# This module handles input and output of PDB files. # # Written by Konrad Hinsen # Last revision: 2001-1-11 # """This module provides classes that represent PDB (Protein Data Bank) files and configurations contained in PDB files. It provides access to PDB files on two levels: low-level (line by line) and high-level (chains, residues, and atoms). Caution: The PDB file format has been heavily abused, and it is probably impossible to write code that can deal with all variants correctly. This modules tries to read the widest possible range of PDB files, but gives priority to a correct interpretation of the PDB format as defined by the Brookhaven National Laboratory. A special problem are atom names. The PDB file format specifies that the first two letters contain the right-justified chemical element name. A later modification allowed the initial space in hydrogen names to be replaced by a digit. Many programs ignore all this and treat the name as an arbitrary left-justified four-character name. This makes it difficult to extract the chemical element accurately; most programs write the '"CA"' for C_alpha in such a way that it actually stands for a calcium atom! For this reason a special element field has been added later, but only few files use it. The low-level routines in this module do not try to deal with the atom name problem; they return and expect four-character atom names including spaces in the correct positions. The high-level routines use atom names without leading or trailing spaces, but provide and use the element field whenever possible. For output, they use the element field to place the atom name correctly, and for input, they construct the element field content from the atom name if no explicit element field is found in the file. Except where indicated, numerical values use the same units and conventions as specified in the PDB format description. Example: >>>conf = Structure('example.pdb') >>>print conf >>>for residue in conf.residues: >>> for atom in residue: >>> print atom """ from Scientific.IO.TextFile import TextFile from Scientific.IO.FortranFormat import FortranFormat, FortranLine from Scientific.Geometry import Vector, Tensor from PDBExportFilters import export_filters import copy, string # # Fortran formats for PDB entries # atom_format = FortranFormat('A6,I5,1X,A4,A1,A4,A1,I4,A1,3X,3F8.3,2F6.2,' + '6X,A4,2A2') anisou_format = FortranFormat('A6,I5,1X,A4,A1,A4,A1,I4,A1,1X,6I7,2X,A4,2A2') conect_format = FortranFormat('A6,11I5') ter_format = FortranFormat('A6,I5,6X,A4,A1,I4,A1') model_format = FortranFormat('A6,4X,I4') header_format = FortranFormat('A6,4X,A40,A9,3X,A4') generic_format = FortranFormat('A6,A74') # # Amino acid and nucleic acid residues # amino_acids = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'CYX', 'GLN', 'GLU', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'ACE', 'NME'] nucleic_acids = [ 'A', 'C', 'G', 'I', 'T', 'U', '+A', '+C', '+G', '+I', '+T', '+U', 'RA', 'RC', 'RG', 'RU', 'DA', 'DC', 'DG', 'DT', 'RA5', 'RC5', 'RG5', 'RU5', 'DA5', 'DC5', 'DG5', 'DT5', 'RA3', 'RC3', 'RG3', 'RU3', 'DA3', 'DC3', 'DG3', 'DT3', 'RAN', 'RCN', 'RGN', 'RUN', 'DAN', 'DCN', 'DGN', 'DTN', ] def defineAminoAcidResidue(symbol): amino_acids.append(string.upper(symbol)) def defineNucleicAcidResidue(symbol): nucleic_acids.append(string.upper(symbol)) # # Low-level file object. It represents line contents as Python dictionaries. # For output, there are additional methods that generate sequence numbers # for everything. # class PDBFile: """PDB file with access at the record level Constructor: PDBFile(|filename|, |mode|='"r"'), where |filename| is the file name and |mode| is '"r"' for reading and '"w"' for writing, The low-level file access is handled by the module Scientific.IO.TextFile, therefore compressed files and URLs (for reading) can be used as well. """ def __init__(self, filename, mode = 'r', subformat = None): self.file = TextFile(filename, mode) self.output = string.lower(mode[0]) == 'w' self.export_filter = None if subformat is not None: export = export_filters.get(subformat, None) if export is not None: self.export_filter = export() self.open = 1 if self.output: self.data = {'serial_number': 0, 'residue_number': 0, 'chain_id': '', 'segment_id': ''} self.het_flag = 0 self.chain_number = -1 def readLine(self): """Returns the contents of the next non-blank line (= record). The return value is a tuple whose first element (a string) contains the record type. For supported record types (HEADER, ATOM, HETATM, ANISOU, TERM, MODEL, CONECT), the items from the remaining fields are put into a dictionary which is returned as the second tuple element. Most dictionary elements are strings or numbers; atom positions are returned as a vector, and anisotropic temperature factors are returned as a rank-2 tensor, already multiplied by 1.e-4. White space is stripped from all strings except for atom names, whose correct interpretation can depend on an initial space. For unsupported record types, the second tuple element is a string containing the remaining part of the record. """ while 1: line = self.file.readline() if not line: return ('END','') if line[-1] == '\n': line = line[:-1] line = string.strip(line) if line: break line = string.ljust(line, 80) type = string.strip(line[:6]) if type == 'ATOM' or type == 'HETATM': line = FortranLine(line, atom_format) data = {'serial_number': line[1], 'name': line[2], 'alternate': string.strip(line[3]), 'residue_name': string.strip(line[4]), 'chain_id': string.strip(line[5]), 'residue_number': line[6], 'insertion_code': string.strip(line[7]), 'position': Vector(line[8:11]), 'occupancy': line[11], 'temperature_factor': line[12], 'segment_id': string.strip(line[13]), 'element': string.strip(line[14]), 'charge': string.strip(line[15])} return type, data elif type == 'ANISOU': line = FortranLine(line, anisou_format) data = {'serial_number': line[1], 'name': line[2], 'alternate': string.strip(line[3]), 'residue_name': string.strip(line[4]), 'chain_id': string.strip(line[5]), 'residue_number': line[6], 'insertion_code': string.strip(line[7]), 'u': 1.e-4*Tensor([[line[8], line[11], line[12]], [line[11], line[9] , line[13]], [line[12], line[13], line[10]]]), 'segment_id': string.strip(line[14]), 'element': string.strip(line[15]), 'charge': string.strip(line[16])} return type, data elif type == 'TER': line = FortranLine(line, ter_format) data = {'serial_number': line[1], 'residue_name': string.strip(line[2]), 'chain_id': string.strip(line[3]), 'residue_number': line[4], 'insertion_code': string.strip(line[5])} return type, data elif type == 'CONECT': line = FortranLine(line, conect_format) data = {'serial_number': line[1], 'bonded': filter(lambda i: i > 0, line[2:6]), 'hydrogen_bonded': filter(lambda i: i > 0, line[6:10]), 'salt_bridged': filter(lambda i: i > 0, line[10:12])} return type, data elif type == 'MODEL': line = FortranLine(line, model_format) data = {'serial_number': line[1]} return type, data elif type == 'HEADER': line = FortranLine(line, header_format) data = {'compound': line[1], 'date': line[2], 'pdb_code': line[3]} return type, data else: return type, line[6:] def writeLine(self, type, data): """Writes a line using record type and data dictionary in the same format as returned by readLine(). Default values are provided for non-essential information, so the data dictionary need not contain all entries. """ if self.export_filter is not None: type, data = self.export_filter.processLine(type, data) if type is None: return line = [type] if type == 'ATOM' or type == 'HETATM': format = atom_format position = data['position'] line = line + [data.get('serial_number', 1), data.get('name'), data.get('alternate', ''), string.rjust(data.get('residue_name', ''), 3), data.get('chain_id', ''), data.get('residue_number', 1), data.get('insertion_code', ''), position[0], position[1], position[2], data.get('occupancy', 0.), data.get('temperature_factor', 0.), data.get('segment_id', ''), string.rjust(data.get('element', ''), 2), data.get('charge', '')] elif type == 'ANISOU': format = anisou_format u = 1.e4*data['u'] u = [int(u[0,0]), int(u[1,1]), int(u[2,2]), int(u[0,1]), int(u[0,2]), int(u[1,2])] line = line + [data.get('serial_number', 1), data.get('name'), data.get('alternate', ''), string.rjust(data.get('residue_name'), 3), data.get('chain_id', ''), data.get('residue_number', 1), data.get('insertion_code', '')] \ + u \ + [data.get('segment_id', ''), string.rjust(data.get('element', ''), 2), data.get('charge', '')] elif type == 'TER': format = ter_format line = line + [data.get('serial_number', 1), string.rjust(data.get('residue_name'), 3), data.get('chain_id', ''), data.get('residue_number', 1), data.get('insertion_code', '')] elif type == 'CONECT': format = conect_format line = line + [data.get('serial_number')] line = line + (data.get('bonded', [])+4*[None])[:4] line = line + (data.get('hydrogen_bonded', [])+4*[None])[:4] line = line + (data.get('salt_bridged', [])+2*[None])[:2] elif type == 'MODEL': format = model_format line = line + [data.get('serial_number')] elif type == 'HEADER': format = header_format line = line + [data.get('compound', ''), data.get('date', ''), data.get('pdb_code')] else: format = generic_format line = line + [data] self.file.write(str(FortranLine(line, format)) + '\n') def writeComment(self, text): """Writes |text| into one or several comment lines. Each line of the text is prefixed with 'REMARK' and written to the file. """ while text: eol = string.find(text,'\n') if eol == -1: eol = len(text) self.file.write('REMARK %s \n' % text[:eol]) text = text[eol+1:] def writeAtom(self, name, position, occupancy=0.0, temperature_factor=0.0, element=''): """Writes an ATOM or HETATM record using the |name|, |occupancy|, |temperature| and |element| information supplied. The residue and chain information is taken from the last calls to the methods nextResidue() and nextChain(). """ if self.het_flag: type = 'HETATM' else: type = 'ATOM' name = string.upper(name) if element != '' and len(element) == 1 and name and name[0] == element: name = ' ' + name self.data['name'] = name self.data['position'] = position self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000 self.data['occupancy'] = occupancy self.data['temperature_factor'] = temperature_factor self.data['element'] = element self.writeLine(type, self.data) def nextResidue(self, name, number = None, terminus = None): """Signals the beginning of a new residue, starting with the next call to writeAtom(). The residue name is |name|, and a |number| can be supplied optionally; by default residues in a chain will be numbered sequentially starting from 1. The value of |terminus| can be 'None', '"C"', or '"N"'; it is passed to export filters that can use this information in order to use different atom or residue names in terminal residues. """ name = string.upper(name) if self.export_filter is not None: name, number = self.export_filter.processResidue(name, number, terminus) self.het_flag = not (name in amino_acids or name in nucleic_acids) self.data['residue_name'] = name self.data['residue_number'] = (self.data['residue_number'] + 1) % 10000 self.data['insertion_code'] = '' if number is not None: if type(number) is type(0): self.data['residue_number'] = number % 10000 else: self.data['residue_number'] = number.number % 10000 self.data['insertion_code'] = number.insertion_code def nextChain(self, chain_id = None, segment_id = ''): """Signals the beginning of a new chain. A chain identifier (string of length one) can be supplied as |chain_id|, by default consecutive letters from the alphabet are used. The equally optional |segment_id| defaults to an empty string. """ if chain_id is None: self.chain_number = (self.chain_number + 1) % len(self._chain_ids) chain_id = self._chain_ids[self.chain_number] if self.export_filter is not None: chain_id, segment_id = \ self.export_filter.processChain(chain_id, segment_id) self.data['chain_id'] = (chain_id+' ')[:1] self.data['segment_id'] = (segment_id+' ')[:4] self.data['residue_number'] = 0 _chain_ids = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' def terminateChain(self): "Signals the end of a chain." if self.export_filter is not None: self.export_filter.terminateChain() self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000 self.writeLine('TER', self.data) self.data['chain_id'] = '' self.data['segment_id'] = '' def close(self): """Closes the file. This method *must* be called for write mode because otherwise the file will be incomplete. """ if self.open: if self.output: self.file.write('END\n') self.file.close() self.open = 0 def __del__(self): self.close() # # High-level object representation of PDB file contents. # # # Representation of objects. # class Atom: """Atom in a PDB structure Constructor: Atom(|name|, |position|, |**properties|), where |name| is the PDB atom name (a string), |position| is a atom position (a vector), and |properties| can include any of the other items that can be stored in an atom record. The properties can be obtained or modified using indexing, as for Python dictionaries. """ def __init__(self, name, position, **properties): self.position = position self.properties = properties if self.properties.get('element', '') == '': if name[0] == ' ' or name[0] in string.digits: self.properties['element'] = name[1] elif name[1] in string.digits: self.properties['element'] = name[0] self.name = string.strip(name) def __getitem__(self, item): try: return self.properties[item] except KeyError: if item == 'name': return self.name elif item == 'position': return self.position else: raise KeyError, "Undefined atom property: " + repr(item) def __setitem__(self, item, value): self.properties[item] = value def __str__(self): return self.__class__.__name__ + ' ' + self.name + \ ' at ' + str(self.position) __repr__ = __str__ def type(self): "Returns the six-letter record type, ATOM or HETATM." return 'ATOM ' def writeToFile(self, file): """Writes an atom record to |file| (a PDBFile object or a string containing a file name).""" close = 0 if type(file) == type(''): file = PDBFile(file, 'w') close = 1 file.writeAtom(self.name, self.position, self.properties.get('occupancy', 0.), self.properties.get('temperature_factor', 0.), self.properties.get('element', '')) if close: file.close() class HetAtom(Atom): """HetAtom in a PDB structure A subclass of Atom, which differs only in the return value of the method type(). Constructor: HetAtom(|name|, |position|, |**properties|). """ def type(self): return 'HETATM' class Group: """Atom group (residue or molecule) in a PDB file This is an abstract base class. Instances can be created using one of the subclasses (Molecule, AminoAcidResidue, NucleotideResidue). Group objects permit iteration over atoms with for-loops, as well as extraction of atoms by indexing with the atom name. """ def __init__(self, name, atoms = None, number = None): self.name = name self.number = number self.atom_list = [] self.atoms = {} if atoms: self.atom_list = atoms for a in atoms: self.atoms[a.name] = a def __len__(self): return len(self.atom_list) def __getitem__(self, item): if type(item) == type(0): return self.atom_list[item] else: return self.atoms[item] def __str__(self): s = self.__class__.__name__ + ' ' + self.name + ':\n' for atom in self.atom_list: s = s + ' ' + `atom` + '\n' return s __repr__ = __str__ def isCompatible(self, residue_data): return residue_data['residue_name'] == self.name \ and residue_data['residue_number'] == self.number def addAtom(self, atom): "Adds |atom| (an Atom object) to the group." self.atom_list.append(atom) self.atoms[atom.name] = atom def deleteAtom(self, atom): """Removes |atom| (an Atom object) from the group. An exception will be raised if |atom| is not part of the group. """ self.atom_list.remove(atom) del self.atoms[atom.name] def deleteHydrogens(self): "Removes all hydrogen atoms." delete = [] for a in self.atom_list: if a.name[0] == 'H' or (a.name[0] in string.digits and a.name[1] == 'H'): delete.append(a) for a in delete: self.deleteAtom(a) def changeName(self, name): "Sets the PDB residue name to |name|." self.name = name def writeToFile(self, file): """Writes the group to |file| (a PDBFile object or a string containing a file name). """ close = 0 if type(file) == type(''): file = PDBFile(file, 'w') close = 1 file.nextResidue(self.name, self.number, self.terminusType()) for a in self.atom_list: a.writeToFile(file) if close: file.close() class Molecule(Group): """Molecule in a PDB file A subclass of Group. Constructor: Molecule(|name|, |atoms|='None', |number|=None), where |name| is the PDB residue name. An optional list of |atoms| can be specified, otherwise the molecule is initially empty. The optional |number| is the PDB residue number. Note: In PDB files, non-chain molecules are treated as residues, there is no separate molecule definition. This modules defines every residue as a molecule that is not an amino acid residue or a nucleotide residue. """ pass class Residue(Group): pass class AminoAcidResidue(Residue): """Amino acid residue in a PDB file A subclass of Group. Constructor: AminoAcidResidue(|name|, |atoms|='None', |number|=None), where |name| is the PDB residue name. An optional list of |atoms| can be specified, otherwise the residue is initially empty. The optional |number| is the PDB residue number. """ is_amino_acid = 1 def isCTerminus(self): """Returns 1 if the residue is in C-terminal configuration, i.e. if it has a second oxygen bound to the carbon atom of the peptide group. """ return self.atoms.has_key('OXT') or self.atoms.has_key('OT2') def isNTerminus(self): """Returns 1 if the residue is in N-terminal configuration, i.e. if it contains more than one hydrogen bound to be nitrogen atom of the peptide group. """ return self.atoms.has_key('1HT') or self.atoms.has_key('2HT') \ or self.atoms.has_key('3HT') def writeToFile(self, file): close = 0 if type(file) == type(''): file = PDBFile(file, 'w') close = 1 terminus = None if self.isCTerminus(): terminus = 'C' if self.isNTerminus(): terminus = 'N' file.nextResidue(self.name, self.number, terminus) for a in self.atom_list: a.writeToFile(file) if close: file.close() class NucleotideResidue(Residue): """Nucleotide residue in a PDB file A subclass of Group. Constructor: NucleotideResidue(|name|, |atoms|='None', |number|=None), where |name| is the PDB residue name. An optional list of |atoms| can be specified, otherwise the residue is initially empty. The optional |number| is the PDB residue number. """ is_nucleotide = 1 def __init__(self, name, atoms = None, number = None): self.pdbname = name name = string.strip(name) if name[0] != 'D' and name[0] != 'R': name = 'D' + name Residue.__init__(self, name, atoms, number) for a in atoms: if a.name == 'O2*' or a.name == "O2'": # Ribose self.name = 'R' + self.name[1:] def isCompatible(self, residue_data): return (residue_data['residue_name'] == self.name or residue_data['residue_name'] == self.pdbname) \ and residue_data['residue_number'] == self.number def addAtom(self, atom): Residue.addAtom(self, atom) if atom.name == 'O2*' or atom.name == "O2'": # Ribose self.name = 'R' + self.name[1:] def hasRibose(self): "Returns 1 if the residue has an atom named O2*." return self.atoms.has_key('O2*') or self.atoms.has_key("O2'") def hasDesoxyribose(self): "Returns 1 if the residue has no atom named O2*." return not self.hasRibose() def hasPhosphate(self): "Returns 1 if the residue has a phosphate group." return self.atoms.has_key('P') def hasTerminalH(self): "Returns 1 if the residue has a 3-terminal H atom." return self.atoms.has_key('H3T') def writeToFile(self, file): close = 0 if type(file) == type(''): file = PDBFile(file, 'w') close = 1 terminus = None if not self.hasPhosphate(): terminus = '5' file.nextResidue(self.name[1:], self.number, terminus) for a in self.atom_list: a.writeToFile(file) if close: file.close() class Chain: """Chain of PDB residues This is an abstract base class. Instances can be created using one of the subclasses (PeptideChain, NucleotideChain). Chain objects respond to len() and return their residues by indexing with integers. """ def __init__(self, residues = None, chain_id = None, segment_id = None): if residues is None: self.residues = [] else: self.residues = residues self.chain_id = chain_id self.segment_id = segment_id def __len__(self): return len(self.residues) def sequence(self): "Returns the list of residue names." return map(lambda r: r.name, self.residues) def __getitem__(self, index): return self.residues[index] def addResidue(self, residue): "Add |residue| at the end of the chain." self.residues.append(residue) def removeResidues(self, first, last): """Remove residues starting from |first| up to (but not including) |last|. If |last| is 'None', remove everything starting from |first|. """ if last is None: del self.residues[first:] else: del self.residues[first:last] def deleteHydrogens(self): "Removes all hydrogen atoms." for r in self.residues: r.deleteHydrogens() def writeToFile(self, file): """Writes the chain to |file| (a PDBFile object or a string containing a file name). """ close = 0 if type(file) == type(''): file = PDBFile(file, 'w') close = 1 file.nextChain(self.chain_id, self.segment_id) for r in self.residues: r.writeToFile(file) file.terminateChain() if close: file.close() class PeptideChain(Chain): """Peptide chain in a PDB file A subclass of Chain. Constructor: PeptideChain(|residues|='None', |chain_id|='None', |segment_id|='None'), where |chain_id| is a one-letter chain identifier and |segment_id| is a multi-character chain identifier, both are optional. A list of AminoAcidResidue objects can be passed as |residues|; by default a peptide chain is initially empty. """ def __getslice__(self, i1, i2): return self.__class__(self.residues[i1:i2]) def isTerminated(self): "Returns 1 if the last residue is in C-terminal configuration." return self.residues and self.residues[-1].isCTerminus() def isCompatible(self, chain_data, residue_data): return chain_data['chain_id'] == self.chain_id and \ chain_data['segment_id'] == self.segment_id and \ residue_data['residue_name'] in amino_acids class NucleotideChain(Chain): """Nucleotide chain in a PDB file A subclass of Chain. Constructor: NucleotideChain(|residues|='None', |chain_id|='None', |segment_id|='None'), where |chain_id| is a one-letter chain identifier and |segment_id| is a multi-character chain identifier, both are optional. A list of NucleotideResidue objects can be passed as |residues|; by default a nucleotide chain is initially empty. """ def __getslice__(self, i1, i2): return self.__class__(self.residues[i1:i2]) def isTerminated(self): # impossible to detect for standard PDB files, but we can still # do something useful for certain non-standard files return self.residues and \ (self.residues[-1].name[-1] == '3' or self.residues[-1].hasTerminalH()) def isCompatible(self, chain_data, residue_data): return chain_data['chain_id'] == self.chain_id and \ chain_data['segment_id'] == self.segment_id and \ residue_data['residue_name'] in nucleic_acids class DummyChain(Chain): def __init__(self, structure, chain_id, segment_id): self.structure = structure self.chain_id = chain_id self.segment_id = segment_id def isTerminated(self): return 0 def addResidue(self, residue): self.structure.addMolecule(residue) def isCompatible(self, chain_data, residue_data): return chain_data['chain_id'] == self.chain_id and \ chain_data['segment_id'] == self.segment_id and \ residue_data['residue_name'] not in amino_acids and \ residue_data['residue_name'] not in nucleic_acids # # Residue number class for dealing with insertion codes # class ResidueNumber: """PDB residue number Most PDB residue numbers are simple integers, but when insertion codes are used a number can consist of an integer plus a letter. Such compound residue numbers are represented by this class. Constructor: ResidueNumber(|number|, |insertion_code|) """ def __init__(self, number, insertion_code): self.number = number self.insertion_code = insertion_code def __cmp__(self, other): if type(other) == type(0): if self.number == other: return 1 else: return cmp(self.number, other) if self.number == other.number: return cmp(self.insertion_code, other.insertion_code) else: return cmp(self.number, other.number) def __str__(self): return str(self.number) + self.insertion_code __repr__ = __str__ # # The configuration class. # class Structure: """A high-level representation of the contents of a PDB file Constructor: Structure(|filename|, |model|='0', |alternate_code|='"A"'), where |filename| is the name of the PDB file. Compressed files and URLs are accepted, as for class PDBFile. The two optional arguments specify which data should be read in case of a multiple-model file or in case of a file that contains alternative positions for some atoms. The components of a system can be accessed in several ways ('s' is an instance of this class): - 's.residues' is a list of all PDB residues, in the order in which they occurred in the file. - 's.peptide_chains' is a list of PeptideChain objects, containing all peptide chains in the file in their original order. - 's.nucleotide_chains' is a list of NucleotideChain objects, containing all nucleotide chains in the file in their original order. - 's.molecules' is a list of all PDB residues that are neither amino acid residues nor nucleotide residues, in their original order. - 's.objects' is a list of all high-level objects (peptide chains, nucleotide chains, and molecules) in their original order. An iteration over a Structure instance by a for-loop is equivalent to an iteration over the residue list. """ def __init__(self, filename, model = 0, alternate_code = 'A'): self.filename = filename self.model = model self.alternate = alternate_code self.pdb_code = '' self.residues = [] self.objects = [] self.peptide_chains = [] self.nucleotide_chains = [] self.molecules = {} self.parseFile(PDBFile(filename)) peptide_chain_constructor = PeptideChain nucleotide_chain_constructor = NucleotideChain molecule_constructor = Molecule def __len__(self): return len(self.residues) def __getitem__(self, item): return self.residues[item] def deleteHydrogens(self): "Removes all hydrogen atoms." for r in self.residues: r.deleteHydrogens() def splitPeptideChain(self, number, position): """Splits the peptide chain indicated by |number| (0 being the first peptide chain in the PDB file) after the residue indicated by |position| (0 being the first residue of the chain). The two chain fragments remain adjacent in the peptide chain list, i.e. the numbers of all following nucleotide chains increase by one. """ self._splitChain(self.peptide_chain_constructor, self.peptide_chains, number, position) def splitNucleotideChain(self, number, position): """Splits the nucleotide chain indicated by |number| (0 being the first nucleotide chain in the PDB file) after the residue indicated by |position| (0 being the first residue of the chain). The two chain fragments remain adjacent in the nucleotide chain list, i.e. the numbers of all following nucleotide chains increase by one. """ self._splitChain(self.nucleotide_chain_constructor, self.nucleotide_chains, number, position) def _splitChain(self, constructor, chain_list, number, position): chain = chain_list[number] part1 = constructor(chain.residues[:position], chain.chain_id, chain.segment_id) part2 = constructor(chain.residues[position:]) chain_list[number:number+1] = [part1, part2] index = self.objects.index(chain) self.objects[index:index+1] = [part1, part2] def joinPeptideChains(self, first, second): """Join the two peptide chains indicated by |first| and |second| into one peptide chain. The new chain occupies the position |first|; the chain at |second| is removed from the peptide chain list. """ self._joinChains(self.peptide_chain_constructor, self.peptide_chains, first, second) def joinNucleotideChains(self, first, second): """Join the two nucleotide chains indicated by |first| and |second| into one nucleotide chain. The new chain occupies the position |first|; the chain at |second| is removed from the nucleotide chain list. """ self._joinChains(self.nucleotide_chain_constructor, self.nucleotide_chains, first, second) def _joinChains(self, constructor, chain_list, first, second): chain1 = chain_list[first] chain2 = chain_list[second] total = constructor(chain1.residues+chain2.residues, chain1.chain_id, chain1.segment_id) chain_list[first] = total del chain_list[second] index = self.objects.index(chain1) self.objects[index] = total index = self.objects.index(chain2) del self.objects[index] def addMolecule(self, molecule): try: molecule_list = self.molecules[molecule.name] except KeyError: molecule_list = [] self.molecules[molecule.name] = molecule_list molecule_list.append(molecule) self.objects.append(molecule) def extractData(self, data): atom_data = {} for name in ['serial_number', 'name', 'position', 'occupancy', 'temperature_factor']: atom_data[name] = data[name] for name in ['alternate', 'charge']: value = data[name] if value: atom_data[name] = value element = data['element'] if element != '': try: string.atoi(element) except ValueError: atom_data['element'] = element residue_data = {'residue_name': data['residue_name']} number = data['residue_number'] insertion = data['insertion_code'] if insertion == '': residue_data['residue_number'] = number else: residue_data['residue_number'] = ResidueNumber(number, insertion) chain_data = {} for name in ['chain_id', 'segment_id']: chain_data[name] = data[name] if chain_data['segment_id'] == self.pdb_code: chain_data['segment_id'] = '' return atom_data, residue_data, chain_data def newResidue(self, residue_data): name = residue_data['residue_name'] residue_number = residue_data['residue_number'] if name in amino_acids: residue = AminoAcidResidue(name, [], residue_number) elif name in nucleic_acids: residue = NucleotideResidue(name, [], residue_number) else: residue = self.molecule_constructor(name, [], residue_number) self.residues.append(residue) return residue def newChain(self, residue, chain_data): if hasattr(residue, 'is_amino_acid'): chain = self.peptide_chain_constructor([], chain_data['chain_id'], chain_data['segment_id']) self.peptide_chains.append(chain) self.objects.append(chain) elif hasattr(residue, 'is_nucleotide'): chain = self.nucleotide_chain_constructor([], chain_data['chain_id'], chain_data['segment_id']) self.nucleotide_chains.append(chain) self.objects.append(chain) else: chain = DummyChain(self, chain_data['chain_id'], chain_data['segment_id']) return chain def parseFile(self, file): atom = None residue = None chain = None read = self.model == 0 while 1: type, data = file.readLine() if type == 'END': break elif type == 'HEADER': self.pdb_code = data['pdb_code'] elif type == 'MODEL': read = data['serial_number'] == self.model if self.model == 0 and len(self.residues) == 0: read = 1 elif type == 'ENDMDL': read = 0 elif read: if type == 'ATOM' or type == 'HETATM': alt = data['alternate'] if alt == '' or alt == self.alternate: atom_data, residue_data, chain_data = \ self.extractData(data) if type == 'ATOM': atom = apply(Atom, (), atom_data) else: atom = apply(HetAtom, (), atom_data) new_chain = chain is None or \ not chain.isCompatible(chain_data, residue_data) new_residue = new_chain or residue is None \ or not residue.isCompatible(residue_data) if new_residue and chain is not None and \ chain.isTerminated(): new_chain = 1 if new_residue: residue = self.newResidue(residue_data) if new_chain: chain = self.newChain(residue, chain_data) chain.addResidue(residue) residue.addAtom(atom) elif type == 'ANISOU': alt = data['alternate'] if alt == '' or alt == self.alternate: if atom is None: raise ValueError, "ANISOU record before " + \ "ATOM record" atom['u'] = data['u'] elif type == 'TERM': if chain is None: raise ValueError, "TERM record before chain" chain = None def renumberAtoms(self): "Renumber all atoms sequentially starting with 1." n = 0 for residue in self.residues: for atom in residue: atom['serial_number'] = n n = n + 1 def __repr__(self): s = self.__class__.__name__ + "(" + repr(self.filename) if self.model != 0: s = s + ", model=" + repr(self.model) if self.alternate != 'A': s = s + ", alternate_code = " + repr(self.alternate_code) s = s + "):\n" for name, list in [("Peptide", self.peptide_chains), ("Nucleotide", self.nucleotide_chains)]: for c in list: s = s + " " + name + " chain " if c.segment_id: s = s + c.segment_id + " " elif c.chain_id: s = s + c.chain_id + " " s = s + "of length " + repr(len(c)) + "\n" for name, list in self.molecules.items(): s = s + " " + repr(len(list)) + " " + name + " molecule" if len(list) == 1: s = s + "\n" else: s = s + "s\n" return s def writeToFile(self, file): """Writes all objects to |file| (a PDBFile object or a string containing a file name). """ close = 0 if type(file) == type(''): file = PDBFile(file, 'w') close = 1 for o in self.objects: o.writeToFile(file) if close: file.close() if __name__ == '__main__': if 0: file = PDBFile('~/3lzt.pdb') copy = PDBFile('test.pdb', 'w', 'xplor') while 1: type, data = file.readLine() if type == 'END': break copy.writeLine(type, data) copy.close() if 1: s = Structure('~/detached/okb.pdb') #s = Structure('./3lzt.pdb') #s = Structure('~/1tka.pdb') print s