bmrblib.kinetics.heteronucl

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 NOE data saveframe category. 24 25 This file is part of the U{BMRB library<https://sourceforge.net/projects/bmrblib>}. 26 27 For example, see http://www.bmrb.wisc.edu/dictionary/3.1html/SaveFramePage.html#heteronucl_NOEs. 28 """ 29 30 # relax module imports. 31 from bmrblib.base_classes import BaseSaveframe, TagCategory, TagCategoryFree 32 33

34 -class HeteronuclNOESaveframe(BaseSaveframe):

35 """The Heteronuclear NOE data saveframe class.""" 36

37 - def pre_ops(self):

38 """Perform some saveframe specific operations prior to XML creation.""" 39 40 # The saveframe description. 41 self.sf_framecode = '%s MHz heteronuclear NOE %s' % (self.frq, self.count)

42 43 44

45 -class HeteronuclNOEList(TagCategoryFree):

46 """Base class for the HeteronuclNOEList tag category.""" 47

48 - def __init__(self, sf):

49 """Setup the HeteronuclNOEList tag category. 50 51 @param sf: The saveframe object. 52 @type sf: saveframe instance 53 """ 54 55 # Initialise the baseclass. 56 super(HeteronuclNOEList, self).__init__(sf) 57 58 # Add the tag info. 59 self.add(key='EntryID', var_name='entry_id', format='str') 60 self.add(key='HeteronuclNOEListID', var_name='count_str', format='int') 61 self.add(key='DataFileName', var_name='data_file_name', format='str') 62 self.add(key='SampleConditionListID', var_name='sample_cond_list_id', format='int') 63 self.add(key='SampleConditionListLabel', var_name='sample_cond_list_label', format='str', default='$conditions_1') 64 self.add(key='SpectrometerFrequency1H', var_name='frq', format='float') 65 self.add(key='TempCalibrationMethod', var_name='temp_calibration', format='str', missing=False) 66 self.add(key='TempControlMethod', var_name='temp_control', format='str', missing=False) 67 self.add(key='HeteronuclearNOEValType', var_name='peak_intensity_type', format='str') 68 self.add(key='NOERefVal', var_name='noe_ref_val', format='float') 69 self.add(key='NOERefDescription', var_name='noe_ref_description', format='str') 70 self.add(key='Details', var_name='details', format='str') 71 self.add(key='TextDataFormat', var_name='text_data_format', format='str') 72 self.add(key='TextData', var_name='text_data', format='str')

73 74 75

76 -class HeteronuclNOEExperiment(TagCategory):

77 """Base class for the HeteronuclNOEExperiment tag category.""" 78

79 - def __init__(self, sf):

80 """Setup the HeteronuclNOEExperiment tag category. 81 82 @param sf: The saveframe object. 83 @type sf: saveframe instance 84 """ 85 86 # Initialise the baseclass. 87 super(HeteronuclNOEExperiment, self).__init__(sf) 88 89 # Add the tag info. 90 self.add(key='ExperimentID', var_name='experiment_id', format='int') 91 self.add(key='ExperimentName', var_name='experiment_name', format='str') 92 self.add(key='SampleID', var_name='sample_id', format='int') 93 self.add(key='SampleLabel', var_name='sample_label', format='str', default='$sample_1') 94 self.add(key='SampleState', var_name='sample_state', format='str') 95 self.add(key='EntryID', var_name='entry_id', format='str') 96 self.add(key='HeteronuclNOEListID', var_name='heteronucl_noe_list_id', format='int')

97 98 99

100 -class HeteronuclNOESoftware(TagCategory):

101 """Base class for the HeteronuclNOESoftware tag category.""" 102

103 - def __init__(self, sf):

104 """Setup the HeteronuclNOESoftware tag category. 105 106 @param sf: The saveframe object. 107 @type sf: saveframe instance 108 """ 109 110 # Initialise the baseclass. 111 super(HeteronuclNOESoftware, self).__init__(sf) 112 113 # Add the tag info. 114 self.add(key='SoftwareID', var_name='software_id', format='int') 115 self.add(key='SoftwareLabel', var_name='software_label', format='str') 116 self.add(key='MethodID', var_name='method_id', format='int') 117 self.add(key='MethodLabel', var_name='method_label', format='str') 118 self.add(key='EntryID', var_name='entry_id', format='str') 119 self.add(key='HeteronuclNOEListID', var_name='heteronucl_noe_list_id', format='int')

120 121

122 -class HeteronuclNOE(TagCategory):

123 """Base class for the HeteronuclNOE tag category.""" 124

125 - def __init__(self, sf):

126 """Setup the HeteronuclNOE tag category. 127 128 @param sf: The saveframe object. 129 @type sf: saveframe instance 130 """ 131 132 # Initialise the baseclass. 133 super(HeteronuclNOE, self).__init__(sf) 134 135 # Add the tag info. 136 self.add(key='HeteronuclNOEID', var_name='data_ids', format='int') 137 self.add(key='AssemblyAtomID1', var_name='assembly_atom_ids', format='int') 138 self.add(key='EntityAssemblyID1', var_name='entity_assembly_ids', format='int') 139 self.add(key='EntityID1', var_name='entity_ids', format='int') 140 self.add(key='CompIndexID1', var_name='res_nums', format='int') 141 self.add(key='SeqID1', var_name='seq_id', format='int') 142 self.add(key='CompID1', var_name='res_names', format='str') 143 self.add(key='AtomID1', var_name='atom_names', format='str') 144 self.add(key='AtomType1', var_name='atom_types', format='str') 145 self.add(key='AtomIsotopeNumber1', var_name='isotope', format='int') 146 self.add(key='AssemblyAtomID2', var_name='assembly_atom_ids_2', format='int') 147 self.add(key='EntityAssemblyID2', var_name='entity_assembly_ids_2', format='int') 148 self.add(key='EntityID2', var_name='entity_ids_2', format='int') 149 self.add(key='CompIndexID2', var_name='res_nums_2', format='int') 150 self.add(key='SeqID2', var_name='seq_id_2', format='int') 151 self.add(key='CompID2', var_name='res_names_2', format='str') 152 self.add(key='AtomID2', var_name='atom_names_2', format='str') 153 self.add(key='AtomType2', var_name='atom_types_2', format='str') 154 self.add(key='AtomIsotopeNumber2', var_name='isotope_2', format='int') 155 self.add(key='Val', var_name='data', format='float') 156 self.add(key='ValErr', var_name='errors', format='float') 157 self.add(key='ResonanceID1', var_name='resonance_id', format='int') 158 self.add(key='ResonanceID2', var_name='resonance_id_2', format='int') 159 self.add(key='AuthEntityAssemblyID1', var_name='auth_entity_assembly_id', format='str') 160 self.add(key='AuthSeqID1', var_name='auth_seq_id', format='str') 161 self.add(key='AuthCompID1', var_name='auth_comp_id', format='str') 162 self.add(key='AuthAtomID1', var_name='auth_atom_id', format='str') 163 self.add(key='AuthEntityAssemblyID2', var_name='auth_entity_assembly_id_2', format='str') 164 self.add(key='AuthSeqID2', var_name='auth_seq_id_2', format='str') 165 self.add(key='AuthCompID2', var_name='auth_comp_id_2', format='str') 166 self.add(key='AuthAtomID2', var_name='auth_atom_id_2', format='str') 167 self.add(key='EntryID', var_name='entry_id', format='str') 168 self.add(key='HeteronuclNOEListID', var_name='count_str', format='int')

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Source Code for Module bmrblib.kinetics.heteronucl_NOEs