generic_fns.structure.api

47 """The structural object base class. 48 49 All API methods are prototyped here as stub methods. 50 """ 51 52 # Identification string. 53 id = 'API' 54 55

56 - def __init__(self):

57 """Initialise the structural object.""" 58 59 # Initialise the empty model list. 60 self.structural_data = ModelList()

61 62

63 - def add_atom(self, 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):

64 """Add a new atom to the structural data object. 65 66 @keyword mol_name: The name of the molecule. 67 @type mol_name: str 68 @keyword atom_name: The atom name, e.g. 'H1'. 69 @type atom_name: str or None 70 @keyword res_name: The residue name. 71 @type res_name: str or None 72 @keyword res_num: The residue number. 73 @type res_num: int or None 74 @keyword pos: The position vector of coordinates. 75 @type pos: list (length = 3) 76 @keyword element: The element symbol. 77 @type element: str or None 78 @keyword atom_num: The atom number. 79 @type atom_num: int or None 80 @keyword chain_id: The chain identifier. 81 @type chain_id: str or None 82 @keyword segment_id: The segment identifier. 83 @type segment_id: str or None 84 @keyword pdb_record: The optional PDB record name, e.g. 'ATOM' or 'HETATM'. 85 @type pdb_record: str or None 86 """ 87 88 # Raise the error. 89 raise RelaxImplementError

90 91

92 - def add_model(self, model=None, coords_from=None):

93 """Add a new model to the store. 94 95 The new model will be constructured with the structural information from the other models currently present. The coords_from argument allows the atomic positions to be taken from a certain model. If this argument is not set, then the atomic positions from the first model will be used. 96 97 @keyword model: The number of the model to create. 98 @type model: int or None 99 @keyword coords_from: The model number to take the coordinates from. 100 @type coords_from: int or None 101 @return: The model container. 102 @rtype: ModelContainer instance 103 """ 104 105 # Raise the error. 106 raise RelaxImplementError

107 108

109 - def add_molecule(self, name=None):

110 """Prototype method stub for adding the given molecule to the store. 111 112 @keyword name: The molecule identification string. 113 @type name: str 114 """ 115 116 # Raise the error. 117 raise RelaxImplementError

118 119

120 - def are_bonded(self, atom_id1=None, atom_id2=None):

121 """Prototype method stub for determining if two atoms are directly bonded to each other. 122 123 @keyword atom_id1: The molecule, residue, and atom identifier string of the first atom. 124 @type atom_id1: str 125 @keyword atom_id2: The molecule, residue, and atom identifier string of the second atom. 126 @type atom_id2: str 127 @return: True if the atoms are directly bonded. 128 @rtype: bool 129 """ 130 131 # Raise the error. 132 raise RelaxImplementError('are_bonded')

133 134

135 - def atom_loop(self, atom_id=None, str_id=None, model_num=None, model_num_flag=False, mol_name_flag=False, res_num_flag=False, res_name_flag=False, atom_num_flag=False, atom_name_flag=False, element_flag=False, pos_flag=False, ave=False):

136 """Prototype generator method stub for looping over all atoms in the structural data object. 137 138 This method should be designed as a generator (http://www.python.org/dev/peps/pep-0255/). 139 It should loop over all atoms of the system yielding the following atomic information, if 140 the corresponding flag is True, in tuple form: 141 142 1. Model number. 143 2. Molecule name. 144 3. Residue number. 145 4. Residue name. 146 5. Atom number. 147 6. Atom name. 148 7. The element name (its atomic symbol and optionally the isotope, e.g. 'N', 'Mg', 149 '17O', '13C', etc). 150 8. The position of the atom in Euclidean space. 151 152 153 @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be yielded. 154 @type atom_id: str 155 @keyword str_id: The structure identifier. This can be the file name, model number, or structure number. If None, then all structures will be looped over. 156 @type str_id: str, int, or None 157 @keyword model_num: Only loop over a specific model. 158 @type model_num: int or None 159 @keyword model_num_flag: A flag which if True will cause the model number to be yielded. 160 @type model_num_flag: bool 161 @keyword mol_name_flag: A flag which if True will cause the molecule name to be yielded. 162 @type mol_name_flag: bool 163 @keyword res_num_flag: A flag which if True will cause the residue number to be yielded. 164 @type res_num_flag: bool 165 @keyword res_name_flag: A flag which if True will cause the residue name to be yielded. 166 @type res_name_flag: bool 167 @keyword atom_num_flag: A flag which if True will cause the atom number to be yielded. 168 @type atom_num_flag: bool 169 @keyword atom_name_flag: A flag which if True will cause the atom name to be yielded. 170 @type atom_name_flag: bool 171 @keyword element_flag: A flag which if True will cause the element name to be yielded. 172 @type element_flag: bool 173 @keyword pos_flag: A flag which if True will cause the atomic position to be yielded. 174 @type pos_flag: bool 175 @keyword ave: A flag which if True will result in this method returning the average atom properties across all loaded structures. 176 @type ave: bool 177 @return: A tuple of atomic information, as described in the docstring. 178 @rtype: tuple consisting of optional molecule name (str), residue number (int), residue name (str), atom number (int), atom name(str), element name (str), and atomic position (array of len 3). 179 """ 180 181 # Raise the error. 182 raise RelaxImplementError

183 184

185 - def attached_atom(self, atom_id=None, attached_atom=None, model=None):

186 """Prototype method stub for finding the atom 'attached_atom' bonded to the atom 'atom_id'. 187 188 @keyword atom_id: The molecule, residue, and atom identifier string. This must 189 correspond to a single atom in the system. 190 @type atom_id: str 191 @keyword attached_atom: The name of the attached atom to return. 192 @type attached_atom: str 193 @keyword model: The model to return the positional information from. If not 194 supplied and multiple models exist, then the returned atomic 195 position will be a list of the positions in each model. 196 @type model: None or int 197 @return: A tuple of information about the bonded atom. 198 @rtype: tuple consisting of the atom number (int), atom name (str), element 199 name (str), and atomic positions for each model (list of numpy 200 arrays) 201 """ 202 203 # Raise the error. 204 raise RelaxImplementError

205 206

207 - def bond_vectors(self, attached_atom=None, model_num=None, mol_name=None, res_num=None, res_name=None, spin_num=None, spin_name=None, return_name=False, return_warnings=False):

208 """Prototype method stub for finding the bond vectors between 'attached_atom' and 'atom_id'. 209 210 @keyword attached_atom: The name of the bonded atom. 211 @type attached_atom: str 212 @keyword model_num: The model of which to return the vectors from. If not supplied 213 and multiple models exist, then vectors from all models will be 214 returned. 215 @type model_num: None or int 216 @keyword mol_name: The name of the molecule that attached_atom belongs to. 217 @type mol_name: str 218 @keyword res_num: The number of the residue that attached_atom belongs to. 219 @type res_num: str 220 @keyword res_name: The name of the residue that attached_atom belongs to. 221 @type res_name: str 222 @keyword spin_num: The number of the spin that attached_atom is attached to. 223 @type spin_num: str 224 @keyword spin_name: The name of the spin that attached_atom is attached to. 225 @type spin_name: str 226 @keyword return_name: A flag which if True will cause the name of the attached atom to 227 be returned together with the bond vectors. 228 @type return_name: bool 229 @keyword return_warnings: A flag which if True will cause warning messages to be returned. 230 @type return_warnings: bool 231 @return: The list of bond vectors for each model. 232 @rtype: list of numpy arrays 233 """ 234 235 # Raise the error. 236 raise RelaxImplementError

237 238

239 - def connect_atom(self, mol_name=None, index1=None, index2=None):

240 """Connect two atoms in the structural data object. 241 242 @keyword mol_name: The name of the molecule. 243 @type mol_name: str 244 @keyword index1: The global index of the first atom. 245 @type index1: str 246 @keyword index2: The global index of the first atom. 247 @type index2: str 248 """ 249 250 # Raise the error. 251 raise RelaxImplementError

252 253

254 - def delete(self):

255 """Prototype method stub for deleting all structural data from the current data pipe.""" 256 257 # Raise the error. 258 raise RelaxImplementError

259 260

261 - def empty(self):

262 """Report if the structural data structure is empty or not. 263 264 @return: True if empty, False otherwise. 265 @rtype: bool 266 """ 267 268 # Check the ModelList structure. 269 if len(self.structural_data) == 0: 270 return True 271 else: 272 return False

273 274

275 - def from_xml(self, str_node, dir=None, id=None, file_version=1):

276 """Recreate the structural object from the XML structural object node. 277 278 @param str_node: The structural object XML node. 279 @type str_node: xml.dom.minicompat.Element instance 280 @keyword dir: The name of the directory containing the results file. 281 @type dir: str 282 @keyword id: The specific structural object ID string. This can be 'scientific', 'internal', etc. 283 @type id: str 284 @keyword file_version: The relax XML version of the XML file. 285 @type file_version: int 286 """ 287 288 # Recreate the model / molecule data structure. 289 model_nodes = str_node.getElementsByTagName('model') 290 self.structural_data.from_xml(model_nodes, id=id, file_version=file_version) 291 292 # The displacement structure. 293 disp_nodes = str_node.getElementsByTagName('displacements') 294 if len(disp_nodes): 295 # Initialise the object. 296 self.displacements = Displacements() 297 298 # Recreate the molecule data structures for the current model. 299 self.displacements.from_xml(disp_nodes[0], file_version=file_version)

300 301

302 - def get_model(self, model):

303 """Return or create the model. 304 305 @param model: The model number. 306 @type model: int or None 307 @return: The ModelContainer corresponding to the model number or that newly created. 308 @rtype: ModelContainer instance 309 """ 310 311 # Check if the target is a single model. 312 if model == None and self.num_models() > 1: 313 raise RelaxError("The target model cannot be determined as there are %s models already present." % self.num_modes()) 314 315 # No model specified. 316 if model == None: 317 # Create the first model, if necessary. 318 if self.num_models(): 319 self.structural_data.add_item() 320 321 # Alias the first model. 322 model_cont = self.structural_data[0] 323 324 # The model has been specified. 325 else: 326 # Get the preexisting model. 327 found = False 328 for model_cont in self.structural_data: 329 if model_cont.num == model: 330 found = True 331 break 332 333 # Add the model if it doesn't exist. 334 if not found: 335 self.structural_data.add_item(model) 336 model_cont = self.structural_data[-1]

337 338

339 - def get_molecule(self, molecule, model=None):

340 """Return the molecule. 341 342 @param molecule: The molecule name. 343 @type molecule: int or None 344 @keyword model: The model number. 345 @type model: int or None 346 @return: The MolContainer corresponding to the molecule name and model number. 347 @rtype: MolContainer instance or None 348 """ 349 350 # Raise the error. 351 raise RelaxImplementError

352 353

354 - def load_pdb(self, file_path, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, verbosity=False):

355 """Prototype method stub for loading structures from a PDB file. 356 357 This inherited prototype method is a stub which, if the functionality is desired, should be 358 overwritten by the derived class. 359 360 361 @param file_path: The full path of the PDB file. 362 @type file_path: str 363 @keyword read_mol: The molecule(s) to read from the file, independent of model. The 364 molecules are determined differently by the different parsers, but 365 are numbered consecutively from 1. If set to None, then all 366 molecules will be loaded. 367 @type read_mol: None, int, or list of int 368 @keyword set_mol_name: Set the names of the molecules which are loaded. If set to None, 369 then the molecules will be automatically labelled based on the file 370 name or other information. 371 @type set_mol_name: None, str, or list of str 372 @keyword read_model: The PDB model to extract from the file. If set to None, then all 373 models will be loaded. 374 @type read_model: None, int, or list of int 375 @keyword set_model_num: Set the model number of the loaded molecule. If set to None, then 376 the PDB model numbers will be preserved, if they exist. 377 @type set_model_num: None, int, or list of int 378 @keyword verbosity: A flag which if True will cause messages to be printed. 379 @type verbosity: bool 380 @return: The status of the loading of the PDB file. 381 @rtype: bool 382 """ 383 384 # Raise the error. 385 raise RelaxImplementError

386 387

388 - def load_xyz(self, file_path, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, verbosity=False):

389 """Method for loading structures from a XYZ file. 390 391 @param file_path: The full path of the XYZ file. 392 @type file_path: str 393 @keyword read_mol: The molecule(s) to read from the file, independent of model. The 394 molecules are determined differently by the different parsers, but 395 are numbered consecutively from 1. If set to None, then all 396 molecules will be loaded. 397 @type read_mol: None, int, or list of int 398 @keyword set_mol_name: Set the names of the molecules which are loaded. If set to None, 399 then the molecules will be automatically labelled based on the file 400 name or other information. 401 @type set_mol_name: None, str, or list of str 402 @keyword read_model: The XYZ model to extract from the file. If set to None, then all 403 models will be loaded. 404 @type read_model: None, int, or list of int 405 @keyword set_model_num: Set the model number of the loaded molecule. If set to None, then 406 the XYZ model numbers will be preserved, if they exist. 407 @type set_model_num: None, int, or list of int 408 @keyword verbosity: A flag which if True will cause messages to be printed. 409 @type verbosity: bool 410 @return: The status of the loading of the XYZ file. 411 @rtype: bool 412 """ 413 414 # Raise the error. 415 raise RelaxImplementError

416 417

418 - def model_loop(self, model=None):

419 """Generator method for looping over the models in numerical order. 420 421 @keyword model: Limit the loop to a single number. 422 @type model: int 423 @return: The model structural object. 424 @rtype: ModelContainer container 425 """ 426 427 # A single model. 428 if model: 429 for i in range(len(self.structural_data)): 430 if self.structural_data[i].num == model: 431 yield self.structural_data[i] 432 433 # All models. 434 else: 435 # The models. 436 model_nums = [] 437 for i in range(len(self.structural_data)): 438 if self.structural_data[i].num != None: 439 model_nums.append(self.structural_data[i].num) 440 441 # Sort. 442 if model_nums: 443 model_nums.sort() 444 445 # Loop over the models in order. 446 for model_num in model_nums: 447 # Find the model. 448 for i in range(len(self.structural_data)): 449 # Yield the model. 450 if self.structural_data[i].num == model_num: 451 yield self.structural_data[i] 452 453 # No models, so just yield the single container. 454 if not model_nums: 455 yield self.structural_data[0]

456 457

458 - def num_models(self):

459 """Method for returning the number of models. 460 461 @return: The number of models in the structural object. 462 @rtype: int 463 """ 464 465 return len(self.structural_data)

466 467

468 - def num_molecules(self):

469 """Method for returning the number of molecules. 470 471 @return: The number of molecules in the structural object. 472 @rtype: int 473 """ 474 475 # Validate the structural object. 476 self.validate() 477 478 # Return the number. 479 return len(self.structural_data[0].mol)

480 481

482 - def pack_structs(self, data_matrix, orig_model_num=None, set_model_num=None, orig_mol_num=None, set_mol_name=None, file_name=None, file_path=None):

483 """From the given structural data, expand the structural data data structure. 484 485 @param data_matrix: A matrix of structural objects. 486 @type data_matrix: list of lists of structural objects 487 @keyword orig_model_num: The original model numbers (for storage). 488 @type orig_model_num: list of int 489 @keyword set_model_num: The new model numbers (for model renumbering). 490 @type set_model_num: list of int 491 @keyword orig_mol_num: The original molecule numbers (for storage). 492 @type orig_mol_num: list of int 493 @keyword set_mol_name: The new molecule names. 494 @type set_mol_name: list of str 495 @keyword file_name: The name of the file from which the molecular data has been 496 extracted. 497 @type file_name: None or str 498 @keyword file_path: The full path to the file specified by 'file_name'. 499 @type file_path: None or str 500 """ 501 502 # Test the number of models. 503 if len(orig_model_num) != len(data_matrix): 504 raise RelaxError("Structural data mismatch, %s original models verses %s in the structural data." % (len(orig_model_num), len(data_matrix))) 505 506 # Test the number of molecules. 507 if len(orig_mol_num) != len(data_matrix[0]): 508 raise RelaxError("Structural data mismatch, %s original molecules verses %s in the structural data." % (len(orig_mol_num), len(data_matrix[0]))) 509 510 # Model numbers do not change. 511 if not set_model_num: 512 set_model_num = orig_model_num 513 514 # Test the model mapping. 515 if len(set_model_num) != len(data_matrix): 516 raise RelaxError("Failure of the mapping of new model numbers, %s new model numbers verses %s models in the structural data." % (len(set_model_num), len(data_matrix))) 517 518 # Test the molecule mapping. 519 if len(set_mol_name) != len(data_matrix[0]): 520 raise RelaxError("Failure of the mapping of new molecule names, %s new molecule names verses %s molecules in the structural data." % (len(set_mol_name), len(data_matrix[0]))) 521 522 # Test that the target models and structures are absent, and get the already existing model numbers. 523 current_models = [] 524 for i in range(len(self.structural_data)): 525 # Create a list of current models. 526 current_models.append(self.structural_data[i].num) 527 528 # Loop over the structures. 529 for j in range(len(self.structural_data[i].mol)): 530 if self.structural_data[i].num in set_model_num and self.structural_data[i].mol[j].mol_name in set_mol_name: 531 raise RelaxError("The molecule '%s' of model %s already exists." % (self.structural_data[i].mol[j].mol_name, self.structural_data[i].num)) 532 533 # Loop over the models. 534 for i in range(len(set_model_num)): 535 # The model doesn't currently exist. 536 if set_model_num[i] not in current_models: 537 # Create the model. 538 self.structural_data.add_item(set_model_num[i]) 539 540 # Add the model number to the current_models list. 541 current_models.append(set_model_num[i]) 542 543 # Get the model. 544 model = self.structural_data[-1] 545 546 # Otherwise get the pre-existing model. 547 else: 548 model = self.structural_data[current_models.index(set_model_num[i])] 549 550 # Loop over the molecules. 551 for j in range(len(set_mol_name)): 552 # Print out. 553 print("Adding molecule '%s' to model %s (from the original molecule number %s of model %s)" % (set_mol_name[j], set_model_num[i], orig_mol_num[j], orig_model_num[i])) 554 555 # Consistency check. 556 index = len(model.mol) 557 if model.num != self.structural_data[0].num and self.structural_data[0].mol[index].mol_name != set_mol_name[j]: 558 raise RelaxError("The new molecule name of '%s' in model %s does not match the corresponding molecule's name of '%s' in model %s." % (set_mol_name[j], set_model_num[i], self.structural_data[0].mol[index].mol_name, self.structural_data[0].num)) 559 560 # Pack the structures. 561 model.mol.add_item(mol_name=set_mol_name[j], mol_cont=data_matrix[i][j]) 562 563 # Set the molecule name and store the structure file info. 564 model.mol[-1].mol_name = set_mol_name[j] 565 model.mol[-1].file_name = file_name 566 model.mol[-1].file_path = file_path 567 model.mol[-1].file_mol_num = orig_mol_num[j] 568 model.mol[-1].file_model = orig_model_num[i]

569 570

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

572 """Method stub for rotating a structure. 573 574 @keyword R: The forwards rotation matrix. 575 @type R: numpy 3D, rank-2 array 576 @keyword origin: The origin of the rotation. 577 @type origin: numpy 3D, rank-1 array 578 @keyword model: The model to rotate. If None, all models will be rotated. 579 @type model: int 580 @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used. 581 @type atom_id: str or None 582 """ 583 584 # Raise the error. 585 raise RelaxImplementError

586 587

588 - def target_mol_name(self, set=None, target=None, index=None, mol_num=None, file=None):

589 """Add the new molecule name to the target data structure. 590 591 @keyword set: The list of new molecule names. If not supplied, the names will be 592 generated from the file name. 593 @type set: None or list of str 594 @keyword target: The target molecule name data structure to which the new name will be 595 appended. 596 @type target: list 597 @keyword index: The molecule index, matching the set argument. 598 @type index: int 599 @keyword mol_num: The molecule number. 600 @type mol_num: int 601 @keyword file: The name of the file, excluding all directories. 602 @type file: str 603 """ 604 605 # Set the target molecule name. 606 if set: 607 target.append(set[index]) 608 else: 609 # Set the name to the file name plus the structure number. 610 target.append(file_root(file) + '_mol' + repr(mol_num))

611 612

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

614 """Method stub for displacing the structural information by the given translation vector. 615 616 @keyword T: The translation vector. 617 @type T: numpy 3D, rank-1 array 618 @keyword model: The model to rotate. If None, all models will be rotated. 619 @type model: int 620 @keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used. 621 @type atom_id: str or None 622 """ 623 624 # Raise the error. 625 raise RelaxImplementError

626 627

628 - def to_xml(self, doc, element):

629 """Prototype method for converting the structural object to an XML representation. 630 631 @param doc: The XML document object. 632 @type doc: xml.dom.minidom.Document instance 633 @param element: The element to add the alignment tensors XML element to. 634 @type element: XML element object 635 """ 636 637 # Create the structural element and add it to the higher level element. 638 str_element = doc.createElement('structure') 639 element.appendChild(str_element) 640 641 # Set the structural attributes. 642 str_element.setAttribute('desc', 'Structural information') 643 str_element.setAttribute('id', self.id) 644 645 # No contents to store, so pack up the structural containers. 646 if not self.structural_data.is_empty(): 647 self.structural_data.to_xml(doc, str_element) 648 649 # The displacement structure. 650 if hasattr(self, 'displacements'): 651 # Create an XML element. 652 disp_element = doc.createElement('displacements') 653 str_element.appendChild(disp_element) 654 655 # Set the attributes. 656 disp_element.setAttribute('desc', 'The rotational and translational displacements between models') 657 658 # Add the displacement data. 659 self.displacements.to_xml(doc, disp_element)

660 661

662 - def validate_models(self):

663 """Check that the models are consistent with each other. 664 665 This checks that the primary structure is identical between the models. 666 """ 667 668 # Raise the error. 669 raise RelaxImplementError

670 671

672 - def write_pdb(self, file, model_num=None):

673 """Prototype method stub for the creation of a PDB file from the structural data. 674 675 The PDB records 676 =============== 677 678 The following information about the PDB records has been taken from the "Protein Data Bank 679 Contents Guide: Atomic Coordinate Entry Format Description" version 3.1, February 11, 2008. 680 681 HET record 682 ---------- 683 684 The HET record describes non-standard residues. The format of the record is:: 685 __________________________________________________________________________________________ 686 | | | | | 687 | Columns | Data type | Field | Definition | 688 |_________|______________|______________|________________________________________________| 689 | | | | | 690 | 1 - 6 | Record name | "HET " | | 691 | 8 - 10 | LString(3) | hetID | Het identifier, right-justified. | 692 | 13 | Character | ChainID | Chain identifier. | 693 | 14 - 17 | Integer | seqNum | Sequence number. | 694 | 18 | AChar | iCode | Insertion code. | 695 | 21 - 25 | Integer | numHetAtoms | Number of HETATM records for the group present | 696 | | | | in the entry. | 697 | 31 - 70 | String | text | Text describing Het group. | 698 |_________|______________|______________|________________________________________________| 699 700 701 HETNAM record 702 ------------- 703 704 The HETNAM associates a chemical name with the hetID from the HET record. The format is of 705 the record is:: 706 __________________________________________________________________________________________ 707 | | | | | 708 | Columns | Data type | Field | Definition | 709 |_________|______________|______________|________________________________________________| 710 | | | | | 711 | 1 - 6 | Record name | "HETNAM" | | 712 | 9 - 10 | Continuation | continuation | Allows concatenation of multiple records. | 713 | 12 - 14 | LString(3) | hetID | Het identifier, right-justified. | 714 | 16 - 70 | String | text | Chemical name. | 715 |_________|______________|______________|________________________________________________| 716 717 718 FORMUL record 719 ------------- 720 721 The chemical formula for non-standard groups. The format of the record is:: 722 __________________________________________________________________________________________ 723 | | | | | 724 | Columns | Data type | Field | Definition | 725 |_________|______________|______________|________________________________________________| 726 | | | | | 727 | 1 - 6 | Record name | "FORMUL" | | 728 | 9 - 10 | Integer | compNum | Component number. | 729 | 13 - 15 | LString(3) | hetID | Het identifier. | 730 | 17 - 18 | Integer | continuation | Continuation number. | 731 | 19 | Character | asterisk | "*" for water. | 732 | 20 - 70 | String | text | Chemical formula. | 733 |_________|______________|______________|________________________________________________| 734 735 736 MODEL record 737 ------------ 738 739 The model number, for multiple structures. The format of the record is:: 740 __________________________________________________________________________________________ 741 | | | | | 742 | Columns | Data type | Field | Definition | 743 |_________|______________|______________|________________________________________________| 744 | | | | | 745 | 1 - 6 | Record name | "MODEL " | | 746 | 11 - 14 | Integer | serial | Model serial number. | 747 |_________|______________|______________|________________________________________________| 748 749 750 ATOM record 751 ----------- 752 753 The ATOM record contains the atomic coordinates for atoms belonging to standard residues. 754 The format of the record is:: 755 __________________________________________________________________________________________ 756 | | | | | 757 | Columns | Data type | Field | Definition | 758 |_________|______________|______________|________________________________________________| 759 | | | | | 760 | 1 - 6 | Record name | "ATOM" | | 761 | 7 - 11 | Integer | serial | Atom serial number. | 762 | 13 - 16 | Atom | name | Atom name. | 763 | 17 | Character | altLoc | Alternate location indicator. | 764 | 18 - 20 | Residue name | resName | Residue name. | 765 | 22 | Character | chainID | Chain identifier. | 766 | 23 - 26 | Integer | resSeq | Residue sequence number. | 767 | 27 | AChar | iCode | Code for insertion of residues. | 768 | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X in Angstroms. | 769 | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y in Angstroms. | 770 | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z in Angstroms. | 771 | 55 - 60 | Real(6.2) | occupancy | Occupancy. | 772 | 61 - 66 | Real(6.2) | tempFactor | Temperature factor. | 773 | 73 - 76 | LString(4) | segID | Segment identifier, left-justified. | 774 | 77 - 78 | LString(2) | element | Element symbol, right-justified. | 775 | 79 - 80 | LString(2) | charge | Charge on the atom. | 776 |_________|______________|______________|________________________________________________| 777 778 779 HETATM record 780 ------------- 781 782 The HETATM record contains the atomic coordinates for atoms belonging to non-standard 783 groups. The format of the record is:: 784 __________________________________________________________________________________________ 785 | | | | | 786 | Columns | Data type | Field | Definition | 787 |_________|______________|______________|________________________________________________| 788 | | | | | 789 | 1 - 6 | Record name | "HETATM" | | 790 | 7 - 11 | Integer | serial | Atom serial number. | 791 | 13 - 16 | Atom | name | Atom name. | 792 | 17 | Character | altLoc | Alternate location indicator. | 793 | 18 - 20 | Residue name | resName | Residue name. | 794 | 22 | Character | chainID | Chain identifier. | 795 | 23 - 26 | Integer | resSeq | Residue sequence number. | 796 | 27 | AChar | iCode | Code for insertion of residues. | 797 | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X. | 798 | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y. | 799 | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z. | 800 | 55 - 60 | Real(6.2) | occupancy | Occupancy. | 801 | 61 - 66 | Real(6.2) | tempFactor | Temperature factor. | 802 | 73 - 76 | LString(4) | segID | Segment identifier; left-justified. | 803 | 77 - 78 | LString(2) | element | Element symbol; right-justified. | 804 | 79 - 80 | LString(2) | charge | Charge on the atom. | 805 |_________|______________|______________|________________________________________________| 806 807 808 TER record 809 ---------- 810 811 The end of the ATOM and HETATM records for a chain. According to the draft atomic 812 coordinate entry format description: 813 814 I{"The TER record has the same residue name, chain identifier, sequence number and insertion 815 code as the terminal residue. The serial number of the TER record is one number greater than 816 the serial number of the ATOM/HETATM preceding the TER."} 817 818 The format of the record is:: 819 __________________________________________________________________________________________ 820 | | | | | 821 | Columns | Data type | Field | Definition | 822 |_________|______________|______________|________________________________________________| 823 | | | | | 824 | 1 - 6 | Record name | "TER " | | 825 | 7 - 11 | Integer | serial | Serial number. | 826 | 18 - 20 | Residue name | resName | Residue name. | 827 | 22 | Character | chainID | Chain identifier. | 828 | 23 - 26 | Integer | resSeq | Residue sequence number. | 829 | 27 | AChar | iCode | Insertion code. | 830 |_________|______________|______________|________________________________________________| 831 832 833 CONECT record 834 ------------- 835 836 The connectivity between atoms. This is required for all HET groups and for non-standard 837 bonds. The format of the record is:: 838 __________________________________________________________________________________________ 839 | | | | | 840 | Columns | Data type | Field | Definition | 841 |_________|______________|______________|________________________________________________| 842 | | | | | 843 | 1 - 6 | Record name | "CONECT" | | 844 | 7 - 11 | Integer | serial | Atom serial number | 845 | 12 - 16 | Integer | serial | Serial number of bonded atom | 846 | 17 - 21 | Integer | serial | Serial number of bonded atom | 847 | 22 - 26 | Integer | serial | Serial number of bonded atom | 848 | 27 - 31 | Integer | serial | Serial number of bonded atom | 849 | 32 - 36 | Integer | serial | Serial number of hydrogen bonded atom | 850 | 37 - 41 | Integer | serial | Serial number of hydrogen bonded atom | 851 | 42 - 46 | Integer | serial | Serial number of salt bridged atom | 852 | 47 - 51 | Integer | serial | Serial number of hydrogen bonded atom | 853 | 52 - 56 | Integer | serial | Serial number of hydrogen bonded atom | 854 | 57 - 61 | Integer | serial | Serial number of salt bridged atom | 855 |_________|______________|______________|________________________________________________| 856 857 858 ENDMDL record 859 ------------- 860 861 The end of model record, for multiple structures. The format of the record is:: 862 __________________________________________________________________________________________ 863 | | | | | 864 | Columns | Data type | Field | Definition | 865 |_________|______________|______________|________________________________________________| 866 | | | | | 867 | 1 - 6 | Record name | "ENDMDL" | | 868 |_________|______________|______________|________________________________________________| 869 870 871 872 MASTER record 873 ------------- 874 875 The control record for bookkeeping. The format of the record is:: 876 __________________________________________________________________________________________ 877 | | | | | 878 | Columns | Data type | Field | Definition | 879 |_________|______________|______________|________________________________________________| 880 | | | | | 881 | 1 - 6 | Record name | "MASTER" | | 882 | 11 - 15 | Integer | numRemark | Number of REMARK records | 883 | 16 - 20 | Integer | "0" | | 884 | 21 - 25 | Integer | numHet | Number of HET records | 885 | 26 - 30 | Integer | numHelix | Number of HELIX records | 886 | 31 - 35 | Integer | numSheet | Number of SHEET records | 887 | 36 - 40 | Integer | numTurn | Number of TURN records | 888 | 41 - 45 | Integer | numSite | Number of SITE records | 889 | 46 - 50 | Integer | numXform | Number of coordinate transformation records | 890 | | | | (ORIGX+SCALE+MTRIX) | 891 | 51 - 55 | Integer | numCoord | Number of atomic coordinate records | 892 | | | | (ATOM+HETATM) | 893 | 56 - 60 | Integer | numTer | Number of TER records | 894 | 61 - 65 | Integer | numConect | Number of CONECT records | 895 | 66 - 70 | Integer | numSeq | Number of SEQRES records | 896 |_________|______________|______________|________________________________________________| 897 898 899 END record 900 ---------- 901 902 The end of the PDB file. The format of the record is:: 903 __________________________________________________________________________________________ 904 | | | | | 905 | Columns | Data type | Field | Definition | 906 |_________|______________|______________|________________________________________________| 907 | | | | | 908 | 1 - 6 | Record name | "END " | | 909 |_________|______________|______________|________________________________________________| 910 911 912 @param file: The PDB file object. This object must be writable. 913 @type file: file object 914 @keyword model_num: The model to place into the PDB file. If not supplied, then all 915 models will be placed into the file. 916 @type model_num: None or int 917 """ 918 919 # Raise the error. 920 raise RelaxImplementError

921 922

923 - def validate(self):

924 """Check the integrity of the structural data. 925 926 The number of molecules must be the same in all models. 927 """ 928 929 # Reference number of molecules. 930 num_mols = len(self.structural_data[0].mol) 931 932 # Loop over all other models. 933 for i in range(1, len(self.structural_data)): 934 # Model alias. 935 model_i = self.structural_data[i] 936 937 # Size check. 938 if num_mols != len(model_i.mol): 939 raise RelaxError("The structural object is not valid - the number of molecules is not the same for all models.") 940 941 # Molecule name check. 942 for j in range(len(model_i.mol)): 943 if model_i.mol[j].mol_name != self.structural_data[0].mol[j].mol_name: 944 raise RelaxError("The molecule name '%s' of model %s does not match the corresponding molecule '%s' of model %s." % (model_i.mol[j].mol_name, model_i.num, self.structural_data[0].mol[j].mol_name, self.structural_data[0].num))

Source Code for Module generic_fns.structure.api_base