extend watfinder to more water models and ions

[jamesmkrieger]

1. add resname SPC to water flag; otherwise it is not selected as water
2. add kwarg considered_atoms_sel to calcWaterBridges to be able to include ion etc instead of just protein
3. add resname SOL to water flag (not worth excluding as only 3 SOL ligands in PDB)
4. add CU2P and CU2 (trimmed to 3-char) to ion flag

[jamesmkrieger]

We now have selections working e.g.

In [1]: from prody import *

In [2]: ag = parsePDB('ionized2_swap.pdb', long_resname=True)
@> 461487 atoms and 1 coordinate set(s) were parsed in 5.64s.

In [3]: set(ag.ion.getResnames())
Out[3]: {'CLA', 'CU2P', 'SOD'}

In [4]: set(ag.ion.getNames())
Out[4]: {'CLA', 'CU2P', 'SOD'}

In [5]: set(ag.water.getResnames())
Out[5]: {'SOL'}

In [6]: set(ag.water.getNames())
Out[6]: {'HW1', 'HW2', 'OW'}

In [7]: ag = parsePDB('ionized2_swap.pdb')
@> 461487 atoms and 1 coordinate set(s) were parsed in 5.74s.

In [8]: set(ag.ion.getResnames())
Out[8]: {'CLA', 'CU2', 'SOD'}

In [9]: set(ag.water.getNames())
Out[9]: {'HW1', 'HW2', 'OW'}

In [10]: set(ag.ion.getNames())
Out[10]: {'CLA', 'CU2P', 'SOD'}