#!/usr/bin/env python
#
# * This library is free software; you can redistribute it and/or
# * modify it under the terms of the GNU Lesser General Public
# * License as published by the Free Software Foundation; either
# * version 2.1 of the License, or (at your option) any later version.
# *
# * This library is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# * Lesser General Public License for more details.
#

#propka3.0, revision 182                                                                      2011-08-09
#-------------------------------------------------------------------------------------------------------
#--                                                                                                   --
#--                                   PROPKA: A PROTEIN PKA PREDICTOR                                 --
#--                                                                                                   --
#--                              VERSION 3.0,  01/01/2011, COPENHAGEN                                 --
#--                              BY MATS H.M. OLSSON AND CHRESTEN R. SONDERGARD                       --
#--                                                                                                   --
#-------------------------------------------------------------------------------------------------------
#
#
#-------------------------------------------------------------------------------------------------------
# References:
#
#   Very Fast Empirical Prediction and Rationalization of Protein pKa Values
#   Hui Li, Andrew D. Robertson and Jan H. Jensen
#   PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005)
#
#   Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes
#   Delphine C. Bas, David M. Rogers and Jan H. Jensen
#   PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)
#
#   PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions
#   Mats H.M. Olsson, Chresten R. Sondergard, Michal Rostkowski, and Jan H. Jensen
#   Journal of Chemical Theory and Computation, 7, 525-537 (2011)
#-------------------------------------------------------------------------------------------------------

import string, re, sys, os, math

import Source.lib as lib
from Source.protein import Protein
 


def main():
    """
    Simple main that creates the proteins, protonates them, and prints new pdb files with hydrogen atoms
    """

    # loading options, flaggs and arguments
    options, pdbfiles = lib.loadOptions()

    for pdbfile in pdbfiles:

      # creating protein object
      myProtein = Protein(pdbfile=pdbfile, options=options)
      filename = "%s_new.pdb" % (myProtein.name)
      myProtein.writePDB(filename=filename, hydrogens=True)


if __name__ == '__main__': main()

