pipe_control.structure.main

1 ############################################################################### 2 # # 3 # Copyright (C) 2003-2013 Edward d'Auvergne # 4 # # 5 # This file is part of the program relax (http://www.nmr-relax.com). # 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 # Python module imports. 23 from minfx.generic import generic_minimise 24 from numpy import array, float64, zeros 25 from numpy.linalg import norm 26 from os import F_OK, access, getcwd 27 from re import search 28 import sys 29 from warnings import warn 30 31 # relax module imports. 32 from lib.errors import RelaxError, RelaxFileError, RelaxNoPdbError, RelaxNoSequenceError 33 from lib.io import get_file_path, open_write_file, write_data, write_spin_data 34 from lib.structure.internal.displacements import Displacements 35 from lib.structure.internal.object import Internal 36 from lib.structure.represent.diffusion_tensor import diffusion_tensor 37 from lib.structure.statistics import atomic_rmsd 38 from lib.structure.superimpose import fit_to_first, fit_to_mean 39 from lib.warnings import RelaxWarning, RelaxNoPDBFileWarning, RelaxZeroVectorWarning 40 from pipe_control import molmol, pipes 41 from pipe_control.interatomic import interatomic_loop 42 from pipe_control.mol_res_spin import create_spin, exists_mol_res_spin_data, generate_spin_id_unique, linear_ave, return_spin, spin_loop 43 from pipe_control.structure.mass import pipe_centre_of_mass 44 from status import Status; status = Status() 45 from target_functions.ens_pivot_finder import Pivot_finder 46 47

48 -def add_atom(mol_name=None, atom_name=None, res_name=None, res_num=None, pos=[None, None, None], element=None, atom_num=None, chain_id=None, segment_id=None, pdb_record=None):

49 """Add a new atom to the structural data object. 50 51 @keyword mol_name: The name of the molecule. 52 @type mol_name: str 53 @keyword atom_name: The atom name, e.g. 'H1'. 54 @type atom_name: str or None 55 @keyword res_name: The residue name. 56 @type res_name: str or None 57 @keyword res_num: The residue number. 58 @type res_num: int or None 59 @keyword pos: The position vector of coordinates. If a rank-2 array is supplied, the length of the first dimension must match the number of models. 60 @type pos: rank-1 or rank-2 array or list of float 61 @keyword element: The element symbol. 62 @type element: str or None 63 @keyword atom_num: The atom number. 64 @type atom_num: int or None 65 @keyword chain_id: The chain identifier. 66 @type chain_id: str or None 67 @keyword segment_id: The segment identifier. 68 @type segment_id: str or None 69 @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or 'HETATM'. 70 @type pdb_record: str or None 71 """ 72 73 # Test if the current data pipe exists. 74 pipes.test() 75 76 # Place the structural object into the relax data store if needed. 77 if not hasattr(cdp, 'structure'): 78 cdp.structure = Internal() 79 80 # Add the atoms. 81 cdp.structure.add_atom(mol_name=mol_name, atom_name=atom_name, res_name=res_name, res_num=res_num, pos=pos, element=element, atom_num=atom_num, chain_id=chain_id, segment_id=segment_id, pdb_record=pdb_record)

82 83

84 -def add_model(model_num=None):

85 """Add a new model to the empty structural data object.""" 86 87 # Test if the current data pipe exists. 88 pipes.test() 89 90 # Place the structural object into the relax data store if needed. 91 if not hasattr(cdp, 'structure'): 92 cdp.structure = Internal() 93 94 # Check the structural object is empty. 95 if cdp.structure.num_molecules() != 0: 96 raise RelaxError("The internal structural object is not empty.") 97 98 # Add a model. 99 cdp.structure.structural_data.add_item(model_num=model_num) 100 print("Created the empty model number %s." % model_num)

101 102

103 -def connect_atom(index1=None, index2=None):

104 """Connect two atoms. 105 106 @keyword index1: The global index of the first atom. 107 @type index1: str 108 @keyword index2: The global index of the first atom. 109 @type index2: str 110 """ 111 112 # Test if the current data pipe exists. 113 pipes.test() 114 115 # Place the structural object into the relax data store if needed. 116 if not hasattr(cdp, 'structure'): 117 cdp.structure = Internal() 118 119 # Add the atoms. 120 cdp.structure.connect_atom(index1=index1, index2=index2)

121 122

123 -def create_cone_pdb(mol=None, cone=None, start_res=1, apex=None, axis=None, R=None, inc=None, scale=30.0, distribution='regular', file=None, dir=None, force=False, axis_flag=True):

124 """Create a PDB representation of the given cone object. 125 126 @keyword mol: The molecule container. 127 @type mol: MolContainer instance 128 @keyword cone: The cone object. This should provide the limit_check() method with determines the limits of the distribution accepting two arguments, the polar angle phi and the azimuthal angle theta, and return True if the point is in the limits or False if outside. It should also provide the theta_max() method for returning the theta value for the given phi, the phi_max() method for returning the phi value for the given theta. 129 @type cone: class instance 130 @keyword start_res: The starting residue number. 131 @type start_res: str 132 @keyword apex: The apex of the cone. 133 @type apex: rank-1, 3D numpy array 134 @keyword axis: The central axis of the cone. If not supplied, the z-axis will be used. 135 @type axis: rank-1, 3D numpy array 136 @keyword R: The rotation matrix. 137 @type R: rank-2, 3D numpy array 138 @keyword inc: The increment number used to determine the number of latitude and longitude lines. 139 @type inc: int 140 @keyword scale: The scaling factor to stretch the unit cone by. 141 @type scale: float 142 @keyword distribution: The type of point distribution to use. This can be 'uniform' or 'regular'. 143 @type distribution: str 144 @keyword file: The name of the PDB file to create. 145 @type file: str 146 @keyword dir: The name of the directory to place the PDB file into. 147 @type dir: str 148 @keyword force: Flag which if set to True will overwrite any pre-existing file. 149 @type force: bool 150 @keyword axis_flag: A flag which if True will create the cone's axis. 151 @type axis_flag: bool 152 """ 153 154 # No molecule supplied. 155 if mol == None: 156 # Create the structural object. 157 structure = Internal() 158 159 # Add a molecule. 160 structure.add_molecule(name='cone') 161 162 # Alias the single molecule from the single model. 163 mol = structure.structural_data[0].mol[0] 164 165 # Create the object. 166 cone(mol=mol, cone=cone, start_res=start_res, apex=apex, axis=axis, R=R, inc=inc, scale=scale, distribution=distribution, axis_flag=axis_flag) 167 168 # Create the PDB file. 169 if file != None: 170 print("\nGenerating the PDB file.") 171 pdb_file = open_write_file(file_name=file, dir=dir, force=force) 172 structure.write_pdb(pdb_file) 173 pdb_file.close() 174 175 # Add the file to the results file list. 176 if not hasattr(cdp, 'result_files'): 177 cdp.result_files = [] 178 cdp.result_files.append(['cone_pdb', 'Cone PDB', get_file_path(file, dir)]) 179 status.observers.result_file.notify()

180 181

182 -def create_diff_tensor_pdb(scale=1.8e-6, file=None, dir=None, force=False):

183 """Create the PDB representation of the diffusion tensor. 184 185 @keyword scale: The scaling factor for the diffusion tensor. 186 @type scale: float 187 @keyword file: The name of the PDB file to create. 188 @type file: str 189 @keyword dir: The name of the directory to place the PDB file into. 190 @type dir: str 191 @keyword force: Flag which if set to True will overwrite any pre-existing file. 192 @type force: bool 193 """ 194 195 # Test if the current data pipe exists. 196 pipes.test() 197 198 # Calculate the centre of mass. 199 com = pipe_centre_of_mass() 200 201 # Create the structural object. 202 structure = Internal() 203 204 # Create an array of data pipes to loop over (hybrid support). 205 if cdp.pipe_type == 'hybrid': 206 pipe_list = cdp.hybrid_pipes 207 else: 208 pipe_list = [pipes.cdp_name()] 209 210 # The molecule names. 211 if cdp.pipe_type == 'hybrid': 212 mol_names = [] 213 for pipe in pipe_list: 214 mol_names.append('diff_tensor_' % pipe) 215 else: 216 mol_names = ['diff_tensor'] 217 218 # Loop over the pipes. 219 for pipe_index in range(len(pipe_list)): 220 # Get the pipe container. 221 pipe = pipes.get_pipe(pipe_list[pipe_index]) 222 223 # Test if the diffusion tensor data is loaded. 224 if not hasattr(pipe, 'diff_tensor'): 225 raise RelaxNoTensorError('diffusion') 226 227 # Test if a structure has been loaded. 228 if not hasattr(cdp, 'structure'): 229 raise RelaxNoPdbError 230 231 # Add a new structure. 232 structure.add_molecule(name=mol_names[pipe_index]) 233 234 # Alias the single molecule from the single model. 235 mol = structure.get_molecule(mol_names[pipe_index]) 236 237 # The diffusion tensor type. 238 diff_type = pipe.diff_tensor.type 239 if diff_type == 'spheroid': 240 diff_type = pipe.diff_tensor.spheroid_type 241 242 # Simulation info. 243 sim_num = None 244 if hasattr(pipe.diff_tensor, 'tm_sim'): 245 # The number. 246 sim_num = len(pipe.diff_tensor.tm_sim) 247 248 # Tensor axes. 249 axes = [] 250 sim_axes = [] 251 if diff_type in ['oblate', 'prolate']: 252 axes.append(pipe.diff_tensor.Dpar * pipe.diff_tensor.Dpar_unit) 253 if sim_num != None: 254 sim_axes.append([]) 255 for i in range(sim_num): 256 sim_axes[0].append(pipe.diff_tensor.Dpar_sim[i] * pipe.diff_tensor.Dpar_unit_sim[i]) 257 258 if diff_type == 'ellipsoid': 259 axes.append(pipe.diff_tensor.Dx * pipe.diff_tensor.Dx_unit) 260 axes.append(pipe.diff_tensor.Dy * pipe.diff_tensor.Dy_unit) 261 axes.append(pipe.diff_tensor.Dz * pipe.diff_tensor.Dz_unit) 262 if sim_num != None: 263 sim_axes.append([]) 264 sim_axes.append([]) 265 sim_axes.append([]) 266 for i in range(sim_num): 267 sim_axes[0].append(pipe.diff_tensor.Dx_sim[i] * pipe.diff_tensor.Dx_unit_sim[i]) 268 sim_axes[1].append(pipe.diff_tensor.Dy_sim[i] * pipe.diff_tensor.Dy_unit_sim[i]) 269 sim_axes[2].append(pipe.diff_tensor.Dz_sim[i] * pipe.diff_tensor.Dz_unit_sim[i]) 270 271 # Create the object. 272 diffusion_tensor(mol=mol, tensor=pipe.diff_tensor.tensor, tensor_diag=pipe.diff_tensor.tensor_diag, diff_type=diff_type, rotation=pipe.diff_tensor.rotation, axes=axes, sim_axes=sim_axes, com=com, scale=scale) 273 274 275 # Create the PDB file. 276 ###################### 277 278 # Print out. 279 print("\nGenerating the PDB file.") 280 281 # Create the PDB file. 282 tensor_pdb_file = open_write_file(file, dir, force=force) 283 structure.write_pdb(tensor_pdb_file) 284 tensor_pdb_file.close() 285 286 # Add the file to the results file list. 287 if not hasattr(cdp, 'result_files'): 288 cdp.result_files = [] 289 if dir == None: 290 dir = getcwd() 291 cdp.result_files.append(['diff_tensor_pdb', 'Diffusion tensor PDB', get_file_path(file, dir)]) 292 status.observers.result_file.notify()

293 294

295 -def delete(atom_id=None):

296 """Delete structural data. 297 298 @keyword atom_id: The molecule, residue, and atom identifier string. This matches the spin ID string format. If not given, then all structural data will be deleted. 299 @type atom_id: str or None 300 """ 301 302 # Test if the current data pipe exists. 303 pipes.test() 304 305 # Run the object method. 306 if hasattr(cdp, 'structure'): 307 print("Deleting structural data from the current pipe.") 308 cdp.structure.delete(atom_id=atom_id) 309 else: 310 print("No structures are present.") 311 312 # Then remove any spin specific structural info. 313 print("Deleting all spin specific structural info.") 314 for spin in spin_loop(selection=atom_id): 315 # Delete positional information. 316 if hasattr(spin, 'pos'): 317 del spin.pos 318 319 # Then remove any interatomic vector structural info. 320 print("Deleting all interatomic vectors.") 321 for interatom in interatomic_loop(selection1=atom_id): 322 # Delete bond vectors. 323 if hasattr(interatom, 'vector'): 324 del interatom.vector

325 326

327 -def displacement(model_from=None, model_to=None, atom_id=None, centroid=None):

328 """Calculate the rotational and translational displacement between two structural models. 329 330 @keyword model_from: The optional model number for the starting position of the displacement. 331 @type model_from: int or None 332 @keyword model_to: The optional model number for the ending position of the displacement. 333 @type model_to: int or None 334 @keyword atom_id: The molecule, residue, and atom identifier string. This matches the spin ID string format. 335 @type atom_id: str or None 336 @keyword centroid: An alternative position of the centroid, used for studying pivoted systems. 337 @type centroid: list of float or numpy rank-1, 3D array 338 """ 339 340 # Test if the current data pipe exists. 341 pipes.test() 342 343 # Convert the model_from and model_to args to lists, is supplied. 344 if model_from != None: 345 model_from = [model_from] 346 if model_to != None: 347 model_to = [model_to] 348 349 # Create a list of all models. 350 models = [] 351 for model in cdp.structure.model_loop(): 352 models.append(model.num) 353 354 # Set model_from or model_to to all models if None. 355 if model_from == None: 356 model_from = models 357 if model_to == None: 358 model_to = models 359 360 # Initialise the data structure. 361 if not hasattr(cdp.structure, 'displacements'): 362 cdp.structure.displacements = Displacements() 363 364 # Loop over the starting models. 365 for i in range(len(model_from)): 366 # Assemble the atomic coordinates. 367 coord_from = [] 368 for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model_from[i], pos_flag=True): 369 coord_from.append(pos[0]) 370 371 # Loop over the ending models. 372 for j in range(len(model_to)): 373 # Assemble the atomic coordinates. 374 coord_to = [] 375 for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model_to[j], pos_flag=True): 376 coord_to.append(pos[0]) 377 378 # Send to the base container for the calculations. 379 cdp.structure.displacements._calculate(model_from=model_from[i], model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to), centroid=centroid)

380 381

382 -def find_pivot(models=None, atom_id=None, init_pos=None, func_tol=1e-5, box_limit=200):

383 """Superimpose a set of structural models. 384 385 @keyword models: The list of models to use. If set to None, then all models will be used. 386 @type models: list of int or None 387 @keyword atom_id: The molecule, residue, and atom identifier string. This matches the spin ID string format. 388 @type atom_id: str or None 389 @keyword init_pos: The starting pivot position for the pivot point optimisation. 390 @type init_pos: list of float or numpy rank-1, 3D array 391 @keyword func_tol: The function tolerance which, when reached, terminates optimisation. Setting this to None turns of the check. 392 @type func_tol: None or float 393 @keyword box_limit: The simplex optimisation used in this function is constrained withing a box of +/- x Angstrom containing the pivot point using the logarithmic barrier function. This argument is the value of x. 394 @type box_limit: int 395 """ 396 397 # Test if the current data pipe exists. 398 pipes.test() 399 400 # Initialised the starting position if needed. 401 if init_pos == None: 402 init_pos = zeros(3, float64) 403 init_pos = array(init_pos) 404 405 # Validate the models. 406 cdp.structure.validate_models() 407 408 # Create a list of all models. 409 if models == None: 410 models = [] 411 for model in cdp.structure.model_loop(): 412 models.append(model.num) 413 414 # Assemble the atomic coordinates of all models. 415 coord = [] 416 for model in models: 417 coord.append([]) 418 for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, pos_flag=True): 419 coord[-1].append(pos[0]) 420 coord[-1] = array(coord[-1]) 421 coord = array(coord) 422 423 # Linear constraints for the pivot position (between -1000 and 1000 Angstrom). 424 A = zeros((6, 3), float64) 425 b = zeros(6, float64) 426 for i in range(3): 427 A[2*i, i] = 1 428 A[2*i+1, i] = -1 429 b[2*i] = -box_limit 430 b[2*i+1] = -box_limit 431 432 # The target function. 433 finder = Pivot_finder(models, coord) 434 results = generic_minimise(func=finder.func, x0=init_pos, min_algor='Log barrier', min_options=('simplex',), A=A, b=b, func_tol=func_tol, print_flag=1) 435 436 # No result. 437 if results == None: 438 return 439 440 # Store the data. 441 cdp.structure.pivot = results 442 443 # Print out. 444 print("Motional pivot found at: %s" % results)

445 446

447 -def get_pos(spin_id=None, str_id=None, ave_pos=False):

448 """Load the spins from the structural object into the relax data store. 449 450 @keyword spin_id: The molecule, residue, and spin identifier string. 451 @type spin_id: str 452 @keyword str_id: The structure identifier. This can be the file name, model number, or structure number. 453 @type str_id: int or str 454 @keyword ave_pos: A flag specifying if the average atom position or the atom position from all loaded structures is loaded into the SpinContainer. 455 @type ave_pos: bool 456 """ 457 458 # Test if the current data pipe exists. 459 pipes.test() 460 461 # Test if the structure exists. 462 if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or not cdp.structure.num_molecules(): 463 raise RelaxNoPdbError 464 465 # Loop over all atoms of the spin_id selection. 466 data = [] 467 for mol_name, res_num, res_name, atom_num, atom_name, element, pos in cdp.structure.atom_loop(atom_id=spin_id, str_id=str_id, mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_num_flag=True, atom_name_flag=True, element_flag=True, pos_flag=True, ave=ave_pos): 468 # Remove the '+' regular expression character from the mol, res, and spin names! 469 if mol_name and search('\+', mol_name): 470 mol_name = mol_name.replace('+', '') 471 if res_name and search('\+', res_name): 472 res_name = res_name.replace('+', '') 473 if atom_name and search('\+', atom_name): 474 atom_name = atom_name.replace('+', '') 475 476 # The spin identification string. 477 id = generate_spin_id_unique(res_num=res_num, res_name=None, spin_num=atom_num, spin_name=atom_name) 478 479 # Get the spin container. 480 spin_cont = return_spin(id) 481 482 # Skip the spin if it doesn't exist. 483 if spin_cont == None: 484 continue 485 486 # Add the position vector to the spin container. 487 spin_cont.pos = pos 488 489 # Store the data for a printout at the end. 490 data.append([id, repr(pos)]) 491 492 # No positions found. 493 if not len(data): 494 raise RelaxError("No positional information matching the spin ID '%s' could be found." % spin_id) 495 496 # Update pseudo-atoms. 497 for spin in spin_loop(): 498 if hasattr(spin, 'members'): 499 # Get the spin positions. 500 positions = [] 501 for atom in spin.members: 502 # Get the spin container. 503 subspin = return_spin(atom) 504 505 # Test that the spin exists. 506 if subspin == None: 507 raise RelaxNoSpinError(atom) 508 509 # Test the position. 510 if not hasattr(subspin, 'pos') or subspin.pos == None or not len(subspin.pos): 511 raise RelaxError("Positional information is not available for the atom '%s'." % atom) 512 513 # Alias the position. 514 pos = subspin.pos 515 516 # Convert to a list of lists if not already. 517 multi_model = True 518 if type(pos[0]) in [float, float64]: 519 multi_model = False 520 pos = [pos] 521 522 # Store the position. 523 positions.append([]) 524 for i in range(len(pos)): 525 positions[-1].append(pos[i].tolist()) 526 527 # The averaging. 528 if spin.averaging == 'linear': 529 # Average pos. 530 ave = linear_ave(positions) 531 532 # Convert to the correct structure. 533 if multi_model: 534 spin.pos = ave 535 else: 536 spin.pos = ave[0] 537 538 # Print out. 539 write_data(out=sys.stdout, headings=["Spin_ID", "Position"], data=data)

540 541

542 -def load_spins(spin_id=None, str_id=None, mol_name_target=None, ave_pos=False):

543 """Load the spins from the structural object into the relax data store. 544 545 @keyword spin_id: The molecule, residue, and spin identifier string. 546 @type spin_id: str 547 @keyword str_id: The structure identifier. This can be the file name, model number, or structure number. 548 @type str_id: int or str 549 @keyword mol_name: The name of target molecule container, overriding the name of the loaded structures 550 @type mol_name: str or None 551 @keyword ave_pos: A flag specifying if the average atom position or the atom position from all loaded structures is loaded into the SpinContainer. 552 @type ave_pos: bool 553 """ 554 555 # Test if the current data pipe exists. 556 pipes.test() 557 558 # Test if the structure exists. 559 if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or not cdp.structure.num_molecules(): 560 raise RelaxNoPdbError 561 562 # Print out. 563 print("Adding the following spins to the relax data store.\n") 564 565 # Init the data for printing out. 566 mol_names = [] 567 res_nums = [] 568 res_names = [] 569 spin_nums = [] 570 spin_names = [] 571 572 # Loop over all atoms of the spin_id selection. 573 for mol_name, res_num, res_name, atom_num, atom_name, element, pos in cdp.structure.atom_loop(atom_id=spin_id, str_id=str_id, mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_num_flag=True, atom_name_flag=True, element_flag=True, pos_flag=True, ave=ave_pos): 574 # Override the molecule name. 575 if mol_name_target: 576 mol_name = mol_name_target 577 578 # Remove the '+' regular expression character from the mol, res, and spin names! 579 if mol_name and search('\+', mol_name): 580 mol_name = mol_name.replace('+', '') 581 if res_name and search('\+', res_name): 582 res_name = res_name.replace('+', '') 583 if atom_name and search('\+', atom_name): 584 atom_name = atom_name.replace('+', '') 585 586 # Generate a spin ID for the current atom. 587 id = generate_spin_id_unique(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=atom_num, spin_name=atom_name) 588 589 # Create the spin. 590 try: 591 spin_cont = create_spin(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=atom_num, spin_name=atom_name) 592 593 # Otherwise, get the spin container. 594 except RelaxError: 595 spin_cont = return_spin(id) 596 597 # Append all the spin ID info for printing later. 598 if mol_name_target: 599 mol_names.append(mol_name_target) 600 else: 601 mol_names.append(mol_name) 602 res_nums.append(res_num) 603 res_names.append(res_name) 604 spin_nums.append(atom_num) 605 spin_names.append(atom_name) 606 607 # Position vector. 608 spin_cont.pos = pos 609 610 # Add the element. 611 spin_cont.element = element 612 613 # Catch no data. 614 if len(mol_names) == 0: 615 warn(RelaxWarning("No spins matching the '%s' ID string could be found." % spin_id)) 616 return 617 618 # Print out. 619 write_spin_data(file=sys.stdout, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names)

620 621

622 -def read_pdb(file=None, dir=None, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, alt_loc=None, verbosity=1, merge=False, fail=True):

623 """The PDB loading function. 624 625 @keyword file: The name of the PDB file to read. 626 @type file: str 627 @keyword dir: The directory where the PDB file is located. If set to None, then the file will be searched for in the current directory. 628 @type dir: str or None 629 @keyword read_mol: The molecule(s) to read from the file, independent of model. The molecules are numbered consecutively from 1. If set to None, then all molecules will be loaded. 630 @type read_mol: None, int, or list of int 631 @keyword set_mol_name: Set the names of the molecules which are loaded. If set to None, then the molecules will be automatically labelled based on the file name or other information. 632 @type set_mol_name: None, str, or list of str 633 @keyword read_model: The PDB model to extract from the file. If set to None, then all models will be loaded. 634 @type read_model: None, int, or list of int 635 @keyword set_model_num: Set the model number of the loaded molecule. If set to None, then the PDB model numbers will be preserved, if they exist. 636 @type set_model_num: None, int, or list of int 637 @keyword alt_loc: The PDB ATOM record 'Alternate location indicator' field value to select which coordinates to use. 638 @type alt_loc: str or None 639 @keyword verbosity: The amount of information to print to screen. Zero corresponds to minimal output while higher values increase the amount of output. The default value is 1. 640 @type verbosity: int 641 @keyword merge: A flag which if set to True will try to merge the PDB structure into the currently loaded structures. 642 @type merge: bool 643 @keyword fail: A flag which, if True, will cause a RelaxError to be raised if the PDB file does not exist. If False, then a RelaxWarning will be trown instead. 644 @type fail: bool 645 @raise RelaxFileError: If the fail flag is set, then a RelaxError is raised if the PDB file does not exist. 646 """ 647 648 # Test if the current data pipe exists. 649 pipes.test() 650 651 # The file path. 652 file_path = get_file_path(file, dir) 653 654 # Try adding file extensions to the end of the file path, if the file can't be found. 655 file_path_orig = file_path 656 if not access(file_path, F_OK): 657 # List of possible extensions. 658 for ext in ['.pdb', '.gz', '.pdb.gz', '.bz2', '.pdb.bz2']: 659 # Add the extension if the file can be found. 660 if access(file_path+ext, F_OK): 661 file_path = file_path + ext 662 663 # Test if the file exists. 664 if not access(file_path, F_OK): 665 if fail: 666 raise RelaxFileError('PDB', file_path_orig) 667 else: 668 warn(RelaxNoPDBFileWarning(file_path)) 669 return 670 671 # Place the internal structural object into the relax data store. 672 if not hasattr(cdp, 'structure'): 673 cdp.structure = Internal() 674 675 # Load the structures. 676 cdp.structure.load_pdb(file_path, read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num, alt_loc=alt_loc, verbosity=verbosity, merge=merge) 677 678 # Load into Molmol (if running). 679 molmol.molmol_obj.open_pdb()

680 681

682 -def read_xyz(file=None, dir=None, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, verbosity=1, fail=True):

683 """The XYZ loading function. 684 685 686 @keyword file: The name of the XYZ file to read. 687 @type file: str 688 @keyword dir: The directory where the XYZ file is located. If set to None, then the 689 file will be searched for in the current directory. 690 @type dir: str or None 691 @keyword read_mol: The molecule(s) to read from the file, independent of model. 692 If set to None, then all molecules will be loaded. 693 @type read_mol: None, int, or list of int 694 @keyword set_mol_name: Set the names of the molecules which are loaded. If set to None, then 695 the molecules will be automatically labelled based on the file name or 696 other information. 697 @type set_mol_name: None, str, or list of str 698 @keyword read_model: The XYZ model to extract from the file. If set to None, then all models 699 will be loaded. 700 @type read_model: None, int, or list of int 701 @keyword set_model_num: Set the model number of the loaded molecule. If set to None, then the 702 XYZ model numbers will be preserved, if they exist. 703 @type set_model_num: None, int, or list of int 704 @keyword fail: A flag which, if True, will cause a RelaxError to be raised if the XYZ 705 file does not exist. If False, then a RelaxWarning will be trown 706 instead. 707 @type fail: bool 708 @keyword verbosity: The amount of information to print to screen. Zero corresponds to 709 minimal output while higher values increase the amount of output. The 710 default value is 1. 711 @type verbosity: int 712 @raise RelaxFileError: If the fail flag is set, then a RelaxError is raised if the XYZ file 713 does not exist. 714 """ 715 716 # Test if the current data pipe exists. 717 pipes.test() 718 719 # The file path. 720 file_path = get_file_path(file, dir) 721 722 # Try adding '.xyz' to the end of the file path, if the file can't be found. 723 if not access(file_path, F_OK): 724 file_path_orig = file_path 725 file_path = file_path + '.xyz' 726 727 # Test if the file exists. 728 if not access(file_path, F_OK): 729 if fail: 730 raise RelaxFileError('XYZ', file_path_orig) 731 else: 732 warn(RelaxNoPDBFileWarning(file_path)) 733 return 734 735 # Place the structural object into the relax data store. 736 if not hasattr(cdp, 'structure'): 737 cdp.structure = Internal() 738 739 # Load the structures. 740 cdp.structure.load_xyz(file_path, read_mol=read_mol, set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num, verbosity=verbosity)

741 742

743 -def rmsd(atom_id=None, models=None):

744 """Calculate the RMSD between the loaded models. 745 746 @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used. 747 @type atom_id: str or None 748 @keyword models: The list of models to calculate the RMDS of. If set to None, then all models will be used. 749 @type models: list of int or None 750 @return: The RMSD value. 751 @rtype: float 752 """ 753 754 # Test if the current data pipe exists. 755 pipes.test() 756 757 # Create a list of all models. 758 if models == None: 759 models = [] 760 for model in cdp.structure.model_loop(): 761 models.append(model.num) 762 763 # Assemble the atomic coordinates of all models. 764 coord = [] 765 for model in models: 766 coord.append([]) 767 for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, pos_flag=True): 768 coord[-1].append(pos[0]) 769 coord[-1] = array(coord[-1]) 770 771 # Calculate the RMSD. 772 cdp.structure.rmsd = atomic_rmsd(coord, verbosity=1) 773 774 # Return the RMSD. 775 return cdp.structure.rmsd

776 777

778 -def rotate(R=None, origin=None, model=None, atom_id=None):

779 """Rotate the structural data about the origin by the specified forwards rotation. 780 781 @keyword R: The forwards rotation matrix. 782 @type R: numpy 3D, rank-2 array or a 3x3 list of floats 783 @keyword origin: The origin of the rotation. If not supplied, the origin will be set to [0, 0, 0]. 784 @type origin: numpy 3D, rank-1 array or list of len 3 or None 785 @keyword model: The model to rotate. If None, all models will be rotated. 786 @type model: int 787 @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used. 788 @type atom_id: str or None 789 """ 790 791 # Test if the current data pipe exists. 792 pipes.test() 793 794 # Test if the structure exists. 795 if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or not cdp.structure.num_molecules(): 796 raise RelaxNoPdbError 797 798 # Set the origin if not supplied. 799 if origin == None: 800 origin = [0, 0, 0] 801 802 # Convert the args to numpy float data structures. 803 R = array(R, float64) 804 origin = array(origin, float64) 805 806 # Call the specific code. 807 cdp.structure.rotate(R=R, origin=origin, model=model, atom_id=atom_id)

808 809

810 -def set_vector(spin=None, xh_vect=None):

811 """Place the XH unit vector into the spin container object. 812 813 @keyword spin: The spin container object. 814 @type spin: SpinContainer instance 815 @keyword xh_vect: The unit vector parallel to the XH bond. 816 @type xh_vect: array of len 3 817 """ 818 819 # Place the XH unit vector into the container. 820 spin.xh_vect = xh_vect

821 822

823 -def superimpose(models=None, method='fit to mean', atom_id=None, centroid=None):

824 """Superimpose a set of structural models. 825 826 @keyword models: The list of models to superimpose. If set to None, then all models will be used. 827 @type models: list of int or None 828 @keyword method: The superimposition method. It must be one of 'fit to mean' or 'fit to first'. 829 @type method: str 830 @keyword atom_id: The molecule, residue, and atom identifier string. This matches the spin ID string format. 831 @type atom_id: str or None 832 @keyword centroid: An alternative position of the centroid to allow for different superpositions, for example of pivot point motions. 833 @type centroid: list of float or numpy rank-1, 3D array 834 """ 835 836 # Check the method. 837 allowed = ['fit to mean', 'fit to first'] 838 if method not in allowed: 839 raise RelaxError("The superimposition method '%s' is unknown. It must be one of %s." % (method, allowed)) 840 841 # Test if the current data pipe exists. 842 pipes.test() 843 844 # Validate the models. 845 cdp.structure.validate_models() 846 847 # Create a list of all models. 848 if models == None: 849 models = [] 850 for model in cdp.structure.model_loop(): 851 models.append(model.num) 852 853 # Assemble the atomic coordinates of all models. 854 coord = [] 855 for model in models: 856 coord.append([]) 857 for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, pos_flag=True): 858 coord[-1].append(pos[0]) 859 coord[-1] = array(coord[-1]) 860 861 # The different algorithms. 862 if method == 'fit to mean': 863 T, R, pivot = fit_to_mean(models=models, coord=coord, centroid=centroid) 864 elif method == 'fit to first': 865 T, R, pivot = fit_to_first(models=models, coord=coord, centroid=centroid) 866 867 868 # Update to the new coordinates. 869 for i in range(len(models)): 870 # Translate the molecule first (the rotational pivot is defined in the first model). 871 translate(T=T[i], model=models[i]) 872 873 # Rotate the molecule. 874 rotate(R=R[i], origin=pivot[i], model=models[i])

875 876

877 -def translate(T=None, model=None, atom_id=None):

878 """Shift the structural data by the specified translation vector. 879 880 @keyword T: The translation vector. 881 @type T: numpy rank-1, 3D array or list of float 882 @keyword model: The model to translate. If None, all models will be rotated. 883 @type model: int or None 884 @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used. 885 @type atom_id: str or None 886 """ 887 888 # Test if the current data pipe exists. 889 pipes.test() 890 891 # Test if the structure exists. 892 if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or not cdp.structure.num_molecules(): 893 raise RelaxNoPdbError 894 895 # Convert the args to numpy float data structures. 896 T = array(T, float64) 897 898 # Call the specific code. 899 cdp.structure.translate(T=T, model=model, atom_id=atom_id)

900 901

902 -def vectors(spin_id1=None, spin_id2=None, model=None, verbosity=1, ave=True, unit=True):

903 """Extract the bond vectors from the loaded structures and store them in the spin container. 904 905 @keyword spin_id1: The spin identifier string of the first spin of the pair. 906 @type spin_id1: str 907 @keyword spin_id2: The spin identifier string of the second spin of the pair. 908 @type spin_id2: str 909 @keyword model: The model to extract the vector from. If None, all vectors will be extracted. 910 @type model: str 911 @keyword verbosity: The higher the value, the more information is printed to screen. 912 @type verbosity: int 913 @keyword ave: A flag which if True will cause the average of all vectors to be extracted. 914 @type ave: bool 915 @keyword unit: A flag which if True will cause the function to calculate the unit vectors. 916 @type unit: bool 917 """ 918 919 # Test if the current data pipe exists. 920 pipes.test() 921 922 # Test if the PDB file has been loaded. 923 if not hasattr(cdp, 'structure'): 924 raise RelaxNoPdbError 925 926 # Test if sequence data is loaded. 927 if not exists_mol_res_spin_data(): 928 raise RelaxNoSequenceError 929 930 # Print out. 931 if verbosity: 932 # Number of models. 933 num_models = cdp.structure.num_models() 934 935 # Multiple models loaded. 936 if num_models > 1: 937 if model: 938 print("Extracting vectors for model '%s'." % model) 939 else: 940 print("Extracting vectors for all %s models." % num_models) 941 if ave: 942 print("Averaging all vectors.") 943 944 # Single model loaded. 945 else: 946 print("Extracting vectors from the single model.") 947 948 # Unit vectors. 949 if unit: 950 print("Calculating the unit vectors.") 951 952 # Loop over the spins. 953 no_vectors = True 954 for spin, mol_name, res_num, res_name in spin_loop(selection=spin_id, full_info=True): 955 # Skip deselected spins. 956 if not spin.select: 957 continue 958 959 # The spin identification string. The residue name and spin num is not included to allow molecules with point mutations to be used as different models. 960 id = generate_spin_id_unique(res_num=res_num, res_name=None, spin_name=spin.name, spin_num=spin.num) 961 962 # Test that the spin number or name are set (one or both are essential for the identification of the atom). 963 if spin.num == None and spin.name == None: 964 warn(RelaxWarning("Either the spin number or name must be set for the spin " + repr(id) + " to identify the corresponding atom in the molecule.")) 965 continue 966 967 # The bond vector already exists. 968 if hasattr(spin, 'vector'): 969 obj = getattr(spin, 'vector') 970 if obj != None: 971 warn(RelaxWarning("The bond vector for the spin " + repr(id) + " already exists.")) 972 continue 973 974 # Get the bond info. 975 bond_vectors, attached_name, warnings = cdp.structure.bond_vectors(attached_atom=attached, model_num=model, res_num=res_num, spin_name=spin.name, spin_num=spin.num, return_name=True, return_warnings=True) 976 id2 = generate_spin_id_unique(res_num=res_num, res_name=None, spin_name=spin.name) 977 978 # No attached atom. 979 if not bond_vectors: 980 # Warning messages. 981 if warnings: 982 warn(RelaxWarning(warnings + " (atom ID " + repr(id) + ").")) 983 984 # Skip the spin. 985 continue 986 987 # Set the attached atom name. 988 if not hasattr(spin, 'attached_atom'): 989 spin.attached_atom = attached_name 990 elif spin.attached_atom != attached_name: 991 raise RelaxError("The " + repr(spin.attached_atom) + " atom already attached to the spin does not match the attached atom " + repr(attached_name) + ".") 992 993 # Initialise the average vector. 994 if ave: 995 ave_vector = zeros(3, float64) 996 997 # Loop over the individual vectors. 998 for i in range(len(bond_vectors)): 999 # Unit vector. 1000 if unit: 1001 # Normalisation factor. 1002 norm_factor = norm(bond_vectors[i]) 1003 1004 # Test for zero length. 1005 if norm_factor == 0.0: 1006 warn(RelaxZeroVectorWarning(spin_id1=id, spin_id2=id2)) 1007 1008 # Calculate the normalised vector. 1009 else: 1010 bond_vectors[i] = bond_vectors[i] / norm_factor 1011 1012 # Sum the vectors. 1013 if ave: 1014 ave_vector = ave_vector + bond_vectors[i] 1015 1016 # Average. 1017 if ave: 1018 vector = ave_vector / float(len(bond_vectors)) 1019 else: 1020 vector = bond_vectors 1021 1022 # Convert to a single vector if needed. 1023 if len(vector) == 1: 1024 vector = vector[0] 1025 1026 # Set the vector. 1027 setattr(spin, 'vector', vector) 1028 1029 # We have a vector! 1030 no_vectors = False 1031 1032 # Print out of modified spins. 1033 if verbosity: 1034 # The number of vectors. 1035 num = len(bond_vectors) 1036 plural = 's' 1037 if num == 1: 1038 plural = '' 1039 1040 if spin.name: 1041 print("Extracted %s %s-%s vector%s for the spin '%s'." % (num, spin.name, attached_name, plural, id)) 1042 else: 1043 print("Extracted %s %s-%s vector%s for the spin '%s'." % (num, spin.num, attached_name, plural, id)) 1044 1045 # Right, catch the problem of missing vectors to prevent massive user confusion! 1046 if no_vectors: 1047 raise RelaxError("No vectors could be extracted.")

1048 1049

1050 -def web_of_motion(file=None, dir=None, models=None, force=False):

1051 """Create a PDB representation of the motion between a set of models. 1052 1053 This will create a PDB file containing the atoms of all models, with identical atoms links using CONECT records. This function only supports the internal structural object. 1054 1055 @keyword file: The name of the PDB file to write. 1056 @type file: str 1057 @keyword dir: The directory where the PDB file will be placed. If set to None, then the file will be placed in the current directory. 1058 @type dir: str or None 1059 @keyword models: The optional list of models to restrict this to. 1060 @type models: list of int or None 1061 @keyword force: The force flag which if True will cause the file to be overwritten. 1062 @type force: bool 1063 """ 1064 1065 # Test if the current data pipe exists. 1066 pipes.test() 1067 1068 # Test if the structure exists. 1069 if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or not cdp.structure.num_molecules(): 1070 raise RelaxNoPdbError 1071 1072 # Validate the models. 1073 cdp.structure.validate_models() 1074 1075 # Initialise the structural object. 1076 web = Internal() 1077 1078 # The model list. 1079 if models == None: 1080 models = [] 1081 for k in range(len(cdp.structure.structural_data)): 1082 models.append(cdp.structure.structural_data[k].num) 1083 1084 # Loop over the molecules. 1085 for i in range(len(cdp.structure.structural_data[0].mol)): 1086 # Alias the molecule of the first model. 1087 mol1 = cdp.structure.structural_data[0].mol[i] 1088 1089 # Loop over the atoms. 1090 for j in range(len(mol1.atom_name)): 1091 # Loop over the models. 1092 for k in range(len(cdp.structure.structural_data)): 1093 # Skip the model. 1094 if cdp.structure.structural_data[k].num not in models: 1095 continue 1096 1097 # Alias. 1098 mol = cdp.structure.structural_data[k].mol[i] 1099 1100 # Add the atom. 1101 web.add_atom(mol_name=mol1.mol_name, atom_name=mol.atom_name[j], res_name=mol.res_name[j], res_num=mol.res_num[j], pos=[mol.x[j], mol.y[j], mol.z[j]], element=mol.element[j], chain_id=mol.chain_id[j], segment_id=mol.seg_id[j], pdb_record=mol.pdb_record[j]) 1102 1103 # Loop over the models again, this time twice. 1104 for k in range(len(models)): 1105 for l in range(len(models)): 1106 # Skip identical atoms. 1107 if k == l: 1108 continue 1109 1110 # The atom index. 1111 index1 = j*len(models) + k 1112 index2 = j*len(models) + l 1113 1114 # Connect to the previous atoms. 1115 web.connect_atom(mol_name=mol1.mol_name, index1=index1, index2=index2) 1116 1117 # Append the PDB extension if needed. 1118 if isinstance(file, str): 1119 # The file path. 1120 file = get_file_path(file, dir) 1121 1122 # Add '.pdb' to the end of the file path if it isn't there yet. 1123 if not search(".pdb$", file): 1124 file += '.pdb' 1125 1126 # Open the file for writing. 1127 file = open_write_file(file, force=force) 1128 1129 # Write the structure. 1130 web.write_pdb(file)

1131 1132

1133 -def write_pdb(file=None, dir=None, model_num=None, compress_type=0, force=False):

1134 """The PDB writing function. 1135 1136 @keyword file: The name of the PDB file to write. 1137 @type file: str 1138 @keyword dir: The directory where the PDB file will be placed. If set to None, then the file will be placed in the current directory. 1139 @type dir: str or None 1140 @keyword model_num: The model to place into the PDB file. If not supplied, then all models will be placed into the file. 1141 @type model_num: None or int 1142 @keyword compress_type: The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression. 1143 @type compress_type: int 1144 @keyword force: The force flag which if True will cause the file to be overwritten. 1145 @type force: bool 1146 """ 1147 1148 # Test if the current data pipe exists. 1149 pipes.test() 1150 1151 # Check if the structural object exists. 1152 if not hasattr(cdp, 'structure'): 1153 raise RelaxError("No structural data is present in the current data pipe.") 1154 1155 # The file path. 1156 file_path = get_file_path(file, dir) 1157 1158 # Add '.pdb' to the end of the file path if it isn't there yet. 1159 if not search(".pdb$", file_path): 1160 file_path = file_path + '.pdb' 1161 1162 # Open the file for writing. 1163 file = open_write_file(file_path, compress_type=compress_type, force=force) 1164 1165 # Write the structures. 1166 cdp.structure.write_pdb(file, model_num=model_num)

1167

Source Code for Module pipe_control.structure.main