add javadocs

[uli-f]

Overall, the javadoc documentation is helpful and sufficient.

I went over all classes and had a look at the javadocs. I added/amended bits and pieces myself.

There are a few javadocs that might benefit from your knowledge of the codebase and the rinchi library:

• [x] RinchiFlag // class // just a sentence what forceEquilibrium does
• [x] ReactionFileFormat // class // in particular: what exactly happens if AUTO is chosen?
• [x] MoleculeUtils // class and all public static methods // please briefly explain what the calculations in getExplicitAtomValencies and setImplicitHydrogenAtoms are based on (e.g., 'Explicit atom valencies are inferred from the bonds and their orders connected to an atom.')
• [x] StereoUtils // class and public methods // some of the methods that are currently public might be changed to private...? If the private methods are not trivial a concise javadoc might still be beneficial as this is one of the more complex parts of the code

[uli-f]

Probably best to merge PR #3 before working on this, as I have already done quite a bit.

[ntk73]

I will see for these javadocs improvements. And yes, after merging your latest pull request.

[ntk73]

Javadocs are ready

[uli-f]

Looks good to me 👍🏼