Re: [Open Babel] obabel SMARTS search with a .sdf and a .fs file (different behaviour)

[David G. A. <ari...@cb...>]

Thank you very much... maybe the documentation could warn about this here:

http://openbabel.org/docs/2.3.1/Fingerprints/fingerprints.html

[...]
Large datasets

First of all, you need to create a fastsearch index (see above). The index
is created with the following command:

babel mymols.sdf -ofs

Substructure searching is as for small datasets, except that the
fastsearch index is used instead of the original file. This command will
find all molecules containing 1,2-dicyanobenzene and return the results as
SMILES strings:

babel mymols.fs -ifs -sN#Cc1ccccc1C#N results.smi
[...]

> This feature is not supported. If you think about it how the
> fastsearch works, you will realise why. The FastSearch uses a
> fingerprint index to quickly filter results before doing a
> substructure match; SMILES strings represent molecules and have
> fingerprints, but SMARTS strings are not molecules and so we cannot
> generate fingerprints.
>
> - Noel
>
> On 31 October 2012 12:17, David García Aristegui <ari...@cb...>
> wrote:
>> Hello, i'm trying to do searches with the SMARTS patterns from
>> SMARTS_InteLigand.txt:
>>
>> obabel FP4.fs -s '[CX4H3][#6]' -O FP4.smi
>> ==============================
>> *** Open Babel Error  in ObtainTarget
>>   Cannot read the SMILES string
>> 0 molecules converted
>>
>> obabel FP4.fs -s '[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]' -O FP4.smi
>> ==============================
>> *** Open Babel Error  in ReadMolecule
>>   [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] contained a character '!' which
>> is
>> invalid in SMILES
>> ==============================
>> *** Open Babel Error  in ObtainTarget
>>   Cannot read the SMILES string
>> 0 molecules converted
>>
>> I have no problems using the FP4.sdf file... or using SMILES strings for
>> the searches (i.e. -s 'CCC').
>>
>> Please, could you tell me what i'm doing wrong using the .fs files to do
>> the SMARTS searches?
>>
>> Best regards.
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_sfd2d_oct
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>