> This gives me a pybel molecule.
> I was wondering if it is possible to turn this into an OBMol object?
Yes. You can get an OBMol object as an attribute from Pybel molecules like this:
mol.OBMol
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html#pybel.Molecule
> 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).
Atoms have multiple attributes like coords:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html#pybel.Atom.coords
> How can I get the force field constants for each atom? (e.g. equivalent of
> GetUFFBondStretchParams from RDKit)
There is, at the moment, no API to get the force field parameters from atoms.
Suggestions are welcome.
Hope that helps,
-Geoff
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