add kwarg strip_icodes to parsePDB parsePQR

[jamesmkrieger]

This enables us to have non-stripped icodes, so they can be used for selections. The default is True to maintain the old behaviour.

This should help with the problem found in #2100

In [1]: from prody import *

In [2]: ag = parsePDB('1ucy', compressed=False)
@> PDB file is found in working directory (1ucy.pdb).
@> 8165 atoms and 1 coordinate set(s) were parsed in 0.07s.

In [3]: ag.select('chain L and resnum 14').getIcodes()
Out[3]: 
array(['', '', '', '', '', '', '', '', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
       'A', 'A', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'C', 'C', 'C', 'C',
       'C', 'C', 'C', 'C', 'C', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
       'D', 'E', 'E', 'E', 'E', 'E', 'E', 'E', 'E', 'E', 'F', 'F', 'F',
       'F', 'F', 'F', 'F', 'F', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G',
       'G', 'G', 'G', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'I',
       'I', 'I', 'I', 'I', 'I', 'J', 'J', 'J', 'J', 'J', 'J', 'J', 'J',
       'J', 'J', 'J', 'J', 'K', 'K', 'K', 'K', 'K', 'K', 'K', 'K', 'L',
       'L', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'M', 'M', 'M', 'M'],
      dtype='<U1')

In [4]: ag.select('chain L and resnum 14 and icode " "')

In [5]: ag = parsePDB('1ucy', compressed=False, strip_icodes=False)
@> PDB file is found in working directory (1ucy.pdb).
@> 8165 atoms and 1 coordinate set(s) were parsed in 0.06s.

In [6]: ag.select('chain L and resnum 14').getIcodes()
Out[6]: 
array([' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', 'A', 'A', 'A', 'A', 'A',
       'A', 'A', 'A', 'A', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'C', 'C',
       'C', 'C', 'C', 'C', 'C', 'C', 'C', 'D', 'D', 'D', 'D', 'D', 'D',
       'D', 'D', 'D', 'E', 'E', 'E', 'E', 'E', 'E', 'E', 'E', 'E', 'F',
       'F', 'F', 'F', 'F', 'F', 'F', 'F', 'G', 'G', 'G', 'G', 'G', 'G',
       'G', 'G', 'G', 'G', 'G', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H',
       'H', 'I', 'I', 'I', 'I', 'I', 'I', 'J', 'J', 'J', 'J', 'J', 'J',
       'J', 'J', 'J', 'J', 'J', 'J', 'K', 'K', 'K', 'K', 'K', 'K', 'K',
       'K', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'L', 'M', 'M', 'M',
       'M'], dtype='<U1')

In [7]: ag.select('chain L and resnum 14 and icode " "')
Out[7]: <Selection: 'chain L and res...4 and icode " "' from 1ucy (8 atoms)>