mb.Compound.save() feature returns a PDB file without bonds

[Pablo-Pomares]

Bug summary

When trying to save to a PDB file, it returns a file without bonds.

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 import Alkane
hex = Alkane(6)

hex.save("hexane.pdb", overwrite=True)

The previous command yields (converted to txt for attachment):

hexane.txt

But the following is expected (converted to txt for attachment):

hexane1.txt

Software versions

• Which version of mBuild are you using? 0.17.0
• Which version of Python (python --version)? 3.11.0
• Which operating system? Pop!_OS 22.04 LTS

[jpotoff]

Normally, we are using the PDB file in connection with the PSF file, which contains all of the connectivity information. To put connectivity information in a PDB file is, therefore, redundant.