Re: [Open Babel] Getting 3d coordinates from mol object

[Geoffrey H. <geo...@gm...>]

> 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