Hi Noel,
thank you very much!
Unfortunately I got an error when I tried the FindPlugin() function.
Code:
*import pybel# Set up converterconv =
pybel.ob.OBConversion()conv.SetOutFormat("mop")conv.AddOption("k",
conv.OUTOPTIONS, "SYMMETRY PM7 UHF STATIC")conv.Convert()gen3d =
openbabel.OBOp.FindPlugin("gen3d")# Get a moleculemol = readstring("smi",
"C=C(C)CCC")gen3d.Do(mol.OBMol)output = conv.WriteString(mol.OBMol)print
(output)*
What did I do wrong?
However I had a look at the Pybel API documentation on Github and I found
the make3D function.
With the following code and your suggestion of getting rid of the
Conversion Object I achieved the result I wanted:
*mol = readstring("smi", "C=C(C)CCC")*
*mol.make3D()output = out = mol.write("mop", opt={"k":"SYMMETRY PM7 UHF
STATIC"})*
*print(output)*
Output:
SYMMETRY PM7 UHF STATIC
C 0.89335 1 0.00286 1 -0.01617 1
C 2.23793 1 0.02055 1 0.00771 1
C 2.97498 1 0.80100 1 1.06089 1
C 3.03015 1 -0.74861 1 -1.03024 1
C 4.54982 1 -0.63509 1 -0.87704 1
C 5.29276 1 -1.42196 1 -1.93888 1
H 0.30804 1 0.54711 1 0.71827 1
H 0.34596 1 -0.55513 1 -0.76914 1
H 2.29548 1 1.31150 1 1.74978 1
H 3.60564 1 1.56767 1 0.59910 1
H 3.60564 1 0.13608 1 1.65997 1
H 2.74736 1 -0.39011 1 -2.02913 1
H 2.74735 1 -1.80860 1 -0.97797 1
H 4.85585 1 -1.00644 1 0.10783 1
H 4.85585 1 0.41523 1 -0.94569 1
H 5.04484 1 -2.48579 1 -1.88112 1
H 6.37179 1 -1.31269 1 -1.79142 1
H 5.04484 1 -1.05708 1 -2.93985 1
Thank you very much Noel!
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
