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 comparable with '--gen3D'.
The only major difference I can think of is that I know obabel runs in parallel on
multiple cores, but I doubt that would make a difference.
On 02/22/2018 11:03 AM, Xianghai Sheng wrote:
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(mol)
mol.AddHydrogens(False, True)
pff = pybel._forcefields['mmff94']
pff.Setup(mol)
pff.SteepestDescent(500, 1.0e-4)
pff.WeightedRotorSearch(250, 50)
pff.SteepestDescent(500, 1.0e-4)
pff.UpdateCoordinates(mol)
It still generates structures with overlapping atoms. Can anybody help please?
Best,
Xianghai
On Thu, Feb 15, 2018 at 3:23 PM, Xianghai Sheng <xsh...@ucmerced.edu
<mailto:xsh...@ucmerced.edu>> wrote:
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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