Hello everyone,
I'm trying to generate some mopac files with some specified key words from
smiles. In obabel in the command line I use the following code for instance:
*obabel -:"C=C(C)CCC" -xk "SYMMETRY PM7 UHF STATIC" -omop -OE1.mop --gen3D*
Now I'm trying to reproduce this in Pybel. SO far I have the following code
with the corresponding output:
*import pybel# Set up converterconv =
pybel.ob.OBConversion()conv.SetOutFormat("mop")conv.AddOption("k",
conv.OUTOPTIONS, "SYMMETRY PM7 UHF STATIC")conv.AddOption("gen3d",
conv.OUTOPTIONS)#conv.Convert()# Get a moleculemol = readstring("smi",
"C=C(C)CCC")output = conv.WriteString(mol.OBMol)print (output)*
Output E1.mop file:
SYMMETRY PM7 UHF STATIC
C 0.00000 1 0.00000 1 0.00000 1
C 0.00000 1 0.00000 1 0.00000 1
C 0.00000 1 0.00000 1 0.00000 1
C 0.00000 1 0.00000 1 0.00000 1
C 0.00000 1 0.00000 1 0.00000 1
C 0.00000 1 0.00000 1 0.00000 1
As you can see the generated E1.mop file has no 3D coordinates. Every
atom is on the same position.
How can I incorporate the option gen3D in pybel for the generation of
valid mopac files?
Thank you very much in advance for any help!
Best regards,
Markus Grimm
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