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/
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