Re: [Open Babel] substructure classification

2012-12-10 Thread David van der Spoel
On 2012-12-10 10:47, Chris Morley wrote: > On 09/12/2012 21:03, David van der Spoel wrote: >> Thanks, I now use this which works: >> >> if (conv.SetOutFormat("fpt")) >>{ >> conv.AddOption("f", OpenBabel::OBConversion::OUTOPTIONS, >> "FP4"); >>

Re: [Open Babel] substructure classification

2012-12-10 Thread Chris Morley
On 09/12/2012 21:03, David van der Spoel wrote: > Thanks, I now use this which works: > > if (conv.SetOutFormat("fpt")) > { > conv.AddOption("f", OpenBabel::OBConversion::OUTOPTIONS, > "FP4"); > conv.AddOption("s"); > conv.Co

Re: [Open Babel] substructure classification

2012-12-10 Thread Noel O'Boyle
On 9 December 2012 21:03, David van der Spoel 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

Re: [Open Babel] substructure classification

2012-12-09 Thread David van der Spoel
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-discu

Re: [Open Babel] substructure classification

2012-12-09 Thread Chris Swain
> > > -- > > 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.

Re: [Open Babel] substructure classification

2012-12-09 Thread David van der Spoel
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 t

Re: [Open Babel] substructure classification

2012-12-09 Thread Chris Morley
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 fro

Re: [Open Babel] substructure classification

2012-12-08 Thread David van der Spoel
On 2012-12-08 17:42, Noel O'Boyle wrote: > Beg pardon, mea culpa and I tell a lie. It should have been: > > 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 functional

Re: [Open Babel] substructure classification

2012-12-08 Thread Noel O'Boyle
Beg pardon, mea culpa and I tell a lie. It should have been: C:\Users\Noel>obabel -:c1(Br)cc(Br)ccc1 -ofpt -xf fp4 -xs > Arylbromide Aromatic 1 molecule converted On 8 December 2012 16:41, Noel O'Boyle wrote: > If you can describe the substructures by a SMARTS string, it's fairly > easy by c

Re: [Open Babel] substructure classification

2012-12-08 Thread Noel O'Boyle
If you can describe the substructures by a SMARTS string, it's fairly easy by customising FP4. Here's the output of FP4 for the arylbromide: C:\Users\Noel>obabel -:c1(Br)ccc(Br)c1 -ofpt -xf fp4 -xs > Secondary_carbonAlkylbromide 1 molecule converted How to customise?... C:\Users\Noel>oba

[Open Babel] substructure classification

2012-12-08 Thread David van der Spoel
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