Check atom names in BSS generated pert files about biosimspace HOT 3 CLOSED

This is what will be done by BioSimSpace when writing the pert file and AMBER prm/rst files as part of the SOMD free energy protocol. I plan on making a copy of the user input molecule, then applying my pert file writer (which has to rename the atoms in order to make them unique). You can look at the _toPertFile method in BioSimSpace/python/_SireWrappers/_molecue.py to see how the renaming works.

I'll leave this issue as a reminder and close when the pert file / free energy protocol is fully implemented.

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On a related note, check also def make_pert_file in
https://github.com/CCPBioSim/fesetup/blob/dev/mutate/topol/pertfile.py

I don't know how BSS merge molecules handle this, but there was some complicated logic in FESetup to make sure that dihedrals and impropers were correctly written in the pert file. The issue is that the same dihedral or improper may be defined with different atom indices in the respective end-states, and care must be taken to avoid accidentally duplicating forcefield terms.

There are also some rules around the values of bond/angles or dihedral/impropers for terms involving dummy atoms that could be controlled with keyword arguments.

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I believe I handle this correctly in both the Gromacs and pert file writer. Since all of the terms are stored as Sire objects, with corresponding BondIDs, AngleIDs, and DihedralDs, it's easy to check for matching terms in the end-states, e.g. by checking the the ID and its mirror.

I'll take a look through the FESetup logic to see if I'm missing anything. For the Gromacs writer, I believe that my procedure is consistent with everything from the latest manual.

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