Source Code for Module data

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003, 2004 Edward d'Auvergne                                  # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23   
 24  from math import pi 
 25  from re import match 
 26  from types import DictType, ListType 
 27   
 28   
 29  # Global data. 
 30  ############## 
 31   
 32 -class Data: 
 33 -    def __init__(self): 
 34          """Class containing all the program data.""" 
 35   
 36          # Fundamental constants. 
 37          #self.h = 6.6260755e-34 
 38          self.h = 6.62606876e-34 
 39          self.h_bar = self.h / ( 2.0*pi ) 
 40          self.mu0 = 4.0 * pi * 1e-7 
 41   
 42          # PDB data. 
 43          self.pdb = SpecificData() 
 44   
 45          # Diffusion data. 
 46          self.diff = SpecificData() 
 47   
 48          # The residue specific data. 
 49          self.res = Residue() 
 50   
 51          # The name of the runs. 
 52          self.run_names = [] 
 53   
 54          # The type of the runs. 
 55          self.run_types = [] 
 56   
 57          # Global minimisation statistics. 
 58          self.chi2 = {} 
 59          self.iter = {} 
 60          self.f_count = {} 
 61          self.g_count = {} 
 62          self.h_count = {} 
 63          self.warning = {} 
 64   
 65   
 66   
 67 -    def __repr__(self): 
 68          text = "The data class containing all permanent program data.\n" 
 69          text = text + "The class contains the following objects:\n" 
 70          for name in dir(self): 
 71              if match("^__", name): 
 72                  continue 
 73              text = text + "  " + name + ", " + `type(getattr(self, name))` + "\n" 
 74          return text 
 75   
 76   
 77   
 78  # Empty data container. 
 79  ####################### 
 80   
 81 -class Element: 
 82 -    def __init__(self): 
 83          """Empty data container.""" 
 84   
 85   
 86 -    def __repr__(self): 
 87          # Header. 
 88          text = "%-25s%-100s\n\n" % ("Data structure", "Value") 
 89   
 90          # Data structures. 
 91          for name in dir(self): 
 92              if match("^__", name): 
 93                  continue 
 94              text = text + "%-25s%-100s\n" % (name, `getattr(self, name)`) 
 95   
 96          # Return the lot. 
 97          return text 
 98   
 99   
100  # Specific data class. 
101  ###################### 
102   
103 -class SpecificData(DictType): 
104 -    def __init__(self): 
105          """Dictionary type class for specific data.""" 
106   
107   
108 -    def __repr__(self): 
109          text = "Data:\n" 
110          if len(self) == 0: 
111              text = text + "  {}\n" 
112          else: 
113              i = 0 
114              for key in self.keys(): 
115                  if i == 0: 
116                      text = text + "  { " 
117                  else: 
118                      text = text + "  , " 
119                  text = text + "Key " + `key` + ":\n" 
120                  for name in dir(self[key]): 
121                      if match("^__", name): 
122                          continue 
123                      text = text + "    " + name + ", " + `type(getattr(self[key], name))` + "\n" 
124                  i = i + 1 
125              text = text + "  }\n" 
126   
127          return text 
128   
129   
130 -    def add_item(self, key): 
131          """Function for adding an empty container to the dictionary.""" 
132   
133          self[key] = Element() 
134   
135   
136   
137  # Residue specific data. 
138  ######################## 
139   
140 -class Residue(DictType): 
141 -    def __init__(self): 
142          """Class containing all the residue specific data.""" 
143   
144   
145 -    def __repr__(self): 
146          text = "Class containing all the residue specific data.\n\n" 
147   
148          # Empty. 
149          if not len(self): 
150              text = text + "The class contains no data.\n" 
151   
152          # Not empty. 
153          else: 
154              text = text + "The residue container contains the following keys:\n" 
155              for key in self: 
156                  text = text + "    " + `key` + "\n" 
157              text = text + "\nThese can be accessed by typing 'self.relax.data.res[key]'.\n" 
158   
159          return text 
160   
161   
162 -    def add_list(self, key): 
163          """Function for adding an empty container to the dictionary.""" 
164   
165          self[key] = ResidueList() 
166   
167   
168 -class ResidueList(ListType): 
169 -    def __init__(self): 
170          """Empty data container for residue specific data.""" 
171   
172   
173 -    def __repr__(self): 
174          text = "Sequence data.\n\n" 
175          text = text + "%-8s%-8s%-8s%-10s" % ("Index", "Number", "Name", "Selected") + "\n" 
176          for i in xrange(len(self)): 
177              text = text + "%-8i%-8i%-8s%-10i" % (i, self[i].num, self[i].name, self[i].select) + "\n" 
178          text = text + "\nThese can be accessed by typing 'self.relax.data.res[key][index]'.\n" 
179          return text 
180   
181   
182 -    def add_item(self): 
183          """Function for appending an empty container to the list.""" 
184   
185          self.append(Element()) 
186