Add function to set atom coordinates of entire system.

[lohedges]

This PR adds a function to set the coordinates of all atoms in the system, which will be wrapped by BioSimSpace.

• 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 added a test for any new functionality in this pull request: [y]
• I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

[lohedges]

Apologies for the large diff. It looks like these wrappers haven't been rebuilt for a while.

[lohedges]

I also realise that I've forgotten to add handling for perturbable molecules. Will add this before review.