pHs are not pKas

[sobolevnrm]

The --ph-calc-method option is incorrect. It should be --pka-calc-method. I've attached a main.py that may fix some of this (at least the problems with the option name and description).

Here's a fixed description but it should be fixed elsewhere, too:

pka_group.add_option('--pka-calc-method', dest='pka_calc_method', metavar='PH_METHOD', choices=('propka', 'pdb2pka'),
                 help='Method used to calculate pKa values. If a pKa calculation method is selected, titratable residue pKa values will be calculated and the residue potentially modified after comparison with the pH value supplied by --with_ph\n'
                 'propka - Use PROPKA to calculate pKa values. Actual PROPKA results will be output to <output-path>.propka.\n'
                 'pdb2pka - Use PDB2PKA to calculate pKa values. Requires the use of the PARSE force field.'
                 'Warning: Larger residues can take a very long time to run using this method. EXPERIMENTAL!')

[kmonson]

Changes will need to be made to runPDB2PQR to make the keyword args consistent with the option name.

Both the OPAL and non OPAL code paths will need to be updated in main_cgi.py especially in the WebOptions class.

When the next release with this change we'll need to work with Nadya to setup testing on OPAL and make sure the OPAL stuff works correctly.

[sobolevnrm]

This was fixed a long time ago.