text: # BSD 3-Clause License
  #
  # Copyright (c) 2016-21, University of Liverpool
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  #
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  # modification, are permitted provided that the following conditions are met:
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  # * Redistributions of source code must retain the above copyright notice, this
  #   list of conditions and the following disclaimer.
  #
  # * Redistributions in binary form must reproduce the above copyright notice,
  #   this list of conditions and the following disclaimer in the documentation
  #   and/or other materials provided with the distribution.
  #
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  #   contributors may be used to endorse or promote products derived from
  #   this software without specific prior written permission.
  #
  # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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  """
  Parser module specific to FreeContact predictions
  """
  
  __author__ = "Felix Simkovic"
  __date__ = "12 Oct 2016"
  __version__ = "0.1"
  
  import re
  
  from conkit.io._parser import ContactFileParser
  from conkit.core.contact import Contact
  from conkit.core.contactmap import ContactMap
  from conkit.core.contactfile import ContactFile
  
  RE_SPLIT = re.compile(r"\s+")
  
  
  class FreeContactParser(ContactFileParser):
      """Class to parse a FreeContact contact file
      """
  
      def __init__(self):
          super(FreeContactParser, self).__init__()
  
      def read(self, f_handle, f_id="freecontact"):
          """Read a contact file
  
          Parameters
          ----------
          f_handle
             Open file handle [read permissions]
          f_id : str, optional
             Unique contact file identifier
  
          Returns
          -------
          :obj:`~conkit.core.contactfile.ContactFile`
  
          """
          hierarchy = ContactFile(f_id)
          contact_map = ContactMap("map_1")
          hierarchy.add(contact_map)
          for line in f_handle:
              line = line.strip()
              if line:
                  res1_seq, res1, res2_seq, res2, raw_score, _ = RE_SPLIT.split(line)
                  contact = Contact(int(res1_seq), int(res2_seq), float(raw_score))
                  contact.res1 = res1
                  contact.res2 = res2
                  contact_map.add(contact)
          hierarchy.method = "Contact map predicted using FreeContact"
          return hierarchy
  
      def write(self, f_handle, hierarchy):
          """Write a contact file instance to to file
  
          Parameters
          ----------
          f_handle
             Open file handle [write permissions]
          hierarchy : :obj:`~conkit.core.contactfile.ContactFile`, :obj:`~conkit.core.contactmap.ContactMap`
                      or :obj:`~conkit.core.contact.Contact`
  
          Raises
          ------
          :exc:`RuntimeError`
             More than one contact map in the hierarchy
  
          """
          contact_file = self._reconstruct(hierarchy)
          if len(contact_file) > 1:
              raise RuntimeError("More than one contact map provided")
          content = ""
          for contact_map in contact_file:
              for contact in contact_map:
                  line = "{res1_seq} {res1} {res2_seq} {res2} {raw_score} 0\n"
                  line = line.format(
                      res1_seq=contact.res1_seq,
                      res2_seq=contact.res2_seq,
                      res1=contact.res1,
                      res2=contact.res2,
                      raw_score=contact.raw_score,
                  )
                  content += line
          f_handle.write(content)
  