No problem - it should say in the error message but I think it is be bing
suppressed (wrapped exceptions) I’ll double check that.
On 8 Nov 2013, at 04:29, Rajarshi Guha <rajarshi.g...@gmail.com> wrote:
> Thanks for the explaination - much clearer now!
>
>
> On Thu, Nov 7, 2013 at 1:05 PM, John May <john...@ebi.ac.uk> wrote:
> 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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>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
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