Fix issue #292

[lohedges]

This PR closes #292, i.e. fixes the issues caused by the previous RDKIt "fix". The issue here is that we must only disable implicit hydrogens when using the customised MDAnalysis inference routine. If used for a general conversion, the use of this option is inconsistent with what RDKit does, e.g. on SDF read, which leads to incorrect stereochemistry when applying the standard sanitization routines.

Additionally, I've switched to just calling the standard RDKit sanitization function since we were missing a few steps. Given all the issues, I want to be as self-consistent as possible. We can separate the stages in future if we find further problems, or provide options to use a sub-set of the routines if needed.

• 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 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]