Fix issue #330

[lohedges]

This PR closes #330 by preserving SMILES based molecule properties when parameterising. Previously, BioSimSpace.Convert.smiles was only used to create an intermediate molecule during parameterisation, so any properties that were generated at this point were not part of the returned molecule. This PR fixes this by adding them to the molecule, hence preserving attributes that are required for stereochemistry.

• 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:

@mb2055

[lohedges]

Looks like this doesn't completely fix #330, rather the specific case of SMILES input. Note that the test that fails is passing locally. Will investigate further.

[lohedges]

Okay, it works locally using the same environment as for the CI. The test involves generating a mapping with RDKit, so I had assumed that this had changed between versions. (It doesn't specify a conformer to use.) If it had failed on a single platform I would have put it down to bad luck, but here it's failed on all of them. (The test is skipped on Windows.)

[lohedges]

Hmm, it seems to fail when all of the tests are run in one go, not individually. This would suggest some possible file caching issue, but the fixtures for this particular test are unique

[lohedges]

It's definitely this PR that makes the test fail, but I can't see what is causing it. (The test passes in isolation, or even when run as part of the subset of the tests.) I feel like there is probably another bug that was masked somehow. Will keep digging.