Source Code for Module bmrblib.NMR_parameters.chem_shift_anisotropy

  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  """The chemical shift anisotropy data saveframe category. 
 24   
 25  For example, see http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_SaveFramePage.html#chem_shift_anisotropy 
 26  """ 
 27   
 28  # relax module imports. 
 29  from bmrblib.base_classes import BaseSaveframe, TagCategory, TagCategoryFree 
 30   
 31   
 32 -class ChemShiftAnisotropySaveframe(BaseSaveframe): 
 33      """The chemical shift anisotropy data saveframe class.""" 
 34   
 35      # Class variables. 
 36      sf_label = 'chem_shift_anisotropy' 
 37   
 38 -    def add_tag_categories(self): 
 39          """Create the tag categories.""" 
 40   
 41          # The tag category objects. 
 42          self.tag_categories.append(ChemShiftAnisotropy(self)) 
 43          self.tag_categories.append(CSAnisotropyExperiment(self)) 
 44          self.tag_categories.append(CSAnisotropySoftware(self)) 
 45          self.tag_categories.append(CSAnisotropy(self)) 
 46   
 47   
 48   
 49 -class ChemShiftAnisotropy(TagCategoryFree): 
 50      """Base class for the ChemShiftAnisotropy tag category.""" 
 51   
 52 -    def __init__(self, sf): 
 53          """Setup the ChemShiftAnisotropy tag category. 
 54   
 55          @param sf:  The saveframe object. 
 56          @type sf:   saveframe instance 
 57          """ 
 58   
 59          # Initialise the baseclass. 
 60          super(ChemShiftAnisotropy, self).__init__(sf) 
 61   
 62          # Add the tag info. 
 63          self.add(key='ChemShiftAnisotropyID',       tag_name='ID',                      var_name='count_str',               format='int') 
 64          self.add(key='DataFileName',                tag_name='Data_file_name',          var_name='file_name') 
 65          self.add(key='SampleConditionListLabel',    tag_name='Sample_conditions_label', var_name='sample_cond_list_label',  default='$conditions_1') 
 66          self.add(key='ValUnits',                    tag_name='Val_units',               var_name='units',                   default='ppm') 
 67   
 68   
 69   
 70 -class CSAnisotropyExperiment(TagCategory): 
 71      """Base class for the CSAnisotropyExperiment tag category.""" 
 72   
 73 -    def __init__(self, sf): 
 74          """Setup the CSAnisotropyExperiment tag category. 
 75   
 76          @param sf:  The saveframe object. 
 77          @type sf:   saveframe instance 
 78          """ 
 79   
 80          # Initialise the baseclass. 
 81          super(CSAnisotropyExperiment, self).__init__(sf) 
 82   
 83          # Add the tag info. 
 84          self.add(key='SampleLabel', tag_name='Sample_label',    var_name='sample_label',    default='$sample_1') 
 85   
 86   
 87   
 88 -class CSAnisotropySoftware(TagCategory): 
 89      """Base class for the CSAnisotropySoftware tag category.""" 
 90   
 91   
 92   
 93 -class CSAnisotropy(TagCategory): 
 94      """Base class for the CSAnisotropy tag category.""" 
 95   
 96 -    def __init__(self, sf): 
 97          """Setup the CSAnisotropy tag category. 
 98   
 99          @param sf:  The saveframe object. 
100          @type sf:   saveframe instance 
101          """ 
102   
103          # Initialise the baseclass. 
104          super(CSAnisotropy, self).__init__(sf) 
105   
106          # Add the tag info. 
107          self.add(key='CSAnisotropyID',          tag_name='ID',                          var_name='data_ids',            format='int') 
108          self.add(key='AssemblyAtomID',          tag_name='Assembly_atom_ID',            var_name='assembly_atom_ids') 
109          self.add(key='EntityAssemblyID',        tag_name='Entity_assembly_ID',          var_name='entity_assembly_ids') 
110          self.add(key='EntityID',                tag_name='Entity_ID',                   var_name='entity_ids',          format='int') 
111          self.add(key='CompIndexID',             tag_name='Residue_seq_code',            var_name='res_nums',            format='int') 
112          self.add(key='SeqID',                   tag_name='Seq_ID',                      var_name='seq_id') 
113          self.add(key='CompID',                  tag_name='Residue_label',               var_name='res_names') 
114          self.add(key='AtomID',                  tag_name='Atom_name',                   var_name='atom_names') 
115          self.add(key='AtomType',                tag_name='Atom_type',                   var_name='atom_types') 
116          self.add(key='AtomIsotopeNumber',       tag_name='Atom_isotope_number',         var_name='isotope',             format='int') 
117          self.add(key='Val',                     tag_name='value',                       var_name='csa',                 format='float') 
118          self.add(key='ValErr',                  tag_name='value_error',                 var_name='csa_error',           format='float') 
119          self.add(key='ChemShiftAnisotropyID',   tag_name='Chem_shift_anisotropy_ID',    var_name='count_str') 
120