[Open Babel] Fail to reproduce obabel --gen3d in pybel

[Xianghai S. <xs...@uc...>]

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