bmrblib.kinetics.relaxation

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 relaxation data BMRB API interface. 24 25 This file is part of the U{BMRB library<https://sourceforge.net/projects/bmrblib>}. 26 """ 27 28 29 # relax module imports. 30 from bmrblib.kinetics.auto_relaxation_v3_1 import AutoRelaxationSaveframe_v3_1 31 from bmrblib.kinetics.heteronucl_NOEs_v2_1 import HeteronuclNOESaveframe_v2_1 32 from bmrblib.kinetics.heteronucl_NOEs_v3_1 import HeteronuclNOESaveframe_v3_1 33 from bmrblib.kinetics.heteronucl_T1_relaxation_v2_1 import HeteronuclT1Saveframe_v2_1 34 from bmrblib.kinetics.heteronucl_T1_relaxation_v3_1 import HeteronuclT1Saveframe_v3_1 35 from bmrblib.kinetics.heteronucl_T2_relaxation_v2_1 import HeteronuclT2Saveframe_v2_1 36 from bmrblib.kinetics.heteronucl_T2_relaxation_v3_1 import HeteronuclT2Saveframe_v3_1 37 38

39 -class Relaxation_v2_1:

40 """Class for the relaxation data part of the BMRB API.""" 41

42 - def __init__(self, datanodes):

43 """Initialise the class, placing the pystarlib data nodes into the namespace. 44 45 @param datanodes: The pystarlib data nodes object. 46 @type datanodes: list 47 """ 48 49 # Initialise the kinetic saveframe supergroups. 50 self.heteronucl_NOEs = HeteronuclNOESaveframe_v2_1(datanodes) 51 self.heteronucl_T1_relaxation = HeteronuclT1Saveframe_v2_1(datanodes) 52 self.heteronucl_T2_relaxation = HeteronuclT2Saveframe_v2_1(datanodes)

53 54

55 - def add(self, **keywords):

56 """Distribute the relaxation data to the appropriate saveframes. 57 58 @keyword data_type: The relaxation data type (one of 'NOE', 'R1', or 'R2'). 59 @type data_type: str 60 @keyword sample_cond_list_id: The sample conditions list ID number. 61 @type sample_cond_list_id: str 62 @keyword sample_cond_list_label: The sample conditions list label. 63 @type sample_cond_list_label: str 64 @keyword temp_calibration: The temperature calibration method (unused). 65 @type temp_calibration: str 66 @keyword temp_control: The temperature control method (unused). 67 @type temp_control: str 68 @keyword peak_intensity_type: The peak intensity type - one of 'height' or 'volume'. 69 @type peak_intensity_type: str 70 @keyword frq: The spectrometer proton frequency, in Hz. 71 @type frq: float 72 @keyword details: The details tag. 73 @type details: None or str 74 @keyword assembly_atom_ids: The assembly atom ID numbers. 75 @type assembly_atom_ids: list of int 76 @keyword entity_assembly_ids: The entity assembly ID numbers. 77 @type entity_assembly_ids: list of int 78 @keyword entity_ids: The entity ID numbers. 79 @type entity_ids: int 80 @keyword res_nums: The residue number list. 81 @type res_nums: list of int 82 @keyword res_names: The residue name list. 83 @type res_names: list of str 84 @keyword atom_names: The atom name list. 85 @type atom_names: list of str 86 @keyword atom_types: The atom types as IUPAC element abbreviations. 87 @type atom_types: list of str 88 @keyword isotope: The isotope type list, ie 15 for '15N'. 89 @type isotope: list of int 90 @keyword assembly_atom_ids_2: The assembly atom ID numbers. This is for the second atom used in the heteronuclear NOE. 91 @type assembly_atom_ids_2: list of int 92 @keyword entity_assembly_ids_2: The entity assembly ID numbers. This is for the second atom used in the heteronuclear NOE. 93 @type entity_assembly_ids_2: list of int 94 @keyword entity_ids_2: The entity ID numbers. This is for the second atom used in the heteronuclear NOE. 95 @type entity_ids_2: int 96 @keyword res_nums_2: The residue number list. This is for the second atom used in the heteronuclear NOE. 97 @type res_nums_2: list of int 98 @keyword res_names_2: The residue name list. This is for the second atom used in the heteronuclear NOE. 99 @type res_names_2: list of str 100 @keyword atom_names_2: The atom name list. This is for the second atom used in the heteronuclear NOE. 101 @type atom_names_2: list of str 102 @keyword atom_types_2: The atom types as IUPAC element abbreviations. This is for the second atom used in the heteronuclear NOE. 103 @type atom_types_2: list of str 104 @keyword isotope_2: The isotope type list, ie 1 for '1H'. This is for the second atom used in the heteronuclear NOE. 105 @type isotope_2: list of int 106 @keyword data: The relaxation data. 107 @type data: list of float 108 @keyword errors: The errors associated with the relaxation data. 109 @type errors: list of float 110 """ 111 112 # Pack specific the data. 113 if keywords['data_type'] == 'R1': 114 self.heteronucl_T1_relaxation.add(**keywords) 115 elif keywords['data_type'] == 'R2': 116 self.heteronucl_T2_relaxation.add(**keywords) 117 elif keywords['data_type'] == 'NOE': 118 self.heteronucl_NOEs.add(**keywords)

119 120

121 - def loop(self):

122 """Generator method for looping over and returning all relaxation data.""" 123 124 # The NOE data. 125 for data in self.heteronucl_NOEs.loop(): 126 data['data_type'] = 'NOE' 127 yield data 128 129 # The R1 data. 130 for data in self.heteronucl_T1_relaxation.loop(): 131 data['data_type'] = 'R1' 132 yield data 133 134 # The R2 data. 135 for data in self.heteronucl_T2_relaxation.loop(): 136 data['data_type'] = 'R2' 137 yield data

138 139 140

141 -class Relaxation_v3_0(Relaxation_v2_1):

142 """Class for the relaxation data part of the BMRB API (v3.0).""" 143

144 - def __init__(self, datanodes):

145 """Initialise the class, placing the pystarlib data nodes into the namespace. 146 147 @param datanodes: The pystarlib data nodes object. 148 @type datanodes: list 149 """ 150 151 # Execute the base class __init__() method. 152 Relaxation_v2_1.__init__(self, datanodes)

153 154 155

156 -class Relaxation_v3_1(Relaxation_v3_0):

157 """Class for the relaxation data part of the BMRB API (v3.1).""" 158

159 - def __init__(self, datanodes):

160 """Initialise the class, placing the pystarlib data nodes into the namespace. 161 162 @param datanodes: The pystarlib data nodes object. 163 @type datanodes: list 164 """ 165 166 # Execute the base class __init__() method. 167 Relaxation_v3_0.__init__(self, datanodes) 168 169 # Initialise the kinetic saveframe supergroups. 170 self.heteronucl_NOEs = HeteronuclNOESaveframe_v3_1(datanodes) 171 self.heteronucl_T1_relaxation = HeteronuclT1Saveframe_v3_1(datanodes) 172 self.heteronucl_T2_relaxation = HeteronuclT2Saveframe_v3_1(datanodes) 173 self.auto_relaxation = AutoRelaxationSaveframe_v3_1(datanodes)

174 175

176 - def add(self, **keywords):

177 """Add relaxation data to the data nodes. 178 179 @keyword data_type: The relaxation data type (one of 'NOE', 'R1', or 'R2'). 180 @type data_type: str 181 @keyword sample_cond_list_id: The sample conditions list ID number. 182 @type sample_cond_list_id: str 183 @keyword sample_cond_list_label: The sample conditions list label. 184 @type sample_cond_list_label: str 185 @keyword temp_calibration: The temperature calibration method. 186 @type temp_calibration: str 187 @keyword temp_control: The temperature control method. 188 @type temp_control: str 189 @keyword peak_intensity_type: The peak intensity type - one of 'height' or 'volume'. 190 @type peak_intensity_type: str 191 @keyword frq: The spectrometer proton frequency, in Hz. 192 @type frq: float 193 @keyword details: The details tag. 194 @type details: None or str 195 @keyword assembly_atom_ids: The assembly atom ID numbers. 196 @type assembly_atom_ids: list of int 197 @keyword entity_assembly_ids: The entity assembly ID numbers. 198 @type entity_assembly_ids: list of int 199 @keyword entity_ids: The entity ID numbers. 200 @type entity_ids: int 201 @keyword res_nums: The residue number list. 202 @type res_nums: list of int 203 @keyword res_names: The residue name list. 204 @type res_names: list of str 205 @keyword atom_names: The atom name list. 206 @type atom_names: list of str 207 @keyword atom_types: The atom types as IUPAC element abbreviations. 208 @type atom_types: list of str 209 @keyword isotope: The isotope type list, ie 15 for '15N'. 210 @type isotope: list of int 211 @keyword assembly_atom_ids_2: The assembly atom ID numbers. This is for the second atom used in the heteronuclear NOE. 212 @type assembly_atom_ids_2: list of int 213 @keyword entity_assembly_ids_2: The entity assembly ID numbers. This is for the second atom used in the heteronuclear NOE. 214 @type entity_assembly_ids_2: list of int 215 @keyword entity_ids_2: The entity ID numbers. This is for the second atom used in the heteronuclear NOE. 216 @type entity_ids_2: int 217 @keyword res_nums_2: The residue number list. This is for the second atom used in the heteronuclear NOE. 218 @type res_nums_2: list of int 219 @keyword res_names_2: The residue name list. This is for the second atom used in the heteronuclear NOE. 220 @type res_names_2: list of str 221 @keyword atom_names_2: The atom name list. This is for the second atom used in the heteronuclear NOE. 222 @type atom_names_2: list of str 223 @keyword atom_types_2: The atom types as IUPAC element abbreviations. This is for the second atom used in the heteronuclear NOE. 224 @type atom_types_2: list of str 225 @keyword isotope_2: The isotope type list, ie 1 for '1H'. This is for the second atom used in the heteronuclear NOE. 226 @type isotope_2: list of int 227 @keyword data: The relaxation data. 228 @type data: list of float 229 @keyword errors: The errors associated with the relaxation data. 230 @type errors: list of float 231 """ 232 233 # Pack specific the data. 234 if keywords['data_type'] in ['R1', 'R2']: 235 self.auto_relaxation.add(**keywords) 236 elif keywords['data_type'] == 'NOE': 237 self.heteronucl_NOEs.add(**keywords)

238 239

240 - def loop(self):

241 """Generator method for looping over and returning all relaxation data.""" 242 243 # The NOE data. 244 for data in self.heteronucl_NOEs.loop(): 245 data['data_type'] = 'NOE' 246 yield data 247 248 # The R1 data. 249 for data in self.heteronucl_T1_relaxation.loop(): 250 data['data_type'] = 'R1' 251 yield data 252 253 # The R2 data. 254 for data in self.heteronucl_T2_relaxation.loop(): 255 data['data_type'] = 'R2' 256 yield data 257 258 259 # The auto-relaxation data. 260 for data in self.auto_relaxation.loop(): 261 data['data_type'] = data['coherence_common_name'] 262 yield data

263

Source Code for Module bmrblib.kinetics.relaxation