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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