On 2012-12-09 11:36, Chris Morley wrote:
> On 08/12/2012 21:32, David van der Spoel wrote:
>> On 2012-12-08 17:42, Noel O'Boyle wrote:
>>> C:\Users\Noel>obabel -:c1(Br)cc(Br)ccc1 -ofpt -xf fp4 -xs
>>>>
>>> Arylbromide Aromatic
>>> 1 molecule converted
>>>
>> Great, I can reproduce that.
>> Is there a simple way of getting this functionality from the source
>> code? I don't see any member functions in OBMol that could provide this?
>
> As well as the core API, OpenBabel has some of its functionality in
> plugins. The code for the above feature is in the API code
> fingerprint.cpp, and in the plugins fingerprintformat.cpp and
> finger3.cpp. Probably the easiest way to access it is to use OB's
> conversion framework (Imitate the command line.). Something like: (untested)
>
> ifstream ifs(13-dibromobenzene.sdf);
> if(!ifs)
> return false;
> OBConversion conv(&ifs, &cout);
> if(!conv.SetInAndOutFormats("sdf", "fpt"))
> return false;
> conv.AddOption("f", OBConversion::OUTOPTIONS, "FP4");
> conv.AddOption("s");
> conv.Convert();
>
> If you already have the OBMol, conv.Write() will do the output half.
>
> See http://openbabel.org/dev-api
Thanks, I now use this which works:
if (conv.SetOutFormat("fpt"))
{
conv.AddOption("f", OpenBabel::OBConversion::OUTOPTIONS,
"FP4");
conv.AddOption("s");
conv.Convert();
cout << conv.WriteString(mol,false);
}
however, it gives me output that is not very nice for e.g.
N,N-dimethylaniline
>
Amine Tertiary_mixed_amine Aromatic C_ONS_bond Rotatable_bond
It would be nicer to get this in a more ordered manner, like a vector of
strings. Also, the first three terms make sense to me but the last two
seem not very useful. Any more tips?
>
> Chris
>
>>>>> is it possible with openbabel to classify a molecule based on
>>>>> substructures?
>>>>>
>>>>> E.g.:
>>>>>
>>>>> 110-dichlorodecane.sdf
>>>>> alkyl chloride
>>>>>
>>>>> 11122334455666-tetradecafluorohexane.sdf
>>>>> alkyl fluoride
>>>>>
>>>>> 111-trimethoxyethane.sdf
>>>>> orthocarboxylic acid derivative
>>>>> orthoester
>>>>>
>>>>> 13-dibromobenzene.sdf
>>>>> aryl bromide
>>>>> aromatic compound
>
>
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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