Thanks Geoffrey, that helps alright but I am still stuck with zero
coordinates when I write to an output file (say mol2 or com). What am I
still missing?
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', outfile_type)
cv.ReadString(mol, smiles_string)
mol.AddHydrogens()
ff = openbabel.OBForceField.FindForceField("MMFF94")
ff.SteepestDescent(1500, 1.0e-4)
ff.WeightedRotorSearch(250, 25)
ff.ConjugateGradients(2500, 1.0e-6)
ff.GetCoordinates(mol)
cv.WriteFile(mol,outfile_name)
Also, I am currently using gen3d to generate my 3D molecule (which already
does a weighted rotor search and steepest descent etc) and then doing a
further weighted rotor search with much stricter energy convergence and much
larger number of conformers to search for (see code below which iterates
over a number of smiles strings).
- I assume this is basically the same as doing the one intensive weighted
rotor search??
- If time is not an issue, should you ideally maximize the number of
conformers and steps in WeightedRotorSearch and for the pre and post
optimization (ie SteepestDescent and ConjugateGradients)??
for smiles_string in smiles_string_list:
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', outfile_type)
cv.ReadString(mol, smiles_string)
mol.AddHydrogens()
gen3d = openbabel.OBOp.FindType("Gen3D")
gen3d.Do(mol)
ff = openbabel.OBForceField.FindForceField("MMFF94")
ff.Setup(mol)
ff.SteepestDescent(ffsd_steps, ffsd_convergence)
ff.WeightedRotorSearch(ffwrs_conformers,ffwrs_steps)
ff.ConjugateGradients(ffcg_steps,ffcg_convergence)
ff.GetCoordinates(mol)
cv.WriteFile(mol,mol_name)
And lastly, how do I write the log to a file?
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
ff.SetLogToStdErr()
I think that is the end of my conformer search questions, so thanks again
for all the help so far!
Scott
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