# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk) # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Parser for PDB files.""" import warnings import numpy as np from Bio.File import as_handle from Bio.PDB.PDBExceptions import PDBConstructionException from Bio.PDB.PDBExceptions import PDBConstructionWarning from Bio.PDB.StructureBuilder import StructureBuilder from Bio.PDB.parse_pdb_header import _parse_pdb_header_list # If PDB spec says "COLUMNS 18-20" this means line[17:20] class PDBParser: """Parse a PDB file and return a Structure object.""" def __init__( self, PERMISSIVE=True, get_header=False, structure_builder=None, QUIET=False, is_pqr=False, ): """Create a PDBParser object. The PDB parser call a number of standard methods in an aggregated StructureBuilder object. Normally this object is instantiated by the PDBParser object itself, but if the user provides his/her own StructureBuilder object, the latter is used instead. Arguments: - PERMISSIVE - Evaluated as a Boolean. If false, exceptions in constructing the SMCRA data structure are fatal. If true (DEFAULT), the exceptions are caught, but some residues or atoms will be missing. THESE EXCEPTIONS ARE DUE TO PROBLEMS IN THE PDB FILE!. - get_header - unused argument kept for historical compatibility. - structure_builder - an optional user implemented StructureBuilder class. - QUIET - Evaluated as a Boolean. If true, warnings issued in constructing the SMCRA data will be suppressed. If false (DEFAULT), they will be shown. These warnings might be indicative of problems in the PDB file! - is_pqr - Evaluated as a Boolean. Specifies the type of file to be parsed. If false (DEFAULT) a .pdb file format is assumed. Set it to true if you want to parse a .pqr file instead. """ # get_header is not used but is left in for API compatibility if structure_builder is not None: self.structure_builder = structure_builder else: self.structure_builder = StructureBuilder() self.header = None self.trailer = None self.line_counter = 0 self.PERMISSIVE = bool(PERMISSIVE) self.QUIET = bool(QUIET) self.is_pqr = bool(is_pqr) # Public methods def get_structure(self, id, file): """Return the structure. Arguments: - id - string, the id that will be used for the structure - file - name of the PDB file OR an open filehandle """ with warnings.catch_warnings(): if self.QUIET: warnings.filterwarnings("ignore", category=PDBConstructionWarning) self.header = None self.trailer = None # Make a StructureBuilder instance (pass id of structure as parameter) self.structure_builder.init_structure(id) with as_handle(file) as handle: lines = handle.readlines() if not lines: raise ValueError("Empty file.") self._parse(lines) self.structure_builder.set_header(self.header) # Return the Structure instance structure = self.structure_builder.get_structure() return structure def get_header(self): """Return the header.""" return self.header def get_trailer(self): """Return the trailer.""" return self.trailer # Private methods def _parse(self, header_coords_trailer): """Parse the PDB file (PRIVATE).""" # Extract the header; return the rest of the file self.header, coords_trailer = self._get_header(header_coords_trailer) # Parse the atomic data; return the PDB file trailer self.trailer = self._parse_coordinates(coords_trailer) def _get_header(self, header_coords_trailer): """Get the header of the PDB file, return the rest (PRIVATE).""" structure_builder = self.structure_builder i = 0 for i in range(len(header_coords_trailer)): structure_builder.set_line_counter(i + 1) line = header_coords_trailer[i] record_type = line[0:6] if record_type in ("ATOM ", "HETATM", "MODEL "): break header = header_coords_trailer[0:i] # Return the rest of the coords+trailer for further processing self.line_counter = i coords_trailer = header_coords_trailer[i:] header_dict = _parse_pdb_header_list(header) return header_dict, coords_trailer def _parse_coordinates(self, coords_trailer): """Parse the atomic data in the PDB file (PRIVATE).""" allowed_records = { "ATOM ", "HETATM", "MODEL ", "ENDMDL", "TER ", "ANISOU", # These are older 2.3 format specs: "SIGATM", "SIGUIJ", # bookkeeping records after coordinates: "MASTER", } local_line_counter = 0 structure_builder = self.structure_builder current_model_id = 0 # Flag we have an open model model_open = 0 current_chain_id = None current_segid = None current_residue_id = None current_resname = None for i in range(len(coords_trailer)): line = coords_trailer[i].rstrip("\n") record_type = line[0:6] global_line_counter = self.line_counter + local_line_counter + 1 structure_builder.set_line_counter(global_line_counter) if not line.strip(): continue # skip empty lines elif record_type == "ATOM " or record_type == "HETATM": # Initialize the Model - there was no explicit MODEL record if not model_open: structure_builder.init_model(current_model_id) current_model_id += 1 model_open = 1 fullname = line[12:16] # get rid of whitespace in atom names split_list = fullname.split() if len(split_list) != 1: # atom name has internal spaces, e.g. " N B ", so # we do not strip spaces name = fullname else: # atom name is like " CA ", so we can strip spaces name = split_list[0] altloc = line[16] resname = line[17:20].strip() chainid = line[21] try: serial_number = int(line[6:11]) except Exception: serial_number = 0 resseq = int(line[22:26].split()[0]) # sequence identifier icode = line[26] # insertion code if record_type == "HETATM": # hetero atom flag if resname == "HOH" or resname == "WAT": hetero_flag = "W" else: hetero_flag = "H" else: hetero_flag = " " residue_id = (hetero_flag, resseq, icode) # atomic coordinates try: x = float(line[30:38]) y = float(line[38:46]) z = float(line[46:54]) except Exception: # Should we allow parsing to continue in permissive mode? # If so, what coordinates should we default to? Easier to abort! raise PDBConstructionException( "Invalid or missing coordinate(s) at line %i." % global_line_counter ) from None coord = np.array((x, y, z), "f") # occupancy & B factor if not self.is_pqr: try: occupancy = float(line[54:60]) except Exception: self._handle_PDB_exception( "Invalid or missing occupancy", global_line_counter ) occupancy = None # Rather than arbitrary zero or one if occupancy is not None and occupancy < 0: # TODO - Should this be an error in strict mode? # self._handle_PDB_exception("Negative occupancy", # global_line_counter) # This uses fixed text so the warning occurs once only: warnings.warn( "Negative occupancy in one or more atoms", PDBConstructionWarning, ) try: bfactor = float(line[60:66]) except Exception: self._handle_PDB_exception( "Invalid or missing B factor", global_line_counter ) bfactor = 0.0 # PDB uses a default of zero if missing elif self.is_pqr: # Attempt to parse charge and radius fields try: pqr_charge = float(line[54:62]) except Exception: self._handle_PDB_exception( "Invalid or missing charge", global_line_counter ) pqr_charge = None # Rather than arbitrary zero or one try: radius = float(line[62:70]) except Exception: self._handle_PDB_exception( "Invalid or missing radius", global_line_counter ) radius = None if radius is not None and radius < 0: # In permissive mode raise fatal exception. message = "Negative atom radius" self._handle_PDB_exception(message, global_line_counter) radius = None segid = line[72:76] element = line[76:78].strip().upper() if current_segid != segid: current_segid = segid structure_builder.init_seg(current_segid) if current_chain_id != chainid: current_chain_id = chainid structure_builder.init_chain(current_chain_id) current_residue_id = residue_id current_resname = resname try: structure_builder.init_residue( resname, hetero_flag, resseq, icode ) except PDBConstructionException as message: self._handle_PDB_exception(message, global_line_counter) elif current_residue_id != residue_id or current_resname != resname: current_residue_id = residue_id current_resname = resname try: structure_builder.init_residue( resname, hetero_flag, resseq, icode ) except PDBConstructionException as message: self._handle_PDB_exception(message, global_line_counter) if not self.is_pqr: # init atom with pdb fields try: structure_builder.init_atom( name, coord, bfactor, occupancy, altloc, fullname, serial_number, element, ) except PDBConstructionException as message: self._handle_PDB_exception(message, global_line_counter) elif self.is_pqr: try: structure_builder.init_atom( name, coord, pqr_charge, radius, altloc, fullname, serial_number, element, pqr_charge, radius, self.is_pqr, ) except PDBConstructionException as message: self._handle_PDB_exception(message, global_line_counter) elif record_type == "ANISOU": anisou = [ float(x) for x in ( line[28:35], line[35:42], line[43:49], line[49:56], line[56:63], line[63:70], ) ] # U's are scaled by 10^4 anisou_array = (np.array(anisou, "f") / 10000.0).astype("f") structure_builder.set_anisou(anisou_array) elif record_type == "MODEL ": try: serial_num = int(line[10:14]) except Exception: self._handle_PDB_exception( "Invalid or missing model serial number", global_line_counter ) serial_num = 0 structure_builder.init_model(current_model_id, serial_num) current_model_id += 1 model_open = 1 current_chain_id = None current_residue_id = None elif record_type == "END " or record_type == "CONECT": # End of atomic data, return the trailer self.line_counter += local_line_counter return coords_trailer[local_line_counter:] elif record_type == "ENDMDL": model_open = 0 current_chain_id = None current_residue_id = None elif record_type == "SIGUIJ": # standard deviation of anisotropic B factor siguij = [ float(x) for x in ( line[28:35], line[35:42], line[42:49], line[49:56], line[56:63], line[63:70], ) ] # U sigma's are scaled by 10^4 siguij_array = (np.array(siguij, "f") / 10000.0).astype("f") structure_builder.set_siguij(siguij_array) elif record_type == "SIGATM": # standard deviation of atomic positions sigatm = [ float(x) for x in ( line[30:38], line[38:46], line[46:54], line[54:60], line[60:66], ) ] sigatm_array = np.array(sigatm, "f") structure_builder.set_sigatm(sigatm_array) elif record_type not in allowed_records: warnings.warn( "Ignoring unrecognized record '{}' at line {}".format( record_type, global_line_counter ), PDBConstructionWarning, ) local_line_counter += 1 # EOF (does not end in END or CONECT) self.line_counter = self.line_counter + local_line_counter return [] def _handle_PDB_exception(self, message, line_counter): """Handle exception (PRIVATE). This method catches an exception that occurs in the StructureBuilder object (if PERMISSIVE), or raises it again, this time adding the PDB line number to the error message. """ message = "%s at line %i." % (message, line_counter) if self.PERMISSIVE: # just print a warning - some residues/atoms may be missing warnings.warn( "PDBConstructionException: %s\n" "Exception ignored.\n" "Some atoms or residues may be missing in the data structure." % message, PDBConstructionWarning, ) else: # exceptions are fatal - raise again with new message (including line nr) raise PDBConstructionException(message) from None