Simplify Chemical System

[MBartkowiakSTFC]

Description of work
Most of the classes derived from ChemicalEntity were only used for a very specific case of a trajectory created by GROMACS with a PDB file describing the topology. Since MDANSE is moving to MDAnalysis for loading GROMACS trajectories, the selection mechanism based on fixed databases needs to be replaced with a more general solution. This is provided by rdkit and substructure matching. Since rdkit introduces its own indexing of atoms, not guaranteed to be consistent with the internal indexing of the ChemicalSystem class, changes are necessary to improve the consistency of the atom indexing.

Fixes

1. ChemicalEntity and all derived classes have been removed from the code.
2. The only database remaining in the Chemistry section is the atoms database.
3. Atom indexing is now fixed and matches the indexing in the coordinate array.
4. New ChemicalSystem implementation stores lists of indices.
5. ChemicalSystem does not have a "configuration" attribute anymore. Configuration is accessed only via the Trajectory class.
6. A backup ChemicalSystem loader allows the users to load old trajectories. The new ChemicalSystem instance will be created in memory and populated with information from the old /chemical_system data structure.
7. The trajectory stores a subset of the atom database, preserving the user-made changes to atom definitions and making trajectories portable even if they use artificial atoms.
8. Atom selection works for trajectories independent of the molecular dynamics engine used to run the simulation. However, it is necessary to detect bonds in the system using the TrajectoryEditor job before it is possible to select structures.
9. Most of the Cython extensions have been replaced with Python equivalents.

To test
All unit tests must pass.
A detailed comparison of the results between this and main branches is necessary due to the fundamental changes to the way the code operates.
Please run TrajectoryEditor with molecule detection on a trajectory and check if all the expected Atom Selection options are working correctly in the GUI.

Jobs that require the most attention:

• CenterOfMassTrajectory
• Voronoi
• SolventAccessibleSurface
• PairDistributionFunction
• VanHoveSelf
• VanHoveDistinct