of Integrative Structural
> and Computational Biology, MB-112A
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
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