On 9 December 2012 21:03, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
> 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?
Just write your own code. All it's doing is SMARTS matching using the
patterns in the text file for FP4.
- Noel
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