Source Code for Module bmrblib.assembly_supercategory.entity

  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 entity 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#entity. 
 28  """ 
 29   
 30  # relax module imports. 
 31  from bmrblib.base_classes import BaseSaveframe, TagCategory, TagCategoryFree 
 32   
 33   
 34 -class EntitySaveframe(BaseSaveframe): 
 35      """The entity saveframe class.""" 
 36   
 37      # Class variables. 
 38      label = 'entity' 
 39      sf_label = 'entity' 
 40   
 41 -    def add_tag_categories(self): 
 42          """Create the tag categories.""" 
 43   
 44          # The tag category objects. 
 45          self.tag_categories.append(Entity(self)) 
 46          self.tag_categories.append(EntityCompIndex(self)) 
 47   
 48   
 49   
 50 -class Entity(TagCategoryFree): 
 51      """Base class for the Entity tag category.""" 
 52   
 53 -    def __init__(self, sf): 
 54          """Setup the Entity tag category. 
 55   
 56          @param sf:  The saveframe object. 
 57          @type sf:   saveframe instance 
 58          """ 
 59   
 60          # Initialise the baseclass. 
 61          super(Entity, self).__init__(sf) 
 62   
 63          # Add the tag info. 
 64          self.add(key='EntityID',                        var_name='count_str',                       format='int') 
 65          self.add(key='BMRBCode',                        var_name='bmrb_code',                       format='str') 
 66          self.add(key='Name',                            var_name='mol_name',                        format='str') 
 67          self.add(key='Type',                            var_name='mol_type',                        format='str') 
 68          self.add(key='PolymerCommonType',               var_name='polymer_common_type',             format='str') 
 69          self.add(key='PolymerType',                     var_name='polymer_type',                    format='str',    allowed=['DNA/RNA hybrid', 'polydeoxyribonucleotide', 'polypeptide(D)', 'polypeptide(L)', 'polyribonucleotide', 'polysaccharide(D)', 'polysaccharide(L)']) 
 70          self.add(key='PolymerTypeDetails',              var_name='polymer_type_details',            format='str') 
 71          self.add(key='PolymerStrandID',                 var_name='polymer_strand_id',               format='str') 
 72          self.add(key='PolymerSeqOneLetterCodeCan',      var_name='polymer_seq_one_letter_code_can', format='str') 
 73          self.add(key='PolymerSeqOneLetterCode',         var_name='polymer_seq_one_letter_code',     format='str') 
 74          self.add(key='TargetIdentifier',                var_name='target_identifier',               format='str') 
 75          self.add(key='PolymerAuthorDefinedSeq',         var_name='polymer_author_defined_seq',      format='str') 
 76          self.add(key='PolymerAuthorSeqDetails',         var_name='polymer_author_seq_details',      format='str') 
 77          self.add(key='AmbiguousConformationalStates',   var_name='ambiguous_conformational_states', format='str') 
 78          self.add(key='AmbiguousChemCompSites',          var_name='ambiguous_chem_comp_sites',       format='str') 
 79          self.add(key='NstdMonomer',                     var_name='nstd_monomer',                    format='str') 
 80          self.add(key='NstdChirality',                   var_name='nstd_chirality',                  format='str') 
 81          self.add(key='NstdLinkage',                     var_name='nstd_linkage',                    format='str') 
 82          self.add(key='NonpolymerCompID',                var_name='nonpolymer_comp_id',              format='str') 
 83          self.add(key='NonpolymerCompLabel',             var_name='nonpolymer_comp_label',           format='str') 
 84          self.add(key='NumberOfMonomers',                var_name='number_of_monomers',              format='int') 
 85          self.add(key='NumberOfNonpolymerComponents',    var_name='number_of_nonpolymer_components', format='int') 
 86          self.add(key='Paramagnetic',                    var_name='paramagnetic',                    format='str') 
 87          self.add(key='ThiolState',                      var_name='thiol_state',                     format='str') 
 88          self.add(key='SrcMethod',                       var_name='src_method',                      format='str') 
 89          self.add(key='ParentEntityID',                  var_name='parent_entity_id',                format='int') 
 90          self.add(key='Fragment',                        var_name='fragment',                        format='str') 
 91          self.add(key='Mutation',                        var_name='mutation',                        format='str') 
 92          self.add(key='ECNumber',                        var_name='ec_number',                       format='str') 
 93          self.add(key='CalcIsoelectricPoint',            var_name='calc_isoelectric_point',          format='float') 
 94          self.add(key='FormulaWeight',                   var_name='molecular_weight',                format='float') 
 95          self.add(key='FormulaWeightExptl',              var_name='molecular_weight_exptl',          format='float') 
 96          self.add(key='FormulaWeightExptlMeth',          var_name='molecular_weight_exptl_meth',     format='str') 
 97          self.add(key='Details',                         var_name='details',                         format='str') 
 98          self.add(key='DBQueryDate',                     var_name='db_query_date',                   format='str') 
 99          self.add(key='DBQueryRevisedLastDate',          var_name='db_query_revised_last_date',      format='str') 
100   
101   
102   
103 -class EntityCompIndex(TagCategory): 
104      """Base class for the EntityCompIndex tag category.""" 
105   
106 -    def __init__(self, sf): 
107          """Setup the Entity tag category. 
108   
109          @param sf:  The saveframe object. 
110          @type sf:   saveframe instance 
111          """ 
112   
113          # Initialise the baseclass. 
114          super(EntityCompIndex, self).__init__(sf) 
115   
116          # Add the tag info. 
117          self.add(key='EntityCompIndexID',   var_name='res_nums',    format='int') 
118          self.add(key='AuthSeqID',           var_name='seq_nums',    format='str') 
119          self.add(key='CompID',              var_name='res_names',   format='str') 
120          self.add(key='CompLabel',           var_name='chem_comp',   format='str') 
121          self.add(key='EntityID',            var_name='count_str',   format='int') 
122