Better support for interactions with DNA

[cbouy]

The "residue" letter codes for DNA is slightly different to the convention used for proteins: it uses 2-letter codes instead of 3. While this isn't a problem for creating prolif.Molecule objects and generating a fingerprint, it might cause some issues when indexing the molecule to look for a particular residue, as shown below:

>>> import prolif as plf
>>> import MDAnalysis as mda
>>> u = mda.Universe("polyAT_vac.prmtop")
>>> dmol = plf.Molecule.from_mda(u)
>>> dmol.residues.name
array(['DA5', 'DA', 'DA', 'DA', 'DA', 'DA', 'DA', 'DA', 'DA', 'DA3',
       'DT5', 'DT', 'DT', 'DT', 'DT', 'DT', 'DT', 'DT', 'DT', 'DT3'],
      dtype=object)
>>> dmol.residues.number
array([ 1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17,
       18, 19, 20], dtype=uint16)
>>> dmol["DA2"]
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-33-840ade3ef100> in <module>
----> 1 dmol["DA2"]

~/projects/ProLIF/prolif/molecule.py in __getitem__(self, key)
    118 
    119     def __getitem__(self, key):
--> 120         return self.residues[key]
    121 
    122     def __repr__(self): # pragma: no cover

~/projects/ProLIF/prolif/residue.py in __getitem__(self, key)
    181         elif isinstance(key, str):
    182             key = ResidueId.from_string(key)
--> 183             return self.data[key]
    184         elif isinstance(key, ResidueId):
    185             return self.data[key]

KeyError: .D

The problem comes from the ResidueId.from_string method which converts DA2 to ResidueId(name=None, number=None, chain="D")

You can still index the molecule correctly by using a ResidueId directly instead of a string: dmol[plf.ResidueId("DA", 2)]. It's less user friendly but also less error prone, since some residue names actually contain numbers like DA5 which correspond to the first residue.

PS: prmtop file from the Amber tutorials

[cbouy]

Just a code snippet for DNA-DNA interactions: