Re: [indigo-general] smirks

[Mikhail Rybalkin]

Hello,

There are two problems with your SMARTS:
1. SMARTS expressions distinguish aromatic and non-aromatic atoms. If
user specify non-aromatic atom, then it do not match aromatic one. You
target is aromatic, and you should explicitly specify this.
2. Another problem is an Indigo-specific problem that we treat "*" as
"anything, except Hydrogen". We have a discussion about it here:
http://blueobelisk.shapado.com/questions/smarts-queries-and-implicit-explicit-hydrogens

To match any atom you should write [H,*] (and not [*,H] because it means
any atom with additional connected hydrogen)

Correct Smirks should be the following:

[H:12][S:7][c:6]1[n:5][c:4][n:3][c:2]2[n:1]([H,*:11])[c:10][n:9][c:8]12>>[H:12][N:5]1[C:4]=[N:3][C:2]2=[C:8]([N:9]=[C:10][N:1]2[H,*:11])[C:6]1=[S:7]

> In general, does anybody know a good tool for converting reaction into
> SMIRKS with mapping feature?
SMIRKS is just a way of reaction representation. With Indigo you can
query reactions loaded directly from rxn-files, and they are attached
(for rxnfiles you cannot specify any atom including hydrogen by the same
reason, and there was no request for it). But you do not need to specify
that Any atom because Indigo will deduce it automatically, because there
was a connection to N, and the third attached reaction works for you.
You can just load these reaction using Indigo Knime node to load query
reaction and pass them to the transformation node.

And if you need tool, then at least in MarvinSketch from ChemAxon you
can work with reaction and save them into SMARTS. Probably, other
molecule sketchers allow this too. And ChemAxon also provides a free
package for Knime to use there Sketcher within Knime.

You can post here other SMIRKS and reaction transformations if they do
not work. This will help us to understand what problems may arise.

PS: file attachments can only be added if you are posting message by
sending it or replaying to indigo-...@googlegroups.com . Google
doesn't provide a way to add an attachment via web interface.

Best regards,
Mikhail

On 5/17/2012 14:57, kxk56 wrote:
> Hi,
>
> I am having problem with thiopurine molecule transformation using
> SMIRKS below:
>
> [*:11][N:1]1[C:2]2[N:3]=[CH:4][N:5]=[C:6]([S:7][H:12])[C:8]=2[N:9]=[CH:
> 10]1>>[*:11][N:1]1[C:2]2[N:3]=[CH:4][N:5]([H:12])[C:6](=[S:7])[C:
> 8]=2[N:9]=[CH:10]1
>
> The above SMIRKS for some reason doesn't apply/recognize to the
> molecule below when used in Knime with molecule transformation node:
> -----
> thiopurine
> SMMXDraw05161213542D
>
> 11 12 0 0 0 0 0 0 0 0999 V2000
> 10.3528 -5.1589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.3951 -5.1583 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 11.3759 -4.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.3951 -6.3398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.3528 -6.3451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 11.3784 -6.9293 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 9.2248 -4.7924 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 9.2247 -6.7116 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
> 8.5276 -5.7519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 11.7500 -2.2500 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> 8.9063 -9.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6 4 2 0 0 0 0
> 5 6 1 0 0 0 0
> 2 3 2 0 0 0 0
> 1 5 2 0 0 0 0
> 4 2 1 0 0 0 0
> 3 1 1 0 0 0 0
> 9 7 2 0 0 0 0
> 8 9 1 0 0 0 0
> 1 7 1 0 0 0 0
> 5 8 1 0 0 0 0
> 3 10 1 0 0 0 0
> 8 11 1 0 0 0 0
> M END
> -----
>
> In general, does anybody know a good tool for converting reaction into
> SMIRKS with mapping feature?
>
> Thanks