specific_fns.jw

45 """Class containing functions specific to reduced spectral density mapping.""" 46

47 - def __init__(self):

48 """Initialise the class by placing API_common methods into the API.""" 49 50 # Execute the base class __init__ method. 51 super(Jw_mapping, self).__init__() 52 53 # Place methods into the API. 54 self.base_data_loop = self._base_data_loop_spin 55 self.create_mc_data = self._create_mc_relax_data 56 self.model_loop = self._model_loop_spin 57 self.return_conversion_factor = self._return_no_conversion_factor 58 self.return_error = self._return_error_relax_data 59 self.return_value = self._return_value_general 60 self.set_param_values = self._set_param_values_spin 61 self.set_selected_sim = self._set_selected_sim_spin 62 self.sim_pack_data = self._sim_pack_relax_data 63 64 # Set up the spin parameters. 65 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) 66 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) 67 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) 68 self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm', desc='CSA value', py_type=float, grace_string='\\qCSA\\Q')

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 spin data has been set. 114 for spin, id in spin_loop(spin_id, return_id=True): 115 # Skip deselected spins. 116 if not spin.select: 117 continue 118 119 # Test if the nuclear isotope type has been set. 120 if not hasattr(spin, 'isotope'): 121 raise RelaxSpinTypeError 122 123 # Test if the CSA value has been set. 124 if not hasattr(spin, 'csa') or spin.csa == None: 125 raise RelaxNoValueError("CSA") 126 127 # Test the interatomic data. 128 interatoms = return_interatom_list(id) 129 for interatom in interatoms: 130 # No relaxation mechanism. 131 if not interatom.dipole_pair: 132 continue 133 134 # The interacting spin. 135 if id != interatom.spin_id1: 136 spin_id2 = interatom.spin_id1 137 else: 138 spin_id2 = interatom.spin_id2 139 spin2 = return_spin(spin_id2) 140 141 # Test if the nuclear isotope type has been set. 142 if not hasattr(spin2, 'isotope'): 143 raise RelaxSpinTypeError 144 145 # Test if the interatomic distance has been set. 146 if not hasattr(interatom, 'r') or interatom.r == None: 147 raise RelaxNoValueError("interatomic distance", spin_id=spin_id, spin_id2=spin_id2) 148 149 # Frequency index. 150 if cdp.jw_frq not in cdp.frq.values(): 151 raise RelaxError("No relaxation data corresponding to the frequency " + repr(cdp.jw_frq) + " has been loaded.") 152 153 # Reduced spectral density mapping. 154 for spin, id in spin_loop(spin_id, return_id=True): 155 # Skip deselected spins. 156 if not spin.select: 157 continue 158 159 # Set the r1, r2, and NOE to None. 160 r1 = None 161 r2 = None 162 noe = None 163 164 # Get the R1, R2, and NOE values corresponding to the set frequency. 165 for ri_id in cdp.ri_ids: 166 # The frequency does not match. 167 if cdp.frq[ri_id] != cdp.jw_frq: 168 continue 169 170 # R1. 171 if cdp.ri_type[ri_id] == 'R1': 172 if sim_index == None: 173 r1 = spin.ri_data[ri_id] 174 else: 175 r1 = spin.ri_data_sim[ri_id][sim_index] 176 177 # R2. 178 if cdp.ri_type[ri_id] == 'R2': 179 if sim_index == None: 180 r2 = spin.ri_data[ri_id] 181 else: 182 r2 = spin.ri_data_sim[ri_id][sim_index] 183 184 # NOE. 185 if cdp.ri_type[ri_id] == 'NOE': 186 if sim_index == None: 187 noe = spin.ri_data[ri_id] 188 else: 189 noe = spin.ri_data_sim[ri_id][sim_index] 190 191 # Skip the spin if not all of the three value exist. 192 if r1 == None or r2 == None or noe == None: 193 continue 194 195 # Loop over the interatomic data. 196 interatoms = return_interatom_list(id) 197 for i in range(len(interatoms)): 198 # No relaxation mechanism. 199 if not interatoms[i].dipole_pair: 200 continue 201 202 # The surrounding spins. 203 if id != interatoms[i].spin_id1: 204 spin_id2 = interatoms[i].spin_id1 205 else: 206 spin_id2 = interatoms[i].spin_id2 207 spin2 = return_spin(spin_id2) 208 209 # Gyromagnetic ratios. 210 gx = return_gyromagnetic_ratio(spin.isotope) 211 gh = return_gyromagnetic_ratio(spin2.isotope) 212 213 # The interatomic distance. 214 r = interatoms[i].r 215 216 # Initialise the function to calculate. 217 self.jw = Mapping(frq=cdp.jw_frq, gx=gx, gh=gh, mu0=mu0, h_bar=h_bar) 218 219 # Calculate the spectral density values. 220 j0, jwx, jwh = self.jw.func(r=r, csa=spin.csa, r1=r1, r2=r2, noe=noe) 221 222 # Reduced spectral density values. 223 if sim_index == None: 224 spin.j0 = j0 225 spin.jwx = jwx 226 spin.jwh = jwh 227 228 # Monte Carlo simulated reduced spectral density values. 229 else: 230 # Initialise the simulation data structures. 231 self.data_init(spin, sim=1) 232 if spin.j0_sim == None: 233 spin.j0_sim = [] 234 spin.jwx_sim = [] 235 spin.jwh_sim = [] 236 237 # Reduced spectral density values. 238 spin.j0_sim.append(j0) 239 spin.jwx_sim.append(jwx) 240 spin.jwh_sim.append(jwh)

241 242

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

244 """Initialise the data structures. 245 246 @param data_cont: The data container. 247 @type data_cont: instance 248 @keyword sim: The Monte Carlo simulation flag, which if true will initialise the simulation data structure. 249 @type sim: bool 250 """ 251 252 # Get the data names. 253 data_names = self.data_names() 254 255 # Loop over the data structure names. 256 for name in data_names: 257 # Simulation data structures. 258 if sim: 259 # Add '_sim' to the names. 260 name = name + '_sim' 261 262 # If the name is not in 'data_cont', add it. 263 if not hasattr(data_cont, name): 264 # Set the attribute. 265 setattr(data_cont, name, None)

266 267 268 default_value_doc = Desc_container("Reduced spectral density mapping default values") 269 default_value_doc.add_paragraph("These default values are found in the file 'physical_constants.py'.") 270 _table = uf_tables.add_table(label="table: J(w) default values", caption="Reduced spectral density mapping default values.") 271 _table.add_headings(["Data type", "Object name", "Value"]) 272 _table.add_row(["CSA", "'csa'", "-172 * 1e-6"]) 273 default_value_doc.add_table(_table.label) 274 275

276 - def overfit_deselect(self, data_check=True, verbose=True):

277 """Deselect spins which _have insufficient data to support calculation. 278 279 @keyword data_check: A flag to signal if the presence of base data is to be checked for. 280 @type data_check: bool 281 @keyword verbose: A flag which if True will allow printouts. 282 @type verbose: bool 283 """ 284 285 # Print out. 286 if verbose: 287 print("\nOver-fit spin deselection:") 288 289 # Test the sequence data exists. 290 if not exists_mol_res_spin_data(): 291 raise RelaxNoSequenceError 292 293 # Loop over spin data. 294 deselect_flag = False 295 for spin, spin_id in spin_loop(return_id=True): 296 # Skip deselected spins. 297 if not spin.select: 298 continue 299 300 # Check if data exists. 301 if not hasattr(spin, 'ri_data'): 302 warn(RelaxDeselectWarning(spin_id, 'missing relaxation data')) 303 spin.select = False 304 deselect_flag = True 305 continue 306 307 # Require 3 or more data points. 308 else: 309 # Count the points. 310 data_points = 0 311 for id in cdp.ri_ids: 312 if id in spin.ri_data and spin.ri_data[id] != None: 313 data_points += 1 314 315 # Not enough. 316 if data_points < 3: 317 warn(RelaxDeselectWarning(spin_id, 'insufficient relaxation data, 3 or more data points are required')) 318 spin.select = False 319 deselect_flag = True 320 continue 321 322 # Final printout. 323 if verbose and not deselect_flag: 324 print("No spins have been deselected.")

325 326 327 return_data_name_doc = Desc_container("Reduced spectral density mapping data type string matching patterns") 328 _table = uf_tables.add_table(label="table: J(w) data types", caption="Reduced spectral density mapping data type string matching patterns.") 329 _table.add_headings(["Data type", "Object name"]) 330 _table.add_row(["J(0)", "'j0'"]) 331 _table.add_row(["J(wX)", "'jwx'"]) 332 _table.add_row(["J(wH)", "'jwh'"]) 333 _table.add_row(["CSA", "'csa'"]) 334 return_data_name_doc.add_table(_table.label) 335 336 337 set_doc = Desc_container("Reduced spectral density mapping set details") 338 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.") 339 340

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

342 """Set the parameter errors. 343 344 @param model_info: The spin container originating from model_loop(). 345 @type model_info: SpinContainer instance 346 @param index: The index of the parameter to set the errors for. 347 @type index: int 348 @param error: The error value. 349 @type error: float 350 """ 351 352 # Alias. 353 spin = model_info 354 355 # Return J(0) sim data. 356 if index == 0: 357 spin.j0_err = error 358 359 # Return J(wX) sim data. 360 if index == 1: 361 spin.jwx_err = error 362 363 # Return J(wH) sim data. 364 if index == 2: 365 spin.jwh_err = error

366 367

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

369 """Return the array of simulation parameter values. 370 371 @param model_info: The spin container originating from model_loop(). 372 @type model_info: SpinContainer instance 373 @param index: The index of the parameter to return the array of values for. 374 @type index: int 375 @return: The array of simulation parameter values. 376 @rtype: list of float 377 """ 378 379 # Alias. 380 spin = model_info 381 382 # Skip deselected spins. 383 if not spin.select: 384 return 385 386 # Return J(0) sim data. 387 if index == 0: 388 return spin.j0_sim 389 390 # Return J(wX) sim data. 391 if index == 1: 392 return spin.jwx_sim 393 394 # Return J(wH) sim data. 395 if index == 2: 396 return spin.jwh_sim

397 398

399 - def sim_return_selected(self, model_info):

400 """Return the array of selected simulation flags. 401 402 @param model_info: The spin container originating from model_loop(). 403 @type model_info: SpinContainer instance 404 @return: The array of selected simulation flags. 405 @rtype: list of int 406 """ 407 408 # Alias. 409 spin = model_info 410 411 # Multiple spins. 412 return spin.select_sim

Source Code for Module specific_fns.jw_mapping