remake_cpouts.py

#!/usr/bin/env python

" This program will deconvolute pH REM cpout files into pH-based cpout files "

import re, os, sys
from optparse import OptionParser

class CpoutError(Exception):
   """ Raised for an error reading/parsing CPOUT file """

#-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-

class RemCpout(object):
   """ cpout file from REM """

   #======================================================

   def __init__(self, fil):
      if type(fil).__name__ != 'file':
         raise TypeError('RemCpout: expected file type!')
      self.file = fil

   #======================================================

   def get_next_record(self):
      """ Gets the next record in this cpout file """
      lines = []
      line = self.file.readline()
      # Hit EOF
      if not line: return
      while line.strip():
         lines.append(line.strip())
         line = self.file.readline()
      return TitrationRecord(lines)

#-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-

class TitrationRecord(object):
   """ A Titration Record from Cpout file """

   full_re = re.compile(r'Solvent pH: *([+-]?\d+\.\d+)')
   rec_re = re.compile(r'Residue *(\d+) State: *(\d+) pH: *([+-]?\d+\.\d+)')
   ph_rec = re.compile(r' *pH: *[+-]?\d+\.\d+')

   #======================================================

   def __init__(self, lines):
      self.lines = lines
      fullmatch = self.full_re.match(lines[0])
      if fullmatch:
         self.full = True
         self.pH = float(fullmatch.groups()[0])
      else:
         self.full = False
         recmatch = self.rec_re.match(lines[0])
         if not recmatch:
            raise CpoutError('Did not find expected line in cpout record!')
         self.pH = float(recmatch.groups()[2])

   #======================================================

   def write_to(self, outfile):
      """ Writes this record somewhere """
      if self.full:
         outfile.write(os.linesep.join(self.lines[:4]))
         outfile.write(os.linesep)
         outfile.write(os.linesep.join([self.ph_rec.sub('',l) for l in self.lines[4:]]))
         outfile.write(os.linesep)
         outfile.write(os.linesep)
         return
      outfile.write(os.linesep.join([self.ph_rec.sub('',l) for l in self.lines]))
      outfile.write(os.linesep)
      outfile.write(os.linesep)

#-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-

def main():
   usage = '%prog [Options] cpout1 cpout2 cpout3 ... cpoutN'
   parser = OptionParser(usage=usage)
   parser.add_option('-p', '--prefix', dest='prefix', default=None,
                     help='Prefix of output cpout files. Output cpout files '
                     'are named <prefix>.pH_<pH>')
   opt, arg = parser.parse_args()

   try:
      cpout_list = [RemCpout(open(f, 'r')) for f in arg]
   except IOError:
      print 'Could not find file %s' % f
      sys.exit(1)

   if not opt.prefix:
      print 'Need a file prefix'
      parser.print_help()
      sys.exit(1)

   records = [cpout.get_next_record() for cpout in cpout_list]

   pH_list = [rec.pH for rec in records]

   files = {}
   for pH in pH_list:
      files[pH] = open(opt.prefix + '.pH_%.2f' % pH, 'w')

   while records[0]:
      for rec in records:
         if rec: rec.write_to(files[rec.pH])
      records = [cpout.get_next_record() for cpout in cpout_list]

   print 'Done!'


if __name__ == '__main__':
   import time
   start = time.time()
   main()
   print 'Took: %.1f sec' % ((time.time() - start))