Improve functions to call PELE's minimization

[martimunicoy]

There are several improvements and bug-fixes that we need to solve on the functions and classes that call PELE's minimization.

[martimunicoy]

Improvements list:

• [x] Replace bash commands by functions from Python libraries (such as os.makedirs() in MoleculeMinimized.py)
• [ ] Skip hardcoded paths to files such in here, use instead relative paths to local files found in the repository.
• [x] Use the offpele's API to parameterize molecules, instead of the main.py such in here
• [ ] Consider handling paths with pathlib's Path class

[martimunicoy]

Regarding the use of offpele's API, below is an example of how to use it:

from offpele.topology import Molecule
from offpele.template import Impact
from offpele.solvent import OBC2

# Create representation of a particular molecule
molecule = Molecule(path_to_pdb_file)

# Generate its rotamer library
rotamer_library = offpele.topology.RotamerLibrary(molecule)
rotamer_library.to_file(rotamer_library_output_path)

# Generate its parameters and template file
molecule.parameterize(forcefield, charges_method=charges_method)
impact = Impact(molecule)
impact.write(impact_output_path)

# Generate its solvent parameters
solvent = OBC2(molecule)
solvent.to_json_file(solvent_output_path)

Besides, the DataLocal's output hierarchy can be constructed through the function handle_output_paths() from main.py

[laumalo]

The following PDB files: benzene.pdb and toluene.pdb present the following error when computing the PELE's minimization.

what(): /!\ Error in MacroBuilder::createMacro: /!\ Error in ImpactTemplateReader::processRESXLine: Incorrect RESX line (wrong format) in file benz!!!! And the same error for tolz.