Fix issue #148

[lohedges]

This PR closes #148 and closes michellab/BioSimSpace#427. The code has been updated to correctly update the water topology to match the GROMACS naming convention in both the Gro87 and GroTop files. Since a user may wish to preserve a particular naming convention, e.g. for crystal waters, I've added an option to disable the topology swap if desired, e.g. if they are just writing to file. A few optimisations have been added following the addition of this parameter, since it means that we can avoid double checking the topology in cases where we know that it has already been swapped, e.g. during the setup of a simulation with a particular engine.

I've not resolved the issue of the Gro87 file being parsed incorrectly. I'm not sure what we can do about this (in a general way, at least) since the file is valid (doesn't trip the existing error handling), but is formatted incorrectly.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@chryswoods

[lohedges]

It looks like the match_water option won't work correctly for the case of writing to GroTop format when different naming schemes are used for the same water topology within a system, e.g. if you have some crystal waters along with regular waters. The GroTop parser deduplicates the molecule types, so you'll only end up with a single type in the top file.

[lohedges]

This has been consumed into a larger crystal water related feature that I'm working on so I'll close this when I submit that PR. I'll still pull out the specific fix implemented here for a backport, i.e. forgetting to update the water topology for Gro87 format on write.

[chryswoods]

👍