I had similar issues using pretty much the same code.
Is there a reason why doing exactly the same thing (number of steps, convergence, etc)
with obabel and Python would give different results?
In my tests, I have to use even several orders of magnitude more steps to get results that
are compa
I tried obgen in openbabel/tools and it generated a reasonable 3D
structure. I tried to reproduce obgen in pybel with the same procedure,
which is
pymol = pybel.readstring('smi', 'CCC(=O)OCC.CCC(=O)OCC.CC[O-]')
mol = pymol.OBMol
builder = ob.OBBuilder()
builder.Build
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:
