Dear all, I'm having a few troubles in calculating properties using Pybel (v.2.3.2) ------------------ import pybel ob = pybel.ob import sys
smi = 'CN1c2ccc(cc2[C@@H]2C1=C1[C@H](C=C2)C(=O)C=CC1=O)OC MOL_1290' descs = pybel.descs m = pybel.readstring('smi', smi) for d in descs: print "DESC [ %s ]" % d, sys.stdout.flush() for k,v in m.calcdesc([d]).items(): print "->", v print "---------------------" print "title:", m.title print "formula:", m.formula ------------------ The output below returns several 'nan' that I can't understand. In particular, I know the molecule has a title (i.e., Molecule.title) but the descriptor can't find it apparently. Same thing with couple more descriptors. DESC [ abonds ] -> 6.0 DESC [ atoms ] -> 24.0 DESC [ bonds ] -> 27.0 DESC [ cansmi ] -> nan DESC [ cansmiNS ] -> nan DESC [ dbonds ] -> 5.0 DESC [ formula ] -> nan DESC [ HBA1 ] -> 6.0 DESC [ HBA2 ] -> 4.0 DESC [ HBD ] -> 0.0 DESC [ InChI ] -> nan DESC [ InChIKey ] -> nan DESC [ L5 ] -> nan DESC [ logP ] -> 2.4417 DESC [ MP ] -> 165.0235 DESC [ MR ] -> 86.134 DESC [ MW ] -> 293.3166 DESC [ nF ] -> 0.0 DESC [ s ] -> nan DESC [ sbonds ] -> 16.0 DESC [ smarts ] -> nan DESC [ tbonds ] -> 0.0 DESC [ title ] -> nan DESC [ TPSA ] -> 46.61 --------------------- title: MOL_1290 formula: C18H15NO3 From what I can tell, all textual descriptors [1] are missing. Also, I was interested in understanding what 'smarts' and 's' descriptors actually mean, but I can't find any documentation on the matter other than this [1]. Advice is welcome. Thanks, S [1] http://open-babel.readthedocs.org/en/latest/Descriptors/descriptors.html -- Stefano Forli, PhD Staff Scientist Molecular Graphics Laboratory Dept. of Integrative Structural and Computational Biology, MB-112F The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037-1000, USA. tel: +1 (858)784-2055 fax: +1 (858)784-2860 email: fo...@scripps.edu http://www.scripps.edu/~forli/ ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss