RE: [PyMOL] displaying pharmacophores

[DeLano, W. <wa...@su...>]

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 =3D Indexed()

# create some atoms

for a in range(1,11):
   at =3D Atom()
   at.name =3D "X%02d"%a
   at.coord =3D [random()*5,random()*5,random()*5]
   model.atom.append(at)

# now create some bonds

for a in range(1,10):
   bd =3D Bond()
   bd.index =3D [a-1,a] # zero-based indices!
   model.bond.append(bd)

# now load and label

cmd.load_model(model,"example")
cmd.label("example","name")

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20


-----Original Message-----
From: Sorich, Michael Joseph - SORMJ001 =
[mailto:Mic...@po...]
Sent: Thursday, June 13, 2002 11:55 PM
To: pym...@li...
Subject: [PyMOL] displaying pharmacophores


Hi,
=20
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...).=20
=20
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?
=20
Also, could someone point me to an example python script to make a =
simple ChemPy molecule and load it with cmd.load_model()?
=20
Thanks for you help
=20
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
=20


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