bmrblib.thermodynamics.model_free_v3

1 ############################################################################# 2 # # 3 # The BMRB library. # 4 # # 5 # Copyright (C) 2009 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 v3.2 Heteronuclear NOE data saveframe category. 24 25 See http://www.bmrb.wisc.edu/dictionary/3.2html/SaveFramePage.html#heteronucl_NOEs. 26 """ 27 28 # relax module imports. 29 from bmrblib.thermodynamics.model_free_v3_1 import ModelFreeSaveframe_v3_1, ModelFreeList_v3_1, ModelFreeExperiment_v3_1, ModelFreeSoftware_v3_1, ModelFree_v3_1 30 31

32 -class ModelFreeSaveframe_v3_2(ModelFreeSaveframe_v3_1):

33 """The v3.2 Model_free data saveframe class.""" 34 35 # Saveframe variables. 36 title = 'model_free' 37

38 - def add_tag_categories(self):

39 """Create the v3.2 tag categories.""" 40 41 # The tag category objects. 42 self.model_free_list = ModelFreeList_v3_2(self) 43 self.model_free_experiment = ModelFreeExperiment_v3_2(self) 44 self.model_free_software = ModelFreeSoftware_v3_2(self) 45 self.model_free = ModelFree_v3_2(self)

46

47 - def specific_setup(self):

48 """Method called by self.add() to set up any version specific data.""" 49 50 self.cat_name = ['model_free']

51 52

53 -class ModelFreeList_v3_2(ModelFreeList_v3_1):

54 """v3.2 ModelFreeList tag category.""" 55

56 - def tag_setup(self, tag_category_label=None, sep=None):

57 """Replacement method for setting up the tag names. 58 59 @keyword tag_category_label: The tag name prefix specific for the tag category. 60 @type tag_category_label: None or str 61 @keyword sep: The string separating the tag name prefix and suffix. 62 @type sep: str 63 """ 64 65 # Category label. 66 if not tag_category_label: 67 tag_category_label='Model_free_list' 68 69 # Execute the base class tag_setup() method. 70 ModelFreeList_v3_1.tag_setup(self, tag_category_label=tag_category_label, sep=sep) 71 72 # Tag names for the relaxation data. 73 self.tag_names['SfCategory'] = 'Sf_category' 74 self.tag_names['ModelFreeListID'] = 'ID' 75 self.tag_names['SampleConditionListLabel'] = 'Sample_condition_list_label'

76 77

78 -class ModelFreeExperiment_v3_2(ModelFreeExperiment_v3_1):

79 """v3.2 ModelFreeExperiment tag category.""" 80

81 - def tag_setup(self, tag_category_label=None, sep=None):

82 """Replacement method for setting up the tag names. 83 84 @keyword tag_category_label: The tag name prefix specific for the tag category. 85 @type tag_category_label: None or str 86 @keyword sep: The string separating the tag name prefix and suffix. 87 @type sep: str 88 """ 89 90 # Category label. 91 if not tag_category_label: 92 tag_category_label='Model_free_experiment' 93 94 # Execute the base class tag_setup() method. 95 ModelFreeExperiment_v3_1.tag_setup(self, tag_category_label=tag_category_label, sep=sep)

96 97

98 -class ModelFreeSoftware_v3_2(ModelFreeSoftware_v3_1):

99 """v3.2 ModelFreeSoftware tag category.""" 100

101 - def tag_setup(self, tag_category_label=None, sep=None):

102 """Replacement method for setting up the tag names. 103 104 @keyword tag_category_label: The tag name prefix specific for the tag category. 105 @type tag_category_label: None or str 106 @keyword sep: The string separating the tag name prefix and suffix. 107 @type sep: str 108 """ 109 110 # Category label. 111 if not tag_category_label: 112 tag_category_label='Model_free_software' 113 114 # Execute the base class tag_setup() method. 115 ModelFreeSoftware_v3_1.tag_setup(self, tag_category_label=tag_category_label, sep=sep)

116 117

118 -class ModelFree_v3_2(ModelFree_v3_1):

119 """v3.2 ModelFree tag category.""" 120

121 - def create(self):

122 """Create the v3.2 ModelFree tag category.""" 123 124 # Keys and objects. 125 info = [ 126 ['ModelFreeID', 'data_ids'], 127 ['AssemblyAtomID', 'assembly_atom_ids'], 128 ['EntityAssemblyID', 'entity_assembly_ids'], 129 ['EntityID', 'entity_ids'], 130 ['CompIndexID', 'res_nums'], 131 ['CompID', 'res_names'], 132 ['AtomID', 'atom_names'], 133 ['AtomType', 'atom_types'], 134 ['AtomIsotopeNumber', 'isotope'], 135 ['S2Val', 's2'], 136 ['S2ValErr', 's2_err'], 137 ['S2fVal', 's2f'], 138 ['S2fValErr', 's2f_err'], 139 ['S2sVal', 's2s'], 140 ['S2sValErr', 's2s_err'], 141 ['LocalTauCVal', 'local_tc'], 142 ['LocalTauCValErr', 'local_tc_err'], 143 ['TauEVal', 'te'], 144 ['TauEValErr', 'te_err'], 145 ['TauFVal', 'tf'], 146 ['TauFValErr', 'tf_err'], 147 ['TauSVal', 'ts'], 148 ['TauSValErr', 'ts_err'], 149 ['RexVal', 'rex'], 150 ['RexValErr', 'rex_err'], 151 ['ChiSquaredVal', 'chi2'], 152 ['ModelFit', 'model_fit'] 153 ] 154 155 # Get the TabTable. 156 table = self.create_tag_table(info) 157 158 # Add the tagtable to the save frame. 159 self.sf.frame.tagtables.append(table)

160 161

162 - def tag_setup(self, tag_category_label=None, sep=None):

163 """Replacement method for setting up the tag names. 164 165 @keyword tag_category_label: The tag name prefix specific for the tag category. 166 @type tag_category_label: None or str 167 @keyword sep: The string separating the tag name prefix and suffix. 168 @type sep: str 169 """ 170 171 # Category label. 172 if not tag_category_label: 173 tag_category_label='Model_free' 174 175 # Execute the base class tag_setup() method. 176 ModelFree_v3_1.tag_setup(self, tag_category_label=tag_category_label, sep=sep) 177 178 # Tag names for the relaxation data. 179 self.tag_names['ModelFreeID'] = 'ID' 180 self.tag_names['AssemblyAtomID'] = 'Assembly_atom_ID' 181 self.tag_names['EntityAssemblyID'] = 'Entity_assembly_ID' 182 self.tag_names['EntityID'] = 'Entity_ID' 183 self.tag_names['CompIndexID'] = 'Comp_index_ID' 184 self.tag_names['CompID'] = 'Comp_ID' 185 self.tag_names['AtomID'] = 'Obs_atom_ID' 186 self.tag_names['AtomType'] = 'Obs_atom_type' 187 self.tag_names['AtomIsotopeNumber'] = 'Obs_atom_isotope_number' 188 self.tag_names['S2Val'] = 'S2_val' 189 self.tag_names['S2ValErr'] = 'S2_val_err' 190 self.tag_names['S2fVal'] = 'S2f_val' 191 self.tag_names['S2fValErr'] = 'S2f_val_err' 192 self.tag_names['S2sVal'] = 'S2s_val' 193 self.tag_names['S2sValErr'] = 'S2s_val_err' 194 self.tag_names['LocalTauCVal'] = 'Local_tau_c_val' 195 self.tag_names['LocalTauCValErr'] = 'Local_tau_c_val_err' 196 self.tag_names['TauEVal'] = 'Tau_e_val' 197 self.tag_names['TauEValErr'] = 'Tau_e_val_err' 198 self.tag_names['TauFVal'] = 'Tau_f_val' 199 self.tag_names['TauFValErr'] = 'Tau_f_val_err' 200 self.tag_names['TauSVal'] = 'Tau_s_val' 201 self.tag_names['TauSValErr'] = 'Tau_s_val_err' 202 self.tag_names['RexVal'] = 'Rex_val' 203 self.tag_names['RexValErr'] = 'Rex_val_err' 204 self.tag_names['ChiSquaredVal'] = 'Chi_squared_val'

205

Source Code for Module bmrblib.thermodynamics.model_free_v3_2