FEAT: Introduce new IParticle classes and refactor of GromacsFragment

[flongford]

This PR takes further steps towards introducing generic chemical objects described in #26 , following on from #27. We now introduce several interface / base classes that can be used as a general representation of a single or collection of particles:

• IParticle: an interface for a single particle object
• IParticleGroup: an interface for a collection of particles, inherits from IParticle so that we can describe a collection of particles as a reduced representation
• BaseParticleGroup: a base class that fulfils the fulfilling the IParticleGroup interface.

Consequently, the following refactoring has taken place:

• IFragment has been refactored to inherit from IParticleGroup
• New GromacsParticle class provides interface to IParticle
• GromacsFragment class now inherits from BaseParticleGroup and represents a collection of GromacsParticles
• Loading of file data into a GromacsFragment now happens upon instantiation, rather than during assignment of the topology attribute
• GromacsTopologyReader has been renamed GromacsMoleculeReader (since technically .itp files are known as 'molecule' files), and now returns a list of GromacsFragments instances from the read method.

Additional changes include

• BaseFileReader class now has _comment attribute, and _remove_comments methods, since these objects are shared between multiple subclasses
• Inclusion of example GROMACS files in force_gromacs/tests/fixtures directory, which can now be used for unit testing
• Added documentation for force_gromacs.chemicals module

[codecov[bot]]

Codecov Report

Merging #30 into master will increase coverage by <.01%. The diff coverage is 98.76%.

@@            Coverage Diff             @@
##           master      #30      +/-   ##
==========================================
+ Coverage    98.7%   98.71%   +<.01%     
==========================================
  Files          65       72       +7     
  Lines        2170     2249      +79     
  Branches      138      158      +20     
==========================================
+ Hits         2142     2220      +78     
- Misses         16       17       +1     
  Partials       12       12

Impacted Files	Coverage Δ
force_gromacs/io/gromacs_coordinate_reader.py	95.08% <100%> (+0.16%)	:arrow_up:
...ources/molecule/tests/test_molecule_data_source.py	100% <100%> (ø)	:arrow_up:
force_gromacs/chemicals/tests/test_molecule.py	100% <100%> (ø)	:arrow_up:
force_gromacs/chemicals/gromacs_particle.py	100% <100%> (ø)
...ources/fragment/tests/test_fragment_data_source.py	100% <100%> (ø)	:arrow_up:
...macs/data_sources/fragment/fragment_data_source.py	100% <100%> (ø)	:arrow_up:
force_gromacs/chemicals/i_particle.py	100% <100%> (ø)
...macs/data_sources/molecule/molecule_data_source.py	100% <100%> (ø)	:arrow_up:
...e_gromacs/io/tests/test_gromacs_topology_writer.py	100% <100%> (ø)	:arrow_up:
...ation_builders/tests/test_gromacs_topology_data.py	100% <100%> (ø)	:arrow_up:
... and 24 more

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