Dear PyMol Users, I found an easy way to count total number of bonds in a molecule, which has been loaded in PyMol viewer:
from chempy import stored, Bond m = cmd.get_model() print “number of total bonds:”, len(m.bond) I hope it will be useful. Cheers Vijay On 3/22/16, Vijay Masand <vijaymas...@gmail.com> wrote: > Dear PyMol Users > > While working with a ligand in a pdb file, which I saved in .mol2 file > format, I used following command: > > get_bond stick_transparency, * > I observed following outcome in Pymol. > Getting: stick_transparency for 63 bonds in > object "testing". > stick_transparency = 0.00000 for object testing > > I know that PyMol can count atoms; the above command is providing > counting of bonds in a molecule. It will be a great help if someone > can tell me the pymol command or API for counting of Bonds in an > object loaded in pymol viewer. > > Thanks in advance. > > From > Vijay > > > -- > Assistant Professor > Department of Chemistry, > Vidya Bharati College, Amravati, 444 602 > Maharashtra, India. > Phone number- +91-9403312628 > https://sites.google.com/site/vijaymasand/ > -- Assistant Professor Department of Chemistry, Vidya Bharati College, Amravati, 444 602 Maharashtra, India. Phone number- +91-9403312628 https://sites.google.com/site/vijaymasand/ ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
