Source Code for Module bmrblib.kinetics.heteronucl_T2_relaxation

  1  ############################################################################# 
  2  #                                                                           # 
  3  # The BMRB library.                                                         # 
  4  #                                                                           # 
  5  # Copyright (C) 2009-2013 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 Heteronuclear T2 data saveframe category. 
 24   
 25  This file is part of the U{BMRB library<https://gna.org/projects/bmrblib>}. 
 26   
 27  For example, see http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_T2_relaxation. 
 28  """ 
 29   
 30  # relax module imports. 
 31  from bmrblib.base_classes import BaseSaveframe, TagCategory, TagCategoryFree 
 32   
 33   
 34 -class HeteronuclT2Saveframe(BaseSaveframe): 
 35      """The Heteronuclear T2 data saveframe class.""" 
 36   
 37   
 38   
 39 -class HeteronuclT2List(TagCategoryFree): 
 40      """Base class for the HeteronuclT2List tag category.""" 
 41   
 42 -    def __init__(self, sf): 
 43          """Setup the HeteronuclT2List tag category. 
 44   
 45          @param sf:  The saveframe object. 
 46          @type sf:   saveframe instance 
 47          """ 
 48   
 49          # Initialise the baseclass. 
 50          super(HeteronuclT2List, self).__init__(sf) 
 51   
 52          # Add the tag info. 
 53          self.add(key='EntryID',                     var_name='entry_id',                format='str') 
 54          self.add(key='HeteronuclT2ListID',          var_name='count_str',               format='int') 
 55          self.add(key='DataFileName',                var_name='data_file_name',          format='str') 
 56          self.add(key='SampleConditionListID',       var_name='sample_cond_list_id',     format='int') 
 57          self.add(key='SampleConditionListLabel',    var_name='sample_cond_list_label',  format='str',  default='$conditions_1') 
 58          self.add(key='SpectrometerFrequency1H',     var_name='frq',                     format='float') 
 59          self.add(key='T2CoherenceType',             var_name='coherence',               format='str',  default='Ny') 
 60          self.add(key='T2ValUnits',                  var_name='units',                   format='str',  default='1/s') 
 61          self.add(key='Details',                     var_name='details',                 format='str') 
 62          self.add(key='TextDataFormat',              var_name='text_data_format',        format='str') 
 63          self.add(key='TextData',                    var_name='text_data',               format='str') 
 64   
 65   
 66   
 67 -class HeteronuclT2Experiment(TagCategory): 
 68      """Base class for the HeteronuclT2Experiment tag category.""" 
 69   
 70 -    def __init__(self, sf): 
 71          """Setup the HeteronuclT2Experiment tag category. 
 72   
 73          @param sf:  The saveframe object. 
 74          @type sf:   saveframe instance 
 75          """ 
 76   
 77          # Initialise the baseclass. 
 78          super(HeteronuclT2Experiment, self).__init__(sf) 
 79   
 80          # Add the tag info. 
 81          self.add(key='ExperimentID',        var_name='experiment_id',           format='int') 
 82          self.add(key='ExperimentName',      var_name='experiment_name',         format='str') 
 83          self.add(key='SampleID',            var_name='sample_id',               format='int') 
 84          self.add(key='SampleLabel',         var_name='sample_label',            format='str',    default='$sample_1') 
 85          self.add(key='SampleState',         var_name='sample_state',            format='str') 
 86          self.add(key='EntryID',             var_name='entry_id',                format='str') 
 87          self.add(key='HeteronuclT2ListID',  var_name='heteronucl_t1_list_id',   format='int') 
 88   
 89   
 90   
 91 -class HeteronuclT2Software(TagCategory): 
 92      """Base class for the HeteronuclT2Software tag category.""" 
 93   
 94 -    def __init__(self, sf): 
 95          """Setup the HeteronuclT2Software tag category. 
 96   
 97          @param sf:  The saveframe object. 
 98          @type sf:   saveframe instance 
 99          """ 
100   
101          # Initialise the baseclass. 
102          super(HeteronuclT2Software, self).__init__(sf) 
103   
104          # Add the tag info. 
105          self.add(key='SoftwareID',          var_name='software_id',             format='int') 
106          self.add(key='SoftwareLabel',       var_name='software_label',          format='str') 
107          self.add(key='MethodID',            var_name='method_id',               format='int') 
108          self.add(key='MethodLabel',         var_name='method_label',            format='str') 
109          self.add(key='EntryID',             var_name='entry_id',                format='str') 
110          self.add(key='HeteronuclT2ListID',  var_name='heteronucl_t1_list_id',   format='int') 
111   
112   
113   
114 -class T2(TagCategory): 
115      """Base class for the T2 tag category.""" 
116   
117 -    def __init__(self, sf): 
118          """Setup the T2 tag category. 
119   
120          @param sf:  The saveframe object. 
121          @type sf:   saveframe instance 
122          """ 
123   
124          # Initialise the baseclass. 
125          super(T2, self).__init__(sf) 
126   
127          # Add the tag info. 
128          self.add(key='RxID',                    var_name='data_ids',                format='int') 
129          self.add(key='AssemblyAtomID',          var_name='assembly_atom_ids',       format='int') 
130          self.add(key='EntityAssemblyID',        var_name='entity_assembly_ids',     format='int') 
131          self.add(key='EntityID',                var_name='entity_ids',              format='int') 
132          self.add(key='CompIndexID',             var_name='res_nums',                format='int') 
133          self.add(key='SeqID',                   var_name='seq_id',                  format='int') 
134          self.add(key='CompID',                  var_name='res_names',               format='str') 
135          self.add(key='AtomID',                  var_name='atom_names',              format='str') 
136          self.add(key='AtomType',                var_name='atom_types',              format='str') 
137          self.add(key='AtomIsotopeNumber',       var_name='isotope',                 format='int') 
138          self.add(key='Val',                     var_name='data',                    format='float') 
139          self.add(key='ValErr',                  var_name='errors',                  format='float') 
140          self.add(key='ResonanceID',             var_name='resonance_id',            format='int') 
141          self.add(key='AuthEntityAssemblyID',    var_name='auth_entity_assembly_id', format='str') 
142          self.add(key='AuthSeqID',               var_name='auth_seq_id',             format='str') 
143          self.add(key='AuthCompID',              var_name='auth_comp_id',            format='str') 
144          self.add(key='AuthAtomID',              var_name='auth_atom_id',            format='str') 
145          self.add(key='EntryID',                 var_name='entry_id',                format='str') 
146          self.add(key='HeteronuclT2ListID',      var_name='heteronucl_t1_list_id',   format='int') 
147