Sorry for spamming, sent to wrong mailing list.
On Wed, Oct 23, 2019 at 7:50 PM Navid Shervani-Tabar <[email protected]>
wrote:
> Hello,
>
> I'm trying to use OB to do some calculation related to the force fields. I
> am using QM9 dataset and reading xyz files provided in the original paper.
>
> def xyz_to_smiles(fname: str) -> str:
> mol = next(pybel.readfile("xyz", fname))
> smi = mol.write(format="smi")
>
> return smi.split()[0].strip()
>
>
> This gives me a pybel molecule.
>
> 1. I was wondering if it is possible to turn this into an OBMol
> object?
> 2. The 3d coordinates for each atom is provided in the xyz file. I
> want to use that and get force filed constants (e.g. stretching force
> constant, natural length) to calculate potential functions (e.g. bond
> stretching). But it seems that the only available way to get atom
> coordinates from the molecule is to use make3D, which optimizes these
> functions rather than giving me what it reads from the xyz file. Is there a
> way to get the coordinates through the molecule object (or OBMol object,
> depending on the answer to first question).
> 3. How can I get the force field constants for each atom? (e.g.
> equivalent of GetUFFBondStretchParams from RDKit)
>
> Even pointing me to the right reading material will suffice.
>
> Thanks in advance,
> Navid
>
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