On Dec 9, 2011, at 12:12 PM, Geoffrey Hutchison wrote:
> As of yet, no. That could be done new scoring function (e.g., minenergy)
> which determines the energy after some minimization. It's a good idea.
OK, that seemed like an easy task, so SVN trunk now has "min" as a score option
with 250 steepest descent steps. Making the # of steps configurable would be
great, but that's about the time I had for coding during my lunch. :-)
# generate 50 conformers, scoring with MMFF94 energies, but default children,
etc.
obabel EtOT5D.cml -O EtOT5D0.xyz --conformer --nconf 50 --score energy
# generate 100 conformers, scoring with MMFF94 energies after geometry
minimization
obabel EtOT5D.cml -O EtOT5D0.xyz --conformer --nconf 50 --score min
I should point out that I *do* have code for using the older conformer searches
from Python -- just not the new GA search:
def globalopt(mol):
pybel._builder.Build(mol.OBMol)
mol.addh()
ff = pybel._forcefields["mmff94"]
success = ff.Setup(mol.OBMol)
if not success:
ff = pybel._forcefields["uff"]
success = ff.Setup(mol.OBMol)
if not success:
sys.exit("Cannot set up forcefield")
# initial cleanup before the weighted search
ff.SteepestDescent(500, 1.0e-4)
ff.WeightedRotorSearch(100, 20)
ff.ConjugateGradients(500, 1.0e-6)
ff.GetCoordinates(mol.OBMol)
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/
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