text: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  #
  # Copyright 2018 João Pedro Rodrigues, 2020 Johannes Hörmann
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #    http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  """
  Give every atom its own residue id, starting from -<number> (default 1).
  
  Restarts numbering every 9999 residues, thus allows for residue number > 99999.
  
  Numbering always restarts at 0, no matter the actual value of <number>.
  Usage:
      python pdb_reres_by_atom_9999.py -<number> <pdb file>
  
  Example:
      python pdb_reres_by_atom_9999.py -10 1CTF.pdb  # renumbers from 10
      python pdb_reres_by_atom_9999.py --1 1CTF.pdb  # renumbers from -1
  
  This program is part of the `pdb-tools` suite of utilities and should not be
  distributed isolatedly. The `pdb-tools` were created to quickly manipulate PDB
  files using the terminal, and can be used sequentially, with one tool streaming
  data to another. They are based on old FORTRAN77 code that was taking too much
  effort to maintain and compile. RIP.
  """
  
  import os
  import sys
  
  __author__ = "Joao Rodrigues"
  __email__ = "j.p.g.l.m.rodrigues@gmail.com"
  
  
  def check_input(args):
      """Checks whether to read from stdin/file and validates user input/options.
      """
  
      # Defaults
      option = 1
      fh = sys.stdin  # file handle
  
      if not len(args):
          # Reading from pipe with default option
          if sys.stdin.isatty():
              sys.stderr.write(__doc__)
              sys.exit(1)
  
      elif len(args) == 1:
          # One of two options: option & Pipe OR file & default option
          if args[0].startswith('-'):
              option = args[0][1:]
              if sys.stdin.isatty():  # ensure the PDB data is streamed in
                  emsg = 'ERROR!! No data to process!\n'
                  sys.stderr.write(emsg)
                  sys.stderr.write(__doc__)
                  sys.exit(1)
  
          else:
              if not os.path.isfile(args[0]):
                  emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
                  sys.stderr.write(emsg.format(args[0]))
                  sys.stderr.write(__doc__)
              sys.exit(1)
  
              fh = open(args[0], 'r')
  
      elif len(args) == 2:
          # Two options: option & File
          if not args[0].startswith('-'):
              emsg = 'ERROR! First argument is not an option: \'{}\'\n'
              sys.stderr.write(emsg.format(args[0]))
              sys.stderr.write(__doc__)
              sys.exit(1)
  
          if not os.path.isfile(args[1]):
              emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
              sys.stderr.write(emsg.format(args[1]))
              sys.stderr.write(__doc__)
              sys.exit(1)
  
          option = args[0][1:]
          fh = open(args[1], 'r')
  
      else:  # Whatever ...
          sys.stderr.write(__doc__)
          sys.exit(1)
  
      # Validate option
      try:
          option = int(option)
      except ValueError:
          emsg = 'ERROR!! You provided an invalid residue number: \'{}\''
          sys.stderr.write(emsg.format(option))
          sys.exit(1)
  
      return (option, fh)
  
  
  def pad_line(line):
      """Helper function to pad line to 80 characters in case it is shorter"""
      size_of_line = len(line)
      if size_of_line < 80:
          padding = 80 - size_of_line + 1
          line = line.strip('\n') + ' ' * padding + '\n'
      return line[:81]  # 80 + newline character
  
  
  def renumber_residues(fhandle, starting_resid):
      """Resets the residue number column to start from a specific number.
      """
      _pad_line = pad_line
      resid = starting_resid - 1  # account for first residue
      records = ('ATOM', 'HETATM', 'TER', 'ANISOU')
      warned = False
      for line in fhandle:
          line = _pad_line(line)
          if line.startswith('MODEL'):
              resid = starting_resid - 1  # account for first residue
              yield line
  
          elif line.startswith(records):
              resid += 1
              if resid > 9999 and not warned:
                  emsg = 'WARNING: residue number above 9999, starting from 0 again.\n'
                  sys.stderr.write(emsg)
                  warned = True
  
              yield line[:22] + str(resid % 10000).rjust(4) + line[26:]
  
          else:
              yield line
  
  
  def main():
      # Check Input
      starting_resid, pdbfh = check_input(sys.argv[1:])
  
      # Do the job
      new_pdb = renumber_residues(pdbfh, starting_resid)
  
      # Output results
      try:
          _buffer = []
          _buffer_size = 5000  # write N lines at a time
          for lineno, line in enumerate(new_pdb):
              if not (lineno % _buffer_size):
                  sys.stdout.write(''.join(_buffer))
                  _buffer = []
              _buffer.append(line)
  
          sys.stdout.write(''.join(_buffer))
          sys.stdout.flush()
      except IOError:
          # This is here to catch Broken Pipes
          # for example to use 'head' or 'tail' without
          # the error message showing up
          pass
  
      # last line of the script
      # Close file handle even if it is sys.stdin, no problem here.
      pdbfh.close()
      sys.exit(0)
  
  
  if __name__ == '__main__':
      main()
  