specific_fns.jw

42 """Class containing functions specific to reduced spectral density mapping.""" 43

44 - def __init__(self):

45 """Initialise the class by placing API_common methods into the API.""" 46 47 # Execute the base class __init__ method. 48 super(Jw_mapping, self).__init__() 49 50 # Place methods into the API. 51 self.base_data_loop = self._base_data_loop_spin 52 self.create_mc_data = self._create_mc_relax_data 53 self.model_loop = self._model_loop_spin 54 self.return_conversion_factor = self._return_no_conversion_factor 55 self.return_error = self._return_error_relax_data 56 self.return_value = self._return_value_general 57 self.set_param_values = self._set_param_values_spin 58 self.set_selected_sim = self._set_selected_sim_spin 59 self.sim_pack_data = self._sim_pack_relax_data 60 61 # Set up the spin parameters. 62 self.PARAMS.add('j0', scope='spin', string='J(0)', desc='Spectral density value at 0 MHz', py_type=float, set='params', grace_string='\\qJ(0)\\Q', err=True, sim=True) 63 self.PARAMS.add('jwx', scope='spin', string='J(wX)', desc='Spectral density value at the frequency of the heteronucleus', py_type=float, set='params', grace_string='\\qJ(\\xw\\f{}\\sX\\N)\\Q', err=True, sim=True) 64 self.PARAMS.add('jwh', scope='spin', string='J(wH)', desc='Spectral density value at the frequency of the proton', py_type=float, set='params', grace_string='\\qJ(\\xw\\f{}\\sH\\N)\\Q', err=True, sim=True) 65 self.PARAMS.add('r', scope='spin', default=NH_BOND_LENGTH, units='Angstrom', desc='Bond length', py_type=float, grace_string='Bond length') 66 self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm', desc='CSA value', py_type=float, grace_string='\\qCSA\\Q') 67 self.PARAMS.add('heteronuc_type', scope='spin', default='15N', desc='The heteronucleus type', py_type=str) 68 self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The proton type', py_type=str)

69 70

71 - def _set_frq(self, frq=None):

72 """Function for selecting which relaxation data to use in the J(w) mapping.""" 73 74 # Test if the current pipe exists. 75 pipes.test() 76 77 # Test if the pipe type is set to 'jw'. 78 function_type = cdp.pipe_type 79 if function_type != 'jw': 80 raise RelaxFuncSetupError(specific_fns.setup.get_string(function_type)) 81 82 # Test if the frequency has been set. 83 if hasattr(cdp, 'jw_frq'): 84 raise RelaxError("The frequency has already been set.") 85 86 # Create the data structure if it doesn't exist. 87 if not hasattr(cdp, 'jw_frq'): 88 cdp.jw_frq = {} 89 90 # Set the frequency. 91 cdp.jw_frq = frq

92 93

94 - def calculate(self, spin_id=None, verbosity=1, sim_index=None):

95 """Calculation of the spectral density values. 96 97 @keyword spin_id: The spin identification string. 98 @type spin_id: None or str 99 @keyword verbosity: The amount of information to print. The higher the value, the greater the verbosity. 100 @type verbosity: int 101 @keyword sim_index: The optional MC simulation index. 102 @type sim_index: None or int 103 """ 104 105 # Test if the frequency has been set. 106 if not hasattr(cdp, 'jw_frq') or not isinstance(cdp.jw_frq, float): 107 raise RelaxError("The frequency has not been set up.") 108 109 # Test if the sequence data is loaded. 110 if not exists_mol_res_spin_data(): 111 raise RelaxNoSequenceError 112 113 # Test if the CSA and bond length values have been set. 114 for spin in spin_loop(spin_id): 115 # Skip deselected spins. 116 if not spin.select: 117 continue 118 119 # Test if the CSA value has been set. 120 if not hasattr(spin, 'csa') or spin.csa == None: 121 raise RelaxNoValueError("CSA") 122 123 # Test if the bond length has been set. 124 if not hasattr(spin, 'r') or spin.r == None: 125 raise RelaxNoValueError("bond length") 126 127 # Test if the spin type has been set. 128 if not hasattr(spin, 'heteronuc_type'): 129 raise RelaxSpinTypeError 130 131 # Test if the type attached proton has been set. 132 if not hasattr(spin, 'proton_type'): 133 raise RelaxProtonTypeError 134 135 # Frequency index. 136 if cdp.jw_frq not in cdp.frq.values(): 137 raise RelaxError("No relaxation data corresponding to the frequency " + repr(cdp.jw_frq) + " has been loaded.") 138 139 # Reduced spectral density mapping. 140 for spin in spin_loop(spin_id): 141 # Skip deselected spins. 142 if not spin.select: 143 continue 144 145 # Set the r1, r2, and NOE to None. 146 r1 = None 147 r2 = None 148 noe = None 149 150 # Get the R1, R2, and NOE values corresponding to the set frequency. 151 for ri_id in cdp.ri_ids: 152 # The frequency does not match. 153 if cdp.frq[ri_id] != cdp.jw_frq: 154 continue 155 156 # R1. 157 if cdp.ri_type[ri_id] == 'R1': 158 if sim_index == None: 159 r1 = spin.ri_data[ri_id] 160 else: 161 r1 = spin.ri_data_sim[ri_id][sim_index] 162 163 # R2. 164 if cdp.ri_type[ri_id] == 'R2': 165 if sim_index == None: 166 r2 = spin.ri_data[ri_id] 167 else: 168 r2 = spin.ri_data_sim[ri_id][sim_index] 169 170 # NOE. 171 if cdp.ri_type[ri_id] == 'NOE': 172 if sim_index == None: 173 noe = spin.ri_data[ri_id] 174 else: 175 noe = spin.ri_data_sim[ri_id][sim_index] 176 177 # Skip the spin if not all of the three value exist. 178 if r1 == None or r2 == None or noe == None: 179 continue 180 181 # Initialise the function to calculate. 182 self.jw = Mapping(frq=cdp.jw_frq, gx=return_gyromagnetic_ratio(spin.heteronuc_type), gh=return_gyromagnetic_ratio(spin.proton_type), mu0=mu0, h_bar=h_bar) 183 184 # Calculate the spectral density values. 185 j0, jwx, jwh = self.jw.func(r=spin.r, csa=spin.csa, r1=r1, r2=r2, noe=noe) 186 187 # Reduced spectral density values. 188 if sim_index == None: 189 spin.j0 = j0 190 spin.jwx = jwx 191 spin.jwh = jwh 192 193 # Monte Carlo simulated reduced spectral density values. 194 else: 195 # Initialise the simulation data structures. 196 self.data_init(spin, sim=1) 197 if spin.j0_sim == None: 198 spin.j0_sim = [] 199 spin.jwx_sim = [] 200 spin.jwh_sim = [] 201 202 # Reduced spectral density values. 203 spin.j0_sim.append(j0) 204 spin.jwx_sim.append(jwx) 205 spin.jwh_sim.append(jwh)

206 207

208 - def data_init(self, data_cont, sim=False):

209 """Initialise the data structures. 210 211 @param data_cont: The data container. 212 @type data_cont: instance 213 @keyword sim: The Monte Carlo simulation flag, which if true will initialise the simulation data structure. 214 @type sim: bool 215 """ 216 217 # Get the data names. 218 data_names = self.data_names() 219 220 # Loop over the data structure names. 221 for name in data_names: 222 # Simulation data structures. 223 if sim: 224 # Add '_sim' to the names. 225 name = name + '_sim' 226 227 # If the name is not in 'data_cont', add it. 228 if not hasattr(data_cont, name): 229 # Set the attribute. 230 setattr(data_cont, name, None)

231 232 233 default_value_doc = Desc_container("Reduced spectral density mapping default values") 234 default_value_doc.add_paragraph("These default values are found in the file 'physical_constants.py'.") 235 _table = uf_tables.add_table(label="table: J(w) default values", caption="Reduced spectral density mapping default values.") 236 _table.add_headings(["Data type", "Object name", "Value"]) 237 _table.add_row(["Bond length", "'r'", "1.02 * 1e-10"]) 238 _table.add_row(["CSA", "'csa'", "-172 * 1e-6"]) 239 _table.add_row(["Heteronucleus type", "'heteronuc_type'", "'15N'"]) 240 _table.add_row(["Proton type", "'proton_type'", "'1H'"]) 241 default_value_doc.add_table(_table.label) 242 243

244 - def overfit_deselect(self):

245 """Deselect spins which _have insufficient data to support calculation.""" 246 247 # Print out. 248 print("\n\nOver-fit spin deselection.\n") 249 250 # Test the sequence data exists. 251 if not exists_mol_res_spin_data(): 252 raise RelaxNoSequenceError 253 254 # Loop over spin data. 255 for spin, spin_id in spin_loop(return_id=True): 256 # Skip deselected spins. 257 if not spin.select: 258 continue 259 260 # Check if data exists. 261 if not hasattr(spin, 'ri_data'): 262 warn(RelaxDeselectWarning(spin_id, 'missing relaxation data')) 263 spin.select = False 264 265 # Require 3 or more data points. 266 else: 267 # Count the points. 268 data_points = 0 269 for id in cdp.ri_ids: 270 if spin.ri_data.has_key(id) and spin.ri_data[id] != None: 271 data_points += 1 272 273 # Not enough. 274 if data_points < 3: 275 warn(RelaxDeselectWarning(spin_id, 'insufficient relaxation data, 3 or more data points are required')) 276 spin.select = False

277 278 279 return_data_name_doc = Desc_container("Reduced spectral density mapping data type string matching patterns") 280 _table = uf_tables.add_table(label="table: J(w) data types", caption="Reduced spectral density mapping data type string matching patterns.") 281 _table.add_headings(["Data type", "Object name"]) 282 _table.add_row(["J(0)", "'j0'"]) 283 _table.add_row(["J(wX)", "'jwx'"]) 284 _table.add_row(["J(wH)", "'jwh'"]) 285 _table.add_row(["Bond length", "'r'"]) 286 _table.add_row(["CSA", "'csa'"]) 287 _table.add_row(["Heteronucleus type", "'heteronuc_type'"]) 288 _table.add_row(["Proton type", "'proton_type'"]) 289 return_data_name_doc.add_table(_table.label) 290 291 292 set_doc = Desc_container("Reduced spectral density mapping set details") 293 set_doc.add_paragraph("In reduced spectral density mapping, three values must be set prior to the calculation of spectral density values: the bond length, CSA, and heteronucleus type.") 294 295

296 - def set_error(self, model_info, index, error):

297 """Set the parameter errors. 298 299 @param model_info: The spin container originating from model_loop(). 300 @type model_info: SpinContainer instance 301 @param index: The index of the parameter to set the errors for. 302 @type index: int 303 @param error: The error value. 304 @type error: float 305 """ 306 307 # Alias. 308 spin = model_info 309 310 # Return J(0) sim data. 311 if index == 0: 312 spin.j0_err = error 313 314 # Return J(wX) sim data. 315 if index == 1: 316 spin.jwx_err = error 317 318 # Return J(wH) sim data. 319 if index == 2: 320 spin.jwh_err = error

321 322

323 - def sim_return_param(self, model_info, index):

324 """Return the array of simulation parameter values. 325 326 @param model_info: The spin container originating from model_loop(). 327 @type model_info: SpinContainer instance 328 @param index: The index of the parameter to return the array of values for. 329 @type index: int 330 @return: The array of simulation parameter values. 331 @rtype: list of float 332 """ 333 334 # Alias. 335 spin = model_info 336 337 # Skip deselected spins. 338 if not spin.select: 339 return 340 341 # Return J(0) sim data. 342 if index == 0: 343 return spin.j0_sim 344 345 # Return J(wX) sim data. 346 if index == 1: 347 return spin.jwx_sim 348 349 # Return J(wH) sim data. 350 if index == 2: 351 return spin.jwh_sim

352 353

354 - def sim_return_selected(self, model_info):

355 """Return the array of selected simulation flags. 356 357 @param model_info: The spin container originating from model_loop(). 358 @type model_info: SpinContainer instance 359 @return: The array of selected simulation flags. 360 @rtype: list of int 361 """ 362 363 # Alias. 364 spin = model_info 365 366 # Multiple spins. 367 return spin.select_sim

Source Code for Module specific_fns.jw_mapping