Optimize tool from python shell

ghutchis · January 24, 2020, 9:03pm

All of the molecular mechanics, optimization, and conformer searching methods in Avogadro v1.x are directly from Open Babel.

You can access these via Python:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python.html

Here’s an example script:

gist.github.com

https://gist.github.com/ghutchis/c6734e91828d0c13daff246d8909e0ae

ob-optimize.py

#!/usr/bin/env python

import sys, os

from openbabel import pybel

# read through multiple files on command-line
for argument in sys.argv[1:]:

    filename, extension = os.path.splitext(argument)

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