Towards #2468 (RDKit interoperability GSOC project)

* Overview of work done in PR

  This PR adds the `RDKitConverter` class which converts MDAnalysis
  `Universe`/`Atomgroup` objects to `RDKit rdchem.Mol` objects.

* Limitations
  - Bonds and elements must be present (the former will be inferred if not
    present).
  - This converter mainly aims at supporting cases where explicit hydrogens
    are present.

* Extra implementation details
  - Bond order and formal charges are inferred via atomic valencies & the
    number of unpaired electrons (see `_infer_bo_and_charges`).
  - In part due to the influence of atom read order on inferring, bond
    conjugation and functional groups are standardized using SMARTS
    reactions (see `_standardize_patterns`).

*  Other changes

   Also includes some PEP8 changes and some cleaning up of the tests for the
   `RDKITReader`.

* References
  For more information on the development process for this PR, see:
  1) https://cbouy.github.io/blog/2020/07/01/rdkit-converter
  2) https://cbouy.github.io/blog/2020/07/22/rdkit-converter-part2

package/CHANGELOG

@@ -79,6 +79,8 @@ Enhancements
   * Added new kwargs `select_remove` and `select_protein` to
     analysis.dihedrals.Janin analysis to give user more fine grained control
     over selections (PR #2899)
+  * Added an RDKit converter that works for any input with all hydrogens
+    explicit in the topology (Issue #2468, PR #2775)
 
 Changes
   * deprecated NumPy type aliases have been replaced with their actual types

package/doc/sphinx/source/conf.py

@@ -346,4 +346,5 @@
                        'https://gsd.readthedocs.io/en/stable/': None,
                        'https://parmed.github.io/ParmEd/html/': None,
                        'https://docs.h5py.org/en/stable': None,
+                       'https://www.rdkit.org/docs/': None,
                        }

package/doc/sphinx/source/documentation_pages/converters.rst

@@ -33,4 +33,5 @@ you will have to specify a package name (case-insensitive). ::
    :maxdepth: 1
 
    converters/ParmEdParser
+   converters/RDKitParser
 

package/doc/sphinx/source/documentation_pages/converters/RDKitParser.rst

@@ -0,0 +1,3 @@
+.. automodule:: MDAnalysis.topology.RDKitParser
+
+.. automodule:: MDAnalysis.coordinates.RDKit

package/doc/sphinx/source/documentation_pages/topology_modules.rst

@@ -43,7 +43,6 @@ topology file format in the *topology_format* keyword argument to
    topology/PDBQTParser
    topology/PQRParser
    topology/PSFParser
-   topology/RDKitParser
    topology/TOPParser
    topology/TPRParser
    topology/TXYZParser