Building ChemPy models is a snap. Just "run" the following Python program from
within PyMOL.
from chempy.models import Indexed
from chempy import Bond, Atom
from whrandom import random
from pymol import cmd
model = Indexed()
# create some atoms
for a in range(1,11):
at = Atom()
at.name = "X%02d"%a
at.coord = [random()*5,random()*5,random()*5]
model.atom.append(at)
# now create some bonds
for a in range(1,10):
bd = Bond()
bd.index = [a-1,a] # zero-based indices!
model.bond.append(bd)
# now load and label
cmd.load_model(model,"example")
cmd.label("example","name")
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
-----Original Message-----
From: Sorich, Michael Joseph - SORMJ001
[mailto:michael.sor...@postgrads.unisa.edu.au]
Sent: Thursday, June 13, 2002 11:55 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] displaying pharmacophores
Hi,
I wish to use pymol to display pharmacophores. A pharmacophore will basically
be a set of points/spheres each colored to represent the atom type it
represents (eg hydrophobe, neg charged atom, hydrogen bond donor...).
I have been using compiled graphics objects to display the pharmacophores,
however, it would probably be more flexible to use a ChemPy object to represent
the pharmacophore. The pharmacophore would be analogous to a molecule and would
contain dummy atoms (eg hydrophobe atom, pos charged atom...) instead of the
usual atom types. Would this be difficult? Does anyone have documentation on
ChemPy?
Also, could someone point me to an example python script to make a simple
ChemPy molecule and load it with cmd.load_model()?
Thanks for you help
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: michael.sor...@postgrads.unisa.edu.au
mike_sor...@hotmail.com
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