Re: [Open Babel] substructure classification
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
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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Re: [Open Babel] Problems with binding Python
I tryed using the latest release of swig (2.0.8) and compile everything from scratch and still got the problem. I am using python 2.7.3. -- View this message in context: http://forums.openbabel.org/Problems-with-binding-Python-tp4655705p4655766.html Sent from the General discussion mailing list archive at Nabble.com. -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] substructure classification
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_amineAromatic 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.sehttp://folding.bmc.uu.se
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Re: [Open Babel] substructure classification
> > > -- > > Message: 2 > Date: Sat, 08 Dec 2012 14:51:44 +0100 > From: David van der Spoel > Subject: [Open Babel] substructure classification > To: openbabel-discuss@lists.sourceforge.net > Message-ID: <50c345f0.4070...@xray.bmc.uu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > 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 > > > -- > 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.sehttp://folding.bmc.uu.se > Have a look at Checkmol http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html Cheers, Chris -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] substructure classification
On 2012-12-09 22:14, Chris Swain wrote: >> >> >> -- >> >> Message: 2 >> Date: Sat, 08 Dec 2012 14:51:44 +0100 >> From: David van der Spoel >> Subject: [Open Babel] substructure classification >> To: openbabel-discuss@lists.sourceforge.net >> Message-ID: <50c345f0.4070...@xray.bmc.uu.se> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi, >> >> 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 >> >> >> -- >> 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.sehttp://folding.bmc.uu.se >> > > > Have a look at Checkmol > > http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html Thanks, I'm aware of that, but was hoping to have that functionality in openbabel instead, in order to streamline my tools (am already using way too many different tools anyway). It seems that openbabel is almost there. -- 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.sehttp://folding.bmc.uu.se -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
