Hi,
I am trying to convert a smiles string into 3D structure in my program, but
the 3D structure I get sometimes have overlapping atoms, especially when
there are multiple fragments in the smiles string. An example is
'CC(=O)OCC.CC(=O)OCC.CC[O-]', and the code I wrote to generate 3D structure
is:
mol = pybel.readstring('smi', 'CC(=O)OCC.CC(=O)OCC.CC[O-]')
mol.addh()
mol.make3D()
mol.write('gjf')
However, when I do 'obabel test.smi -O test.gjf --gen3d' in the command
line, I get a reasonable 3D structure. I can see how make3D() is
implemented in pybel but I am wondering how it is implemented in obabel to
treat the multi-fragment problem and how I can generate reasonable 3D
structure in python.
Best,
Xianghai
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