Construct offpele's molecule from SMILES

[martimunicoy]

We can construct molecules from SMILES tags. This method would ease the automatization workflows that employ offpele. For this purpose, we need three main features:

• Build RDKit's molecule from smiles using the method Chem.MolFromSmiles.
• New function to automatically assign atom names to the molecule (as we no longer will feed from a PDB file).
• A function to write the new molecule to a PDB file for PELE (PELE will still need a PDB file with the correct conformation and atom names assigned).