From: Rajeev R. <raj...@gm...> - 2013-03-29 08:32:44
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On 28/03/2013 12:17, Pascal Muller wrote: > Hi, > >> Is there a way to append ROTATABLE_BOND as a descriptor in openbabel, If is >> there any then please help me. > > http://forums.openbabel.org/number-of-rotatable-bonds-td959206.html > > Should be easy to add the corresponding line in > openbabel-2.3.1/tools/obprop.cpp, recompile, and run obprop, if that > is what you want. > > Or just run e.g. > > #!/usr/bin/python > import pybel > for mol in pybel.readfile("smi", "file.smi"): > print mol.OBMol.NumRotors(), "\t", mol.OBMol.GetTitle() If you would prefer the number of rotatable bonds as a descriptor and without having to recompile, add the following item to data/plugindefines.txt SmartsDescriptor rotors [!$(*#*)&!D1]-!@[!$(*#*)&!D1] Number of rotatable bonds\n From http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#ROTATE Use like: obabel mols.xxx -O out.yyy --append rotors obabel mols.xxx -O out.yyy --sort rotors+ obabel mols.xxx -O out.yyy --filter "rotors>2" obabel mols.xxx -O out.yyy --largest 3 rotors+ I have tried both ways, as suggested by Mr. Muller & Mr. Morley, and I found Mr. Morley's method easier and it worked in a single attempt. Thanks to both of you for your help. On Thu, Mar 28, 2013 at 10:46 AM, Chris Morley <c.m...@ga...> wrote: > On 28/03/2013 12:17, Pascal Muller wrote: > > Hi, > > > >> Is there a way to append ROTATABLE_BOND as a descriptor in openbabel, > If is > >> there any then please help me. > > > > http://forums.openbabel.org/number-of-rotatable-bonds-td959206.html > > > > Should be easy to add the corresponding line in > > openbabel-2.3.1/tools/obprop.cpp, recompile, and run obprop, if that > > is what you want. > > > > Or just run e.g. > > > > #!/usr/bin/python > > import pybel > > for mol in pybel.readfile("smi", "file.smi"): > > print mol.OBMol.NumRotors(), "\t", mol.OBMol.GetTitle() > > If you would prefer the number of rotatable bonds as a descriptor and > without having to recompile, add the following item to > data/plugindefines.txt > > SmartsDescriptor > rotors > [!$(*#*)&!D1]-!@[!$(*#*)&!D1] > Number of rotatable bonds\n > From > > http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#ROTATE > > Use like: > obabel mols.xxx -O out.yyy --append rotors > obabel mols.xxx -O out.yyy --sort rotors+ > obabel mols.xxx -O out.yyy --filter "rotors>2" > obabel mols.xxx -O out.yyy --largest 3 rotors+ > > Chris > > > > > ------------------------------------------------------------------------------ > Own the Future-Intel® Level Up Game Demo Contest 2013 > Rise to greatness in Intel's independent game demo contest. > Compete for recognition, cash, and the chance to get your game > on Steam. $5K grand prize plus 10 genre and skill prizes. > Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d > _______________________________________________ > OpenBabel-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Regards, Rajeev Ranjan Roy Project Assistant Prof. A. Surolia's Laboratory Molecular Biophysics Unit (MBU) Indian Institute of Sciences , Bangalore M.Sc, [Biotechnology], (2010-12) Department of Bio Sciences & Bio Engineering Indian Institute of Technology, Bombay |