On Feb 4, 2008 4:00 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Snoze,
I'm going to guess, like Elaine, that your purpose is to add partial charges. If your 1000 compounds are in one big mol2 file, here is a script that would do the job:

from chimera import openModels, Molecule
from AddCharge import addNonstandardResCharges, estimateFormalCharge, ChargeError
mols = openModels.list(modelTypes=[Molecule])
log = open("errlog", "w")

for m in mols:
residues = m.residues
atoms = [a for r in residues for a in r.atoms]
fc = estimateFormalCharge(atoms)

try:
addNonstandardResCharges(m.residues, fc)
except ChargeError:
print>>log, "Charge estimate (%d) or protonation wrong for %s (%s)" % (
fc, m.name, m.oslIdent())

from WriteMol2 import writeMol2
writeMol2(mols, "output.mol2")
log.close()

If you save the above in a file named script.py and your 1000 compounds are in a file named input.mol2, then running:

chimera --nogui input.mol2 script.py

will produce a file named output.mol2 with the charges included. Any problems it had charging particular compounds will be saved in a file named errlog.

--Eric

  Eric Pettersen

  UCSF Computer Graphics Lab

                     http://www.cgl.ucsf.edu

On Feb 1, 2008, at 10:36 AM, Elaine Meng wrote: