OpenBabel energy minimization fails if Compound.name does not contain an element symbol

[chrisiacovella]

Bug summary

The way energy minimization is currently handled, it relies on outputting a temporary .mol2 file. This .mol2 file populates fields solely using Compound.name info, and not Compound.element. While the energy_minimize function does check if Compound.element is not set and tries to infer the element, the element information is not used.

Code to reproduce the behavior

Please include a code snippet that can be used to reproduce this bug.

import mbuild as mb

from mbuild.lib.recipes.alkane import Alkane

test_mol = Alkane(n=6)

for particle in test_mol: particle.name = 'junk'

test_mol.energy_minimize()

Software versions

• Which version of mBuild are you using? 0.15.1
• Which version of Python (python --version)? 3.9
• Which operating system? MacOS 12.6.2 M1 chip