Source Code for Module bmrblib.misc

  1  ############################################################################# 
  2  #                                                                           # 
  3  # The BMRB library.                                                         # 
  4  #                                                                           # 
  5  # Copyright (C) 2009-2010 Edward d'Auvergne                                 # 
  6  #                                                                           # 
  7  # This program is free software: you can redistribute it and/or modify      # 
  8  # it under the terms of the GNU General Public License as published by      # 
  9  # the Free Software Foundation, either version 3 of the License, or         # 
 10  # (at your option) any later version.                                       # 
 11  #                                                                           # 
 12  # This program is distributed in the hope that it will be useful,           # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of            # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             # 
 15  # GNU General Public License for more details.                              # 
 16  #                                                                           # 
 17  # You should have received a copy of the GNU General Public License         # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.     # 
 19  #                                                                           # 
 20  ############################################################################# 
 21   
 22  # Module docstring. 
 23  """Functions for manipulating NMR-STAR dictionary data.""" 
 24   
 25  # Python module imports. 
 26  from numpy import ndarray 
 27  from warnings import warn 
 28   
 29   
 30 -def no_missing(data, name): 
 31      """Check that there are no None values in the data. 
 32   
 33      @param data:    The data to check. 
 34      @type data:     anything 
 35      @param name:    The name associated with the data. 
 36      @type name:     str 
 37      """ 
 38   
 39      # Init. 
 40      missing = False 
 41   
 42      # List data. 
 43      if isinstance(data, list): 
 44          # Loop over the data. 
 45          for i in range(len(data)): 
 46              if data[i] == None or data[i] == 'None': 
 47                  missing = True 
 48   
 49      # None. 
 50      if data == None: 
 51          missing = True 
 52   
 53      # Fail. 
 54      if missing: 
 55          raise NameError("Data is missing from the " + name + '.') 
 56   
 57   
 58 -def translate(data, format='str', reverse=False): 
 59      """Translate all values back-and-forth between Python structures and NMR-STAR strings. 
 60   
 61      @param data:        The data to translate. 
 62      @type data:         anything 
 63      @keyword format:    The format to convert to.  This can be 'str', 'int', or 'float'. 
 64      @type format:       str 
 65      """ 
 66   
 67      # From Python to NMR-STAR. 
 68      if not reverse: 
 69          # List data (including numpy arrays). 
 70          if isinstance(data, list) or isinstance(data, ndarray): 
 71              # Loop over the data. 
 72              new_data = [] 
 73              for i in range(len(data)): 
 74                  if data[i] == None or data[i] == 'None': 
 75                      new_data.append('?') 
 76                  else: 
 77                      new_data.append(str(data[i])) 
 78   
 79          # None. 
 80          elif data == None: 
 81              new_data = '?' 
 82   
 83          # Otherwise normal conversion. 
 84          else: 
 85              new_data = str(data) 
 86   
 87      # The data is None. 
 88      elif data == None: 
 89          new_data = None 
 90   
 91      # From NMR-STAR to Python. 
 92      else: 
 93          # Conversion function. 
 94          if format == 'str': 
 95              convert = str 
 96          elif format == 'int': 
 97              convert = int 
 98          elif format == 'float': 
 99              convert = float 
100   
101          # List data. 
102          if isinstance(data, list): 
103              # Loop over the data. 
104              new_data = [] 
105              for i in range(len(data)): 
106                  if data[i] in ['?', '.']: 
107                      new_data.append(None) 
108                  else: 
109                      new_data.append(convert(data[i])) 
110   
111          # None. 
112          elif data in ['?', '.']: 
113              new_data = None 
114   
115          # Otherwise normal conversion. 
116          else: 
117              new_data = convert(data) 
118   
119      # Return the translated result. 
120      return new_data 
121