Source Code for Module bmrblib.kinetics.heteronucl_NOEs_v3_2

  1  ############################################################################# 
  2  #                                                                           # 
  3  # The BMRB library.                                                         # 
  4  #                                                                           # 
  5  # Copyright (C) 2009 Edward d'Auvergne                                      # 
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 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.misc import translate 
 30  from bmrblib.kinetics.heteronucl_NOEs_v3_1 import HeteronuclNOESaveframe_v3_1, HeteronuclNOEList_v3_1, HeteronuclNOEExperiment_v3_1, HeteronuclNOESoftware_v3_1, HeteronuclNOE_v3_1 
 31  from bmrblib.pystarlib.TagTable import TagTable 
 32   
 33   
 34 -class HeteronuclNOESaveframe_v3_2(HeteronuclNOESaveframe_v3_1): 
 35      """The v3.2 Heteronuclear NOE data saveframe class.""" 
 36   
 37 -    def add(self, sample_cond_list_id=None, sample_cond_list_label='$conditions_1', temp_calibration=None, temp_control=None, peak_intensity_type=None, frq=None, details=None, assembly_atom_ids=None, entity_assembly_ids=None, entity_ids=None, res_nums=None, seq_id=None, res_names=None, atom_names=None, atom_types=None, isotope=None, assembly_atom_ids_2=None, entity_assembly_ids_2=None, entity_ids_2=None, res_nums_2=None, seq_id_2=None, res_names_2=None, atom_names_2=None, atom_types_2=None, isotope_2=None, data=None, errors=None): 
 38          """Add relaxation data to the data nodes. 
 39   
 40          @keyword sample_cond_list_id:       The sample conditions list ID number. 
 41          @type sample_cond_list_id:          str 
 42          @keyword sample_cond_list_label:    The sample conditions list label. 
 43          @type sample_cond_list_label:       str 
 44          @keyword temp_calibration:          The temperature calibration method. 
 45          @type temp_calibration:             str 
 46          @keyword temp_control:              The temperature control method. 
 47          @type temp_control:                 str 
 48          @keyword peak_intensity_type:       The peak intensity type - one of 'height' or 'volume'. 
 49          @type peak_intensity_type:          str 
 50          @keyword frq:                       The spectrometer proton frequency, in Hz. 
 51          @type frq:                          float 
 52          @keyword details:                   The details tag. 
 53          @type details:                      None or str 
 54          @keyword assembly_atom_ids:         The assembly atom ID numbers. 
 55          @type assembly_atom_ids:            list of int 
 56          @keyword entity_assembly_ids:       The entity assembly ID numbers. 
 57          @type entity_assembly_ids:          list of int 
 58          @keyword entity_ids:                The entity ID numbers. 
 59          @type entity_ids:                   int 
 60          @keyword res_nums:                  The residue number list. 
 61          @type res_nums:                     list of int 
 62          @keyword res_names:                 The residue name list. 
 63          @type res_names:                    list of str 
 64          @keyword atom_names:                The atom name list. 
 65          @type atom_names:                   list of str 
 66          @keyword atom_types:                The atom types as IUPAC element abbreviations. 
 67          @type atom_types:                   list of str 
 68          @keyword isotope:                   The isotope type list, ie 15 for '15N'. 
 69          @type isotope:                      list of int 
 70          @keyword assembly_atom_ids_2:       The assembly atom ID numbers.  This is for the second atom used in the heteronuclear NOE. 
 71          @type assembly_atom_ids_2:          list of int 
 72          @keyword entity_assembly_ids_2:     The entity assembly ID numbers.  This is for the second atom used in the heteronuclear NOE. 
 73          @type entity_assembly_ids_2:        list of int 
 74          @keyword entity_ids_2:              The entity ID numbers.  This is for the second atom used in the heteronuclear NOE. 
 75          @type entity_ids_2:                 int 
 76          @keyword res_nums_2:                The residue number list.  This is for the second atom used in the heteronuclear NOE. 
 77          @type res_nums_2:                   list of int 
 78          @keyword res_names_2:               The residue name list.  This is for the second atom used in the heteronuclear NOE. 
 79          @type res_names_2:                  list of str 
 80          @keyword atom_names_2:              The atom name list.  This is for the second atom used in the heteronuclear NOE. 
 81          @type atom_names_2:                 list of str 
 82          @keyword atom_types_2:              The atom types as IUPAC element abbreviations.  This is for the second atom used in the heteronuclear NOE. 
 83          @type atom_types_2:                 list of str 
 84          @keyword isotope_2:                 The isotope type list, ie 1 for '1H'.  This is for the second atom used in the heteronuclear NOE. 
 85          @type isotope_2:                    list of int 
 86          @keyword data:                      The relaxation data. 
 87          @type data:                         list of float 
 88          @keyword errors:                    The errors associated with the relaxation data. 
 89          @type errors:                       list of float 
 90          """ 
 91   
 92          # Check the args. 
 93          if not temp_calibration: 
 94              raise NameError("The temperature calibration method has not been specified.") 
 95          if not temp_control: 
 96              raise NameError("The temperature control method has not been specified.") 
 97          if not peak_intensity_type: 
 98              raise NameError("The peak intensity type has not been specified.") 
 99   
100          # Place the args into the namespace. 
101          self.temp_calibration = translate(temp_calibration) 
102          self.temp_control = translate(temp_control) 
103          self.peak_intensity_type = translate(peak_intensity_type) 
104   
105          # Execute the v3.1 add method. 
106          HeteronuclNOESaveframe_v3_1.add(self, 
107                                          sample_cond_list_id=sample_cond_list_id, 
108                                          sample_cond_list_label=sample_cond_list_label, 
109                                          frq=frq, 
110                                          details=details, 
111                                          assembly_atom_ids=assembly_atom_ids, 
112                                          entity_assembly_ids=entity_assembly_ids, 
113                                          entity_ids=entity_ids, 
114                                          res_nums=res_nums, 
115                                          seq_id=seq_id, 
116                                          res_names=res_names, 
117                                          atom_names=atom_names, 
118                                          atom_types=atom_types, 
119                                          isotope=isotope, 
120                                          assembly_atom_ids_2=assembly_atom_ids_2, 
121                                          entity_assembly_ids_2=entity_assembly_ids_2, 
122                                          entity_ids_2=entity_ids_2, 
123                                          res_nums_2=res_nums_2, 
124                                          seq_id_2=seq_id_2, 
125                                          res_names_2=res_names_2, 
126                                          atom_names_2=atom_names_2, 
127                                          atom_types_2=atom_types_2, 
128                                          isotope_2=isotope_2, 
129                                          data=data, 
130                                          errors=errors) 
131   
132   
133 -    def add_tag_categories(self): 
134          """Create the v3.2 tag categories.""" 
135   
136          # The tag category objects. 
137          self.heteronuclRxlist = HeteronuclNOEList_v3_2(self) 
138          self.heteronuclRxexperiment = HeteronuclNOEExperiment_v3_1(self) 
139          self.heteronuclRxsoftware = HeteronuclNOESoftware_v3_1(self) 
140          self.Rx = HeteronuclNOE_v3_1(self) 
141   
142   
143   
144 -class HeteronuclNOEList_v3_2(HeteronuclNOEList_v3_1): 
145      """v3.1 HeteronuclNOEList tag category.""" 
146   
147 -    def create(self): 
148          """Create the HeteronuclNOEList tag category.""" 
149   
150          # The save frame category. 
151          self.sf.frame.tagtables.append(self.create_tag_table([['SfCategory', 'cat_name']], free=True)) 
152          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['SfFramecode']], tagvalues=[[self.sf.sf_label]])) 
153   
154          # NOE ID number. 
155          if 'HeteronuclNOEListID' in self.tag_names: 
156              self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['HeteronuclNOEListID']], tagvalues=[[str(self.sf.noe_inc)]])) 
157   
158          # Sample info. 
159          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['SampleConditionListID']], tagvalues=[[self.sf.sample_cond_list_id]])) 
160          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['SampleConditionListLabel']], tagvalues=[['$conditions_1']])) 
161   
162          # NMR info. 
163          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['TempCalibrationMethod']], tagvalues=[[self.sf.temp_calibration]])) 
164          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['TempControlMethod']], tagvalues=[[self.sf.temp_control]])) 
165          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['SpectrometerFrequency1H']], tagvalues=[[str(self.sf.frq/1e6)]])) 
166          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['HeteronuclearNOEValType']], tagvalues=[[self.sf.peak_intensity_type]])) 
167          self.sf.frame.tagtables.append(TagTable(free=True, tagnames=[self.tag_names_full['Details']], tagvalues=[[self.sf.details]])) 
168   
169   
170 -    def tag_setup(self, tag_category_label=None, sep=None): 
171          """Set up the tag names. 
172   
173          @keyword tag_category_label:    The tag name prefix specific for the tag category. 
174          @type tag_category_label:       None or str 
175          @keyword sep:                   The string separating the tag name prefix and suffix. 
176          @type sep:                      str 
177          """ 
178   
179          # Execute the base class tag_setup() method. 
180          HeteronuclNOEList_v3_1.tag_setup(self, tag_category_label='Heteronucl_NOE_list', sep=sep) 
181   
182          # Tag names for the relaxation data. 
183          self.tag_names['TempCalibrationMethod'] = 'Temp_calibration_method' 
184          self.tag_names['TempControlMethod'] = 'Temp_control_method' 
185          self.tag_names['HeteronuclearNOEValType'] = 'Heteronuclear_NOE_val_type' 
186