Source Code for Module bmrblib.structure.tensor

  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 tensor saveframe category. 
 24   
 25  For example, see http://www.bmrb.wisc.edu/dictionary/3.1html_frame/frame_SaveFramePage.html#tensor 
 26  """ 
 27   
 28  # Python module imports. 
 29  from numpy import array 
 30   
 31  # relax module imports. 
 32  from bmrblib.base_classes import BaseSaveframe, TagCategory, TagCategoryFree 
 33   
 34   
 35 -class TensorSaveframe(BaseSaveframe): 
 36      """The tensor saveframe class.""" 
 37   
 38      # Saveframe variables. 
 39      sf_label = 'tensor' 
 40   
 41 -    def add_tag_categories(self): 
 42          """Create the tag categories.""" 
 43   
 44          # The tag category objects. 
 45          self.tag_categories.append(TensorList(self)) 
 46          self.tag_categories.append(Tensor(self)) 
 47   
 48   
 49   
 50 -class TensorList(TagCategoryFree): 
 51      """Base class for the TensorList tag category.""" 
 52   
 53 -    def __init__(self, sf): 
 54          """Setup the TensorList tag category. 
 55   
 56          @param sf:  The saveframe object. 
 57          @type sf:   saveframe instance 
 58          """ 
 59   
 60          # Initialise the baseclass. 
 61          super(TensorList, self).__init__(sf) 
 62   
 63          # The category name. 
 64          self.tag_category_label = 'Tensor_list' 
 65   
 66          # Add the tag info. 
 67          self.add(key='EntryID',                 tag_name='Entry_ID',                var_name=None) 
 68          self.add(key='SfID',                    tag_name='Sf_ID',                   var_name=None) 
 69          self.add(key='TensorID',                tag_name='ID',                      var_name='data_ids',            format='str') 
 70          self.add(key='TensorType',              tag_name='Tensor_type',             var_name='tensor_type') 
 71          self.add(key='GeometricShape',          tag_name='Geometric_shape',         var_name='geometric_shape',     allowed=['sphere', 'spheroid', 'oblate spheroid', 'prolate spheroid', 'ellipsoid']) 
 72          self.add(key='TensorSymmetry',          tag_name='Tensor_symmetry',         var_name='tensor_symmetry',     allowed=['isotropic', 'anisotropic', 'axial symmetry', 'oblate axial symmetry', 'prolate axial symmetry', 'rhombic']) 
 73          self.add(key='MatrixValUnits',          tag_name='Matrix_val_units',        var_name='matrix_val_units') 
 74          self.add(key='AngleUnits',              tag_name='Angle_units',             var_name='angle_units',         allowed=[None, 'deg', 'rad']) 
 75          self.add(key='IsotropicValFormula',     tag_name='Isotropic_val_formula',   var_name='iso_val_formula') 
 76          self.add(key='AnisotropicValFormula',   tag_name='Anisotropic_val_formula', var_name='aniso_val_formula') 
 77          self.add(key='RhombicValFormula',       tag_name='Rhombic_val_formula',     var_name='rhomb_val_formula') 
 78          self.add(key='EulerAngleType',          tag_name='Euler_angle_type',        var_name='euler_type') 
 79          self.add(key='DataFileName',            tag_name='Data_file_name',          var_name='file_name') 
 80          self.add(key='Details',                 tag_name='Details',                 var_name='details') 
 81   
 82          # Change tag names. 
 83          self['SfCategory'].tag_name = 'Sf_category' 
 84          self['SfFramecode'].tag_name = 'Sf_framecode' 
 85   
 86   
 87   
 88 -class Tensor(TagCategory): 
 89      """Base class for the Tensor tag category.""" 
 90   
 91 -    def __init__(self, sf): 
 92          """Setup the Tensor tag category. 
 93   
 94          @param sf:  The saveframe object. 
 95          @type sf:   saveframe instance 
 96          """ 
 97   
 98          # Initialise the baseclass. 
 99          super(Tensor, self).__init__(sf) 
100   
101          # The category name. 
102          self.tag_category_label = 'Tensor' 
103   
104          # Add the tag info. 
105          self.add(key='TensorID',                    tag_name='ID',                              var_name='data_ids') 
106          self.add(key='InteratomicDistanceListID',   tag_name='Interatomic_distance_list_ID',    var_name=None) 
107          self.add(key='InteratomicDistSetID',        tag_name='Interatomic_dist_set_ID',         var_name=None) 
108          self.add(key='CalcTypeID',                  tag_name='Calc_type_ID',                    var_name=None) 
109          self.add(key='AssemblyAtomID',              tag_name='Assembly_atom_ID',                var_name='assembly_atom_ids') 
110          self.add(key='EntityAssemblyID',            tag_name='Entity_assembly_ID',              var_name='entity_assembly_ids') 
111          self.add(key='EntityID',                    tag_name='Entity_ID',                       var_name='entity_ids',                      format='int',   missing=False) 
112          self.add(key='CompIndexID',                 tag_name='Comp_index_ID',                   var_name='res_nums',                        format='int',   missing=False) 
113          self.add(key='SeqID',                       tag_name='Seq_ID',                          var_name=None) 
114          self.add(key='CompID',                      tag_name='Residue_label',                   var_name='res_names',                       missing=False) 
115          self.add(key='AtomID',                      tag_name='Atom_name',                       var_name='atom_names',                      missing=False) 
116          self.add(key='AtomType',                    tag_name='Atom_type',                       var_name='atom_types') 
117          self.add(key='AtomIsotopeNumber',           tag_name='Atom_isotope_number',             var_name='isotope',                         format='int') 
118          self.add(key='AxialSymAxisPolarAngle',      tag_name='Axial_sym_axis_polar_angle',      var_name='axial_sym_axis_polar_angle',      format='float') 
119          self.add(key='AxialSymAxisAzimuthalAngle',  tag_name='Axial_sym_axis_azimuthal_angle',  var_name='axial_sym_axis_azimuthal_angle',  format='float') 
120          self.add(key='IsotropicVal',                tag_name='Isotropic_val',                   var_name='iso_val',                         format='float') 
121          self.add(key='AnisotropicVal',              tag_name='Anisotropic_val',                 var_name='aniso_val',                       format='float') 
122          self.add(key='RhombicVal',                  tag_name='Rhombic_val',                     var_name='rhombic_val',                     format='float') 
123          self.add(key='EulerAngleAlpha',             tag_name='Euler_angle_alpha',               var_name='euler_alpha',                     format='float') 
124          self.add(key='EulerAngleBeta',              tag_name='Euler_angle_beta',                var_name='euler_beta',                      format='float') 
125          self.add(key='EulerAngleGamma',             tag_name='Euler_angle_gamma',               var_name='euler_gamma',                     format='float') 
126          self.add(key='IsotropicComp11Val',          tag_name='Isotropic_comp_1_1_val',          var_name='iso_comp_11',                     format='float') 
127          self.add(key='IsotropicComp22Val',          tag_name='Isotropic_comp_2_2_val',          var_name='iso_comp_22',                     format='float') 
128          self.add(key='IsotropicComp33Val',          tag_name='Isotropic_comp_3_3_val',          var_name='iso_comp_33',                     format='float') 
129          self.add(key='AntiSymComp12Val',            tag_name='Anti_sym_comp_1_2_val',           var_name='antisym_comp_12',                 format='float') 
130          self.add(key='AntiSymComp13Val',            tag_name='Anti_sym_comp_1_3_val',           var_name='antisym_comp_13',                 format='float') 
131          self.add(key='AntiSymComp23Val',            tag_name='Anti_sym_comp_2_3_val',           var_name='antisym_comp_23',                 format='float') 
132          self.add(key='SymTracelessComp11Val',       tag_name='Sym_traceless_comp_1_1_val',      var_name=None,                              format='float') 
133          self.add(key='SymTracelessComp12Val',       tag_name='Sym_traceless_comp_1_2_val',      var_name=None,                              format='float') 
134          self.add(key='SymTracelessComp13Val',       tag_name='Sym_traceless_comp_1_3_val',      var_name=None,                              format='float') 
135          self.add(key='SymTracelessComp22Val',       tag_name='Sym_traceless_comp_2_2_val',      var_name=None,                              format='float') 
136          self.add(key='SymTracelessComp23Val',       tag_name='Sym_traceless_comp_2_3_val',      var_name=None,                              format='float') 
137          self.add(key='ReduceableMatrix11Val',       tag_name='Reduceable_matrix_1_1_val',       var_name='tensor_11',                       format='float') 
138          self.add(key='ReduceableMatrix12Val',       tag_name='Reduceable_matrix_1_2_val',       var_name='tensor_12',                       format='float') 
139          self.add(key='ReduceableMatrix13Val',       tag_name='Reduceable_matrix_1_3_val',       var_name='tensor_13',                       format='float') 
140          self.add(key='ReduceableMatrix21Val',       tag_name='Reduceable_matrix_2_1_val',       var_name='tensor_21',                       format='float') 
141          self.add(key='ReduceableMatrix22Val',       tag_name='Reduceable_matrix_2_2_val',       var_name='tensor_22',                       format='float') 
142          self.add(key='ReduceableMatrix23Val',       tag_name='Reduceable_matrix_2_3_val',       var_name='tensor_23',                       format='float') 
143          self.add(key='ReduceableMatrix31Val',       tag_name='Reduceable_matrix_3_1_val',       var_name='tensor_31',                       format='float') 
144          self.add(key='ReduceableMatrix32Val',       tag_name='Reduceable_matrix_3_2_val',       var_name='tensor_32',                       format='float') 
145          self.add(key='ReduceableMatrix33Val',       tag_name='Reduceable_matrix_3_3_val',       var_name='tensor_33',                       format='float') 
146          self.add(key='AuthEntityAssemblyID',        tag_name='Auth_entity_assembly_ID',         var_name=None) 
147          self.add(key='AuthSeqID',                   tag_name='Auth_seq_ID',                     var_name=None) 
148          self.add(key='AuthCompID',                  tag_name='uth_comp_ID',                     var_name=None) 
149          self.add(key='AuthAtomID',                  tag_name='Auth_atom_ID',                    var_name=None) 
150          self.add(key='EntryID',                     tag_name='Entry_ID',                        var_name=None) 
151          self.add(key='TensorListID',                tag_name='Tensor_list_ID',                  var_name='count_str',                       format='float') 
152