Fix issue #194

[lohedges]

This PR closes #194 by skipping BioSimSpace position restraint include directives when parsing GROMACS topology files. I'm not sure if there is a more general way of fixing this issue, but this will work for the purposes of being able to read GROMACS files that were written as input to a BioSimSpac.Process.Gromacs simulation using position restraints. Here the restraints will be ignored, but they would be re-written if the user wanted to run the same protocol. In this instance, they just want to be able to read the system back in, i.e. the topology.

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Suggested reviewers:

@chryswoods

[chryswoods]

Are these restraints used only by BioSimSpace? If so, then I am happy to approve. Just want to check that we aren't ignoring something that another program would expect us to read.

[lohedges]

This is the standard way of adding position restraints in GROMACS topology files, so similar directives might be present in other files too (which would also cause the parser to fail). Here I've explicitly skipped the records when the exact BioSimSpace naming convention is found, but I could also update that to be more unique, e.g. include bss in the string.

Another solution would be adding support for parsing these records, but I'm not sure how useful that would be.

[chryswoods]

Ok - we can use this skip for now, while I think about how to add support for parsing the record. It may be useful to have these as extra properties of the molecule or system.