Hi all,
Yep the SMILES parser changed on master and won’t accept invalid SMILES by
default. Notice how daylight rejects it also. It should now be the case now
that if CDK rejects it - daylight also rejects it (If not then it’s a bug). The
new parser automatically kekulises on load, verifying the bond orders can be
assigned to aromatic systems. This is much friendly for the CDK as you don’t
have molecules with all single aromatic bonds floating about. When we added
this it fixed 2 failing unit tests.
In the molecule you're missing a hydrogen of one or more nitrogens, to know
which ones is the problem.
The SMILES should be:
> c4ccc2c(cc1=Nc3[nH]cccc3(Cn12))c4
>
Some toolkits will fix this by default but that’s making several assumptions
and it’s nothing more than an hack for broken SMILES input. To fix this you
need to change the formula of the molecule which is never a good start. You
can still parse it with the CDK by turning on ‘preserve aromaticity’ (need to
rename) this disables electron checking but I strongly discourage that. The
actual fix involves checking every possible combination of hydrogens on
aromatic nitrogens and phosphates, checkout the fixarom core from
http://www.daylight.com/download/contrib/.
Now where this molecules come from is probably more interesting. Most likely
it’s people using the aromaticity models on formats which don’t support it. The
MDL model for example doesn’t allow lone pair contributions. If you have marvin
sketch, try loading ‘[nH]1cccc1’ and then generating an MDL mol file. You’ll
notice they have there own non-portable work around to ensure the hydrogen is
kept. Of course everyone knows you should never store aromaticity in the mol
file :-).
Mrv0541 11071317592D
5 5 0 0 0 0 999 V2000
1.2964 0.6723 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.9639 0.1874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7089 -0.5972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8839 -0.5972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6290 0.1874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
4 5 4 0 0 0 0
1 5 4 0 0 0 0
3 4 4 0 0 0 0
M STY 1 1 DAT
M SAL 1 1 1
M SDT 1 MRV_IMPLICIT_H
M SDD 1 0.0000 0.0000 DR ALL 0 0
M SED 1 IMPL_H1
M END
Oh some more examples which are now correctly rejected.
> C/1.C/C=C/1
> C-1.C/C=C=1
> ccc
> ccccc
> p1cccc1 <- generated by older CDK versions!
Cheers,
J
On 7 Nov 2013, at 16:33, Nina Jeliazkova <jeliazkova.n...@gmail.com> wrote:
>
>
>
> On 7 November 2013 18:26, Nina Jeliazkova <jeliazkova.n...@gmail.com> wrote:
>
>
>
> On 7 November 2013 18:18, Rajarshi Guha <rajarshi.g...@gmail.com> wrote:
> It seems
> c4ccc2c(cc1=Nc3ncccc3(Cn12))c4
>
> does not parse using the latest CDK master, but does parse fine using
> http://apps.ideaconsult.net:8080/ambit2/depict?search=c4ccc2c%28cc1%3DNc3ncccc3%28Cn12%29%29c4&smarts=
>
> I'm not sure what version ambit is using
>
>
> cdk 1.4.11
>
> There is also a test version using cdk 1.5.3 (Sep 2013) and seems to parse
> fine
> http://apps.ideaconsult.net:8080/bioclipse/depict?search=c4ccc2c%28cc1%3DNc3ncccc3%28Cn12%29%29c4&smarts=
>
>
> Nina
>
> Regards,
> Nina
> but could somebody confirm this issue with the latest master?
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
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