Source Code for Module file_ops

  1  from os import mkdir, chmod 
  2  from re import match 
  3  from string import split 
  4  import sys 
  5   
  6 -class file_ops: 
  7 -        def __init__(self, mf): 
  8                  "Class containing the file operations" 
  9   
 10                  self.mf = mf 
 11   
 12   
 13 -        def close_mf_files(self, dir): 
 14                  "Close the mfin, mfdata, mfmodel, mfpar, and run files, and make the run file executable." 
 15   
 16                  self.mf.mfin.close() 
 17                  self.mf.mfdata.close() 
 18                  self.mf.mfmodel.close() 
 19                  self.mf.mfpar.close() 
 20                  self.mf.run.close() 
 21                  chmod(dir + '/run', 0777) 
 22                   
 23           
 24 -        def init_log_file(self, title): 
 25                  "Initialize the log file." 
 26                   
 27                  self.mf.log = open('log.stage' + self.mf.data.stage, 'w') 
 28                  self.mf.log.write(title) 
 29   
 30   
 31 -        def open_file(self, file_name): 
 32                  "Open the file 'file' and return all the data." 
 33                   
 34                  file = open(file_name, 'r') 
 35                  lines = file.readlines() 
 36                  data = [] 
 37                  i = 0 
 38                  for line in lines: 
 39                          if i != 0: 
 40                                  j = i - 1 
 41                                  row = split(line) 
 42                                  data.append([]) 
 43                                  data[j].append(row[0]) 
 44                                  data[j].append(row[1]) 
 45                                  for k in range(len(row)): 
 46                                          if k > 1: 
 47                                                  data[j].append(float(row[k])) 
 48                          i = i + 1 
 49                  return data 
 50   
 51   
 52 -        def open_input(self): 
 53                  "Open the input file." 
 54   
 55                  try: 
 56                          open("input", 'r') 
 57                  except IOError: 
 58                          print "Input file \"input\" does not exist, quitting script!\n" 
 59                          sys.exit() 
 60                  input = open("input", 'r') 
 61                  return input 
 62   
 63   
 64 -        def mkdir(self, dir): 
 65                  "Create the given directory, or exit if the directory exists." 
 66   
 67                  self.mf.log.write("Making directory " + dir + "\n") 
 68                  try: 
 69                          mkdir(dir) 
 70                  except OSError: 
 71                          print "Directory ./" + dir + " already exists, quitting script.\n" 
 72                          sys.exit() 
 73   
 74   
 75 -        def open_mf_files(self, dir): 
 76                  "Open the mfin, mfdata, mfmodel, mfpar, and run files for writing." 
 77   
 78                  self.mf.mfin = open(dir + '/mfin', 'w') 
 79                  self.mf.mfdata = open(dir + '/mfdata', 'w') 
 80                  self.mf.mfmodel = open(dir + '/mfmodel', 'w') 
 81                  self.mf.mfpar = open(dir + '/mfpar', 'w') 
 82                  self.mf.run = open(dir + '/run', 'w') 
 83           
 84           
 85 -        def read_file(self, file_name): 
 86                  "Attempt to read the file, or quit the script if it does not exist." 
 87   
 88                  try: 
 89                          open(file_name, 'r') 
 90                  except IOError: 
 91                          print "The file '" + file_name + "' does not exist, quitting script.\n\n" 
 92                          sys.exit() 
 93                  file = open(file_name, 'r') 
 94                  return file 
 95   
 96   
 97 -        def relax_data(self, file): 
 98                  """Open the relaxation data in the file 'file' and return all the data. 
 99                   
100                  It is assumed that the file has four columns separated by whitespace.  The columns should be: 
101                          0 - Residue numbers 
102                          1 - Residue names 
103                          2 - R1, R2, or NOE values 
104                          3 - The errors 
105                  """ 
106                   
107                  lines = open(file, 'r') 
108                  lines = lines.readlines() 
109                  data = [] 
110                  i = 0 
111                  for line in lines: 
112                          if i != 0: 
113                                  j = i - 1 
114                                  row = split(line) 
115                                  data.append([]) 
116                                  data[j].append(row[0]) 
117                                  data[j].append(row[1]) 
118                                  data[j].append(float(row[2])) 
119                                  data[j].append(float(row[3])) 
120                          i = i + 1 
121                  return data 
122