Source Code for Module bmrblib.misc

  1  ############################################################################# 
  2  #                                                                           # 
  3  # The BMRB library.                                                         # 
  4  #                                                                           # 
  5  # Copyright (C) 2009-2015 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  This file is part of the U{BMRB library<https://gna.org/projects/bmrblib>}. 
 26  """ 
 27   
 28  # Python module imports. 
 29  from numpy import ndarray 
 30  from warnings import warn 
 31   
 32   
 33 -def no_missing(data, name): 
 34      """Check that there are no None values in the data. 
 35   
 36      @param data:    The data to check. 
 37      @type data:     anything 
 38      @param name:    The name associated with the data. 
 39      @type name:     str 
 40      """ 
 41   
 42      # Init. 
 43      missing = False 
 44   
 45      # List data. 
 46      if isinstance(data, list): 
 47          # Loop over the data. 
 48          for i in range(len(data)): 
 49              if data[i] is None or data[i] == 'None': 
 50                  missing = True 
 51   
 52      # None. 
 53      if data is None: 
 54          missing = True 
 55   
 56      # Fail. 
 57      if missing: 
 58          raise NameError("Data is missing from the " + name + '.') 
 59   
 60   
 61 -def translate(data, format='str', reverse=False): 
 62      """Translate all values back-and-forth between Python structures and NMR-STAR strings. 
 63   
 64      @param data:        The data to translate. 
 65      @type data:         anything 
 66      @keyword format:    The format to convert to.  This can be 'str', 'int', or 'float'. 
 67      @type format:       str 
 68      """ 
 69   
 70      # From Python to NMR-STAR. 
 71      if not reverse: 
 72          # List data (including numpy arrays). 
 73          if isinstance(data, list) or isinstance(data, ndarray): 
 74              # Loop over the data. 
 75              new_data = [] 
 76              for i in range(len(data)): 
 77                  if data[i] is None or data[i] == 'None': 
 78                      new_data.append('?') 
 79                  else: 
 80                      new_data.append(str(data[i])) 
 81   
 82          # None. 
 83          elif data is None: 
 84              new_data = '?' 
 85   
 86          # Otherwise normal conversion. 
 87          else: 
 88              new_data = str(data) 
 89   
 90      # The data is None. 
 91      elif data is None: 
 92          new_data = None 
 93   
 94      # From NMR-STAR to Python. 
 95      else: 
 96          # Conversion function. 
 97          if format == 'str': 
 98              convert = str 
 99          elif format == 'int': 
100              convert = int 
101          elif format == 'float': 
102              convert = float 
103   
104          # List data. 
105          if isinstance(data, list): 
106              # Loop over the data. 
107              new_data = [] 
108              for i in range(len(data)): 
109                  if data[i] in ['?', '.']: 
110                      new_data.append(None) 
111                  else: 
112                      new_data.append(convert(data[i])) 
113   
114          # None. 
115          elif data in ['?', '.']: 
116              new_data = None 
117   
118          # Otherwise normal conversion. 
119          else: 
120              new_data = convert(data) 
121   
122      # Return the translated result. 
123      return new_data 
124