X as a Dummy atom/Input.py

[jacquelinzak]

Currently X is defined as a dummy atom in atoms.py, but in different software such as macromodel, you have the ability to add in your own custom atom.types and define it as Du (or have a section for custom atom types to be defined especially for validation of custom forcefields like Q2MM)

Lastly, the capability in makeinput.py to find and delete a dummy atom would be beneficial

[ajs99778]

I've added the ability to define dummy atom types in the config file. It looks like the config documentation has disappeared from the docs, but in $AARONLIB/config.ini you can put

[AtomTypes]
dummy = X Du

to define both X and Du as dummy types.

As for finding and deleting dummy atoms, I think we'd prefer to keep that sort of thing in the findAtoms.py script rather than makeInput.py. I've changed findAtoms.py to be able to print an XYZ file for the atoms it found. You should be able to do

findAtoms.py your_structure.xyz --dummy --invert -xyz

You could either save the XYZ file or pipe it into makeInput.py directly. If that doesn't fit with your workflow, let us know.