Thanks for the explaination - much clearer now!
On Thu, Nov 7, 2013 at 1:05 PM, John May <[email protected]> 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 <[email protected]>
> wrote:
>
>
>
>
> On 7 November 2013 18:26, Nina Jeliazkova <[email protected]>wrote:
>
>>
>>
>>
>> On 7 November 2013 18:18, Rajarshi Guha <[email protected]> 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=<http://apps.ideaconsult.net:8080/bioclipse/depict?search=c4ccc2c(cc1=Nc3ncccc3(Cn12))c4&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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>>
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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from the latest Intel processors and coprocessors. See abstracts and register
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