Source Code for Module bmrblib.kinetics.heteronucl_T2_relaxation_v2_1

  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.                                       # 
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 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 v2.1 Heteronuclear T2 data saveframe category. 
 24   
 25  This file is part of the U{BMRB library<https://gna.org/projects/bmrblib>}. 
 26   
 27  See http://www.bmrb.wisc.edu/dictionary/htmldocs/nmr_star/dictionary_files/complete_form_v21.txt. 
 28  """ 
 29   
 30  # relax module imports. 
 31  from bmrblib.kinetics.heteronucl_T2_relaxation import HeteronuclT2Saveframe, HeteronuclT2List, HeteronuclT2Experiment, HeteronuclT2Software, T2 
 32   
 33   
 34 -class HeteronuclT2Saveframe_v2_1(HeteronuclT2Saveframe): 
 35      """The v2.1 Heteronuclear T2 data saveframe class.""" 
 36   
 37      # Class variables. 
 38      name = 'T2' 
 39      label = 'heteronucl_T2' 
 40      sf_label = 'T2_relaxation' 
 41   
 42 -    def add_tag_categories(self): 
 43          """Create the v2.1 tag categories.""" 
 44   
 45          # The tag category objects. 
 46          self.tag_categories.append(HeteronuclT2List_v2_1(self)) 
 47          self.tag_categories.append(HeteronuclT2Experiment_v2_1(self)) 
 48          self.tag_categories.append(HeteronuclT2Software_v2_1(self)) 
 49          self.tag_categories.append(T2_v2_1(self)) 
 50   
 51   
 52 -    def pre_ops(self): 
 53          """Perform some saveframe specific operations prior to XML creation.""" 
 54   
 55          # The saveframe description. 
 56          self.sf_framecode = '%s MHz heteronuclear R1 %s' % (self.frq, self.count) 
 57   
 58   
 59   
 60 -class HeteronuclT2List_v2_1(HeteronuclT2List): 
 61      """v2.1 HeteronuclT2List tag category.""" 
 62   
 63 -    def __init__(self, sf): 
 64          """Setup the HeteronuclT2List_v2_1 tag category. 
 65   
 66          @param sf:  The saveframe object. 
 67          @type sf:   saveframe instance 
 68          """ 
 69   
 70          # Initialise the baseclass. 
 71          super(HeteronuclT2List_v2_1, self).__init__(sf) 
 72   
 73          # Add the tag info. 
 74          self['Details'].tag_name =                  'Details' 
 75          self['SampleConditionListLabel'].tag_name = 'Sample_conditions_label' 
 76          self['SpectrometerFrequency1H'].tag_name =  'Spectrometer_frequency_1H' 
 77          self['T2CoherenceType'].tag_name =          'T2_coherence_type' 
 78          self['T2ValUnits'].tag_name =               'T2_value_units' 
 79          self['TextDataFormat'].tag_name =           'Text_data_format' 
 80          self['TextData'].tag_name =                 'Text_data' 
 81   
 82   
 83   
 84 -class HeteronuclT2Experiment_v2_1(HeteronuclT2Experiment): 
 85      """v2.1 HeteronuclT2Experiment tag category.""" 
 86   
 87 -    def __init__(self, sf): 
 88          """Setup the HeteronuclT2Experiment_v2_1 tag category. 
 89   
 90          @param sf:  The saveframe object. 
 91          @type sf:   saveframe instance 
 92          """ 
 93   
 94          # Initialise the baseclass. 
 95          super(HeteronuclT2Experiment_v2_1, self).__init__(sf) 
 96   
 97          # Add the tag info. 
 98          self['ExperimentName'].tag_name = 'Experiment_label' 
 99          self['SampleLabel'].tag_name = 'Sample_label' 
100   
101   
102   
103 -class HeteronuclT2Software_v2_1(HeteronuclT2Software): 
104      """v2.1 HeteronuclT2Software tag category.""" 
105   
106 -    def __init__(self, sf): 
107          """Setup the HeteronuclT2Software tag category. 
108   
109          @param sf:  The saveframe object. 
110          @type sf:   saveframe instance 
111          """ 
112   
113          # Initialise the baseclass. 
114          super(HeteronuclT2Software_v2_1, self).__init__(sf) 
115   
116          # Add the tag info. 
117          self['SoftwareLabel'].tag_name =       'Software_label' 
118   
119   
120   
121 -class T2_v2_1(T2): 
122      """v2.1 T2 tag category.""" 
123   
124 -    def __init__(self, sf): 
125          """Setup the T2_v2_1 tag category. 
126   
127          @param sf:  The saveframe object. 
128          @type sf:   saveframe instance 
129          """ 
130   
131          # Initialise the baseclass. 
132          super(T2_v2_1, self).__init__(sf) 
133   
134          # Change tag names. 
135          self['CompIndexID'].tag_name =          'Residue_seq_code' 
136          self['CompID'].tag_name =               'Residue_label' 
137          self['AtomID'].tag_name =               'Atom_name' 
138          self['Val'].tag_name =                  'T2_value' 
139          self['ValErr'].tag_name =               'T2_value_error' 
140