Fix issue #347

[lohedges]

This PR closes #347 by allowing the Antechamber acdoctor mode to be disabled via a kwarg when using BioSimSpace.Parameters.gaff/gaff2, or via BioSimSpace.Parameters.parameterise.

I'll re-trigger the CI once the Sire development packages have finished building.

@noahharrison64: Tagging you in so that you can test.

• 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]

[noahharrison64]

Testing on my side looks good: can confirm this branch allows the successful parsing of acdoctor = False as a keyword arg to the gaff2 parameterisation function. Doing so sets -dr no in the antechamber command and allows for parameterisation of molecules with unusual valences that antechamber may not be set up to handle (negatively charged nitrogens in my use case)

Thanks @lohedges