That's great, many thanks for the help. One other thing, I mentioned pybel
because I haven't got the OBMol conversion from input smiles string to
output file with 3D coordinates. Would you mind giving a quick example of
this (or directing me to online documentation, I couldn't find much here)?
What I have been trying:
mol = openbabel.OBMol()
conversion = openbabel.OBConversion()
conversion.SetInAndOutFormats('smi', 'com')
conversion.ReadString(mol, 'cc')
mol.AddHydrogens()
#Next step is what I'm not sure of, how do I get the coordinates so that I
can optimize and write to file??
cv.GetCoordinates()
cv.WriteFile(mol, 'test.com')
# But this just gives the coordinates as 0
With pybel I found the make3d() and localopt() functions very handy for this
but can't get a similar setup going with openbabel.
Apologies if this is a bit of a new thread.
Cheers,
Scott
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