Identify copies of same ligand (OOP refactor)

[jaimergp]

Compare topologies of identifies ligand to match those that are the same in different positions. Each copy should have a different molecule.name but identical residue.type.

• molecule.basename (derived from molecule.name) is used to identify copies of the same ligand, because is the part used for *.pdb (coordinates source).
• residue.type is used to identify the residue type in terms of parameters. It's not clear if we need one mol2/frcmod for each pdb or one for each type (have to look it up), but if needed, it is just a matter of copying them with the appropriate names (molecule.basename). The contents would still list the same residue.type.

Since this is getting messy, a small OOP refactor will be needed.

[jaimergp]

Tentative tasklist (to be copied over to the PR(s) when available)

• [ ] Design a OOP interface which differentiates between metals, residues, and protein(s). Each component of the MCPB.py puzzle should be a separate object. Decide if it's better to have individual objects (Metal, Residue, Protein) to be merged by residue type or collective objects with an attribute for the different copies. The classes should have the needed stuff to generate the files for each component. My first impression is that we should have an object for each residue type, that handles the needed copies.
• [ ] Topological comparisons to identify copies of the same ligand.