class PerlGenPDBParser:
"""
Parse a PDB file generated by and return a Chain object.
"""
def __init__(self, filename):
assert (isinstance(filename, str))
self.__chain = self.__current_residue = None
self._parse_coordinates(open(filename).readlines())
def get_chain(self):
return self.__chain
def _parse_coordinates(self, lines):
self.__chain = Chain(lines[0].split()[4])
for i in range(len(lines)):
items = lines[i].split()
atom_serial_num = int(items[1])
atom_name = items[2]
element = lines[i][13]
residue_name = items[3]
residue_serial_num = int(items[5])
coords = array([items[6], items[7], items[8]], 'f')
if self.__current_residue is None or self.__current_residue.sequence_number(
) != residue_serial_num:
self.__current_residue = Residue(residue_serial_num,
residue_name)
self.__chain.add_residue(self.__current_residue)
self.__current_residue.add_atom(
Atom(atom_serial_num, atom_name, coords, element))
class PerlGenPDBParser:
"""
Parse a PDB file generated by and return a Chain object.
"""
def __init__(self, filename):
assert(isinstance(filename, str))
self.__chain = self.__current_residue = None
self._parse_coordinates(open(filename).readlines())
def get_chain(self):
return self.__chain
def _parse_coordinates(self, lines):
self.__chain = Chain(lines[0].split()[4])
for i in range(len(lines)):
items = lines[i].split()
atom_serial_num = int(items[1])
atom_name = items[2]
element = lines[i][13]
residue_name = items[3]
residue_serial_num = int(items[5])
coords = array([items[6], items[7], items[8]], 'f')
if self.__current_residue is None or self.__current_residue.sequence_number() != residue_serial_num:
self.__current_residue = Residue(residue_serial_num, residue_name)
self.__chain.add_residue(self.__current_residue)
self.__current_residue.add_atom(Atom(atom_serial_num, atom_name, coords, element))
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.current_model.has_chain_with_id(chain_id):
self.current_chain = self.current_model.chains(chain_id)
warnings.warn(
"WARNING: Chain %s is discontinuous at line %i." %
(chain_id, self.line_counter), PDBConstructionWarning)
else:
self.current_chain = Chain(chain_id)
self.current_model.add_chain(self.current_chain)
def _parse_coordinates(self, lines):
self.__chain = Chain(lines[0].split()[4])
for i in range(len(lines)):
items = lines[i].split()
atom_serial_num = int(items[1])
atom_name = items[2]
element = lines[i][13]
residue_name = items[3]
residue_serial_num = int(items[5])
coords = array([items[6], items[7], items[8]], 'f')
if self.__current_residue is None or self.__current_residue.sequence_number(
) != residue_serial_num:
self.__current_residue = Residue(residue_serial_num,
residue_name)
self.__chain.add_residue(self.__current_residue)
self.__current_residue.add_atom(
Atom(atom_serial_num, atom_name, coords, element))
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.current_model.has_chain_with_id(chain_id):
self.current_chain = self.current_model.chains(chain_id)
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
% (chain_id, self.line_counter),
PDBConstructionWarning)
else:
self.current_chain = Chain(chain_id)
self.current_model.add_chain(self.current_chain)
def _parse_coordinates(self, lines):
self.__chain = Chain(lines[0].split()[4])
for i in range(len(lines)):
items = lines[i].split()
atom_serial_num = int(items[1])
atom_name = items[2]
element = lines[i][13]
residue_name = items[3]
residue_serial_num = int(items[5])
coords = array([items[6], items[7], items[8]], 'f')
if self.__current_residue is None or self.__current_residue.sequence_number() != residue_serial_num:
self.__current_residue = Residue(residue_serial_num, residue_name)
self.__chain.add_residue(self.__current_residue)
self.__current_residue.add_atom(Atom(atom_serial_num, atom_name, coords, element))
class StructureBuilder:
"""
Deals with constructing the Structure object. The StructureBuilder class is used
by the PDBCoordsParser classes to translate a file to a Structure object.
"""
def __init__(self):
self.line_counter = 0
self.all_models_generated = []
def _is_completely_disordered(self, residue):
"Returns True if all atoms in the residue have a non blank altloc."
for atom in residue.all_atoms():
if atom.altloc() == " ":
return False
return True
# Public methods called by the Parser classes
def set_line_counter(self, line_counter):
"""
The line counter keeps track of the line in the PDB file that
is being parsed.
Arguments:
o line_counter - int
"""
assert (isinstance(line_counter, int))
self.line_counter = line_counter
def init_model(self, model_id, serial_num=None):
"""Initiate a new Model object with given id.
Arguments:
o id - int
o serial_num - int
"""
assert (isinstance(model_id, int)
and (isinstance(serial_num, int) or serial_num is None))
self.all_models_generated.append(Model(model_id, serial_num))
self.current_model = self.all_models_generated[-1]
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.current_model.has_chain_with_id(chain_id):
self.current_chain = self.current_model.chains(chain_id)
warnings.warn(
"WARNING: Chain %s is discontinuous at line %i." %
(chain_id, self.line_counter), PDBConstructionWarning)
else:
self.current_chain = Chain(chain_id)
self.current_model.add_chain(self.current_chain)
def init_seg(self, segid):
"""Flag a change in segid.
Arguments:
o segid - string
"""
assert (isinstance(segid, str))
self.segid = segid
def init_residue(self, resname, field, resseq, icode):
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if field == "H":
# The hetero field consists of H_ + the residue name (e.g. H_FUC)
field = "H_" + resname
res_id = (field, resseq, icode)
if field == " ":
if self.current_chain.has_residue_with_id(res_id):
# There already is a residue with the id (field, resseq, icode).
# This only makes sense in the case of a point mutation.
warnings.warn(
"WARNING: Residue ('%s', %i, '%s') "
"redefined at line %i." %
(field, resseq, icode, self.line_counter),
PDBConstructionWarning)
duplicate_residue = self.current_chain.residues(res_id)
if duplicate_residue.is_disordered() == 2:
# The residue in the chain is a DisorderedResidue object.
# So just add the last Residue object.
if duplicate_residue.has_residue_with_name(resname):
# The residue was already made
self.current_residue = duplicate_residue
duplicate_residue.set_main_disorder_identifier(resname)
else:
# Make a new residue and add it to the already
# present DisorderedResidue
new_residue = Residue(res_id, resname, self.segid)
duplicate_residue.add_residue(new_residue)
self.current_residue = duplicate_residue
return
else:
# Make a new DisorderedResidue object and put all
# the Residue objects with the id (field, resseq, icode) in it.
# These residues each should have non-blank altlocs for all their atoms.
# If not, the PDB file probably contains an error.
if not self._is_completely_disordered(duplicate_residue):
# if this exception is ignored, a residue will be missing
self.current_residue = None
raise PDBConstructionException(\
"Blank altlocs in duplicate residue %s ('%s', %i, '%s')" \
% (resname, field, resseq, icode))
self.current_chain.remove_residue_with_id(res_id)
new_residue = Residue(res_id, resname, self.segid)
disordered_residue = DisorderedResidue(res_id)
self.current_chain.add_residue(disordered_residue)
disordered_residue.add_residue(duplicate_residue)
disordered_residue.add_residue(new_residue)
self.current_residue = disordered_residue
return
residue = Residue(res_id, resname, self.segid)
self.current_chain.add_residue(residue)
self.current_residue = residue
def init_atom(self,
name,
coord,
b_factor,
occupancy,
altloc,
fullname,
serial_number=None,
element=None):
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
o element - string, upper case, e.g. "HG" for mercury
"""
residue = self.current_residue
# if residue is None, an exception was generated during
# the construction of the residue
if residue is None:
return
# First check if this atom is already present in the residue.
# If it is, it might be due to the fact that the two atoms have atom
# names that differ only in spaces (e.g. "CA.." and ".CA.",
# where the dots are spaces). If that is so, use all spaces
# in the atom name of the current atom.
if residue.has_atom_with_id(name):
duplicate_atom = residue.atoms(name)
# atom name with spaces of duplicate atom
duplicate_fullname = duplicate_atom.fullname()
if duplicate_fullname != fullname:
# name of current atom now includes spaces
name = fullname
warnings.warn(
"WARNING: atom names %s and %s differ "
"only in spaces at line %i." %
(duplicate_fullname, fullname, self.line_counter),
PDBConstructionWarning)
atom = self.current_atom = Atom(serial_number, name, coord, element)
atom.pdb_atom_post_initialize(b_factor, occupancy, altloc, fullname)
if altloc != " ":
# The atom is disordered
if residue.has_atom_with_id(name):
# Residue already contains this atom
duplicate_atom = residue.atoms(name)
if duplicate_atom.is_disordered() is 2:
duplicate_atom.add_atom(atom)
else:
# This is an error in the PDB file:
# a disordered atom is found with a blank altloc
# Detach the duplicate atom, and put it in a
# DisorderedAtom object together with the current
# atom.
residue.remove_atom_with_id(name)
disordered_atom = DisorderedAtom(name)
residue.add_atom(disordered_atom)
disordered_atom.add_atom(atom)
disordered_atom.add_atom(duplicate_atom)
residue.flag_disordered()
warnings.warn(
"WARNING: disordered atom found "
"with blank altloc before line %i.\n" %
self.line_counter, PDBConstructionWarning)
else:
# The residue does not contain this disordered atom
# so we create a new one.
disordered_atom = DisorderedAtom(name)
residue.add_atom(disordered_atom)
# Add the real atom to the disordered atom, and the
# disordered atom to the residue
disordered_atom.add_atom(atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add_atom(atom)
def set_anisou(self, anisou_array):
"Set anisotropic B factor of current Atom."
self.current_atom.set_anisou(anisou_array)
def set_siguij(self, siguij_array):
"Set standard deviation of anisotropic B factor of current Atom."
self.current_atom.set_siguij(siguij_array)
def set_sigatm(self, sigatm_array):
"Set standard deviation of atom position of current Atom."
self.current_atom.set_sigatm(sigatm_array)
class StructureBuilder:
"""
Deals with constructing the Structure object. The StructureBuilder class is used
by the PDBCoordsParser classes to translate a file to a Structure object.
"""
def __init__(self):
self.line_counter = 0
self.all_models_generated = []
def _is_completely_disordered(self, residue):
"Returns True if all atoms in the residue have a non blank altloc."
for atom in residue.all_atoms():
if atom.altloc() == " ":
return False
return True
# Public methods called by the Parser classes
def set_line_counter(self, line_counter):
"""
The line counter keeps track of the line in the PDB file that
is being parsed.
Arguments:
o line_counter - int
"""
assert(isinstance(line_counter, int))
self.line_counter = line_counter
def init_model(self, model_id, serial_num=None):
"""Initiate a new Model object with given id.
Arguments:
o id - int
o serial_num - int
"""
assert(isinstance(model_id, int) and (isinstance(serial_num, int) or serial_num is None))
self.all_models_generated.append(Model(model_id,serial_num))
self.current_model = self.all_models_generated[-1]
def init_chain(self, chain_id):
"""Initiate a new Chain object with given id.
Arguments:
o chain_id - string
"""
if self.current_model.has_chain_with_id(chain_id):
self.current_chain = self.current_model.chains(chain_id)
warnings.warn("WARNING: Chain %s is discontinuous at line %i."
% (chain_id, self.line_counter),
PDBConstructionWarning)
else:
self.current_chain = Chain(chain_id)
self.current_model.add_chain(self.current_chain)
def init_seg(self, segid):
"""Flag a change in segid.
Arguments:
o segid - string
"""
assert(isinstance(segid, str))
self.segid=segid
def init_residue(self, resname, field, resseq, icode):
"""
Initiate a new Residue object.
Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for
hetero residues, otherwise blank.
o resseq - int, sequence identifier
o icode - string, insertion code
"""
if field == "H":
# The hetero field consists of H_ + the residue name (e.g. H_FUC)
field = "H_" + resname
res_id=(field, resseq, icode)
if field == " ":
if self.current_chain.has_residue_with_id(res_id):
# There already is a residue with the id (field, resseq, icode).
# This only makes sense in the case of a point mutation.
warnings.warn("WARNING: Residue ('%s', %i, '%s') "
"redefined at line %i."
% (field, resseq, icode, self.line_counter),
PDBConstructionWarning)
duplicate_residue = self.current_chain.residues(res_id)
if duplicate_residue.is_disordered() == 2:
# The residue in the chain is a DisorderedResidue object.
# So just add the last Residue object.
if duplicate_residue.has_residue_with_name(resname):
# The residue was already made
self.current_residue = duplicate_residue
duplicate_residue.set_main_disorder_identifier(resname)
else:
# Make a new residue and add it to the already
# present DisorderedResidue
new_residue = Residue(res_id, resname, self.segid)
duplicate_residue.add_residue(new_residue)
self.current_residue = duplicate_residue
return
else:
# Make a new DisorderedResidue object and put all
# the Residue objects with the id (field, resseq, icode) in it.
# These residues each should have non-blank altlocs for all their atoms.
# If not, the PDB file probably contains an error.
if not self._is_completely_disordered(duplicate_residue):
# if this exception is ignored, a residue will be missing
self.current_residue = None
raise PDBConstructionException(\
"Blank altlocs in duplicate residue %s ('%s', %i, '%s')" \
% (resname, field, resseq, icode))
self.current_chain.remove_residue_with_id(res_id)
new_residue = Residue(res_id, resname, self.segid)
disordered_residue = DisorderedResidue(res_id)
self.current_chain.add_residue(disordered_residue)
disordered_residue.add_residue(duplicate_residue)
disordered_residue.add_residue(new_residue)
self.current_residue = disordered_residue
return
residue = Residue(res_id, resname, self.segid)
self.current_chain.add_residue(residue)
self.current_residue = residue
def init_atom(self, name, coord, b_factor, occupancy, altloc, fullname,
serial_number=None, element=None):
"""
Initiate a new Atom object.
Arguments:
o name - string, atom name, e.g. CA, spaces should be stripped
o coord - Numeric array (Float0, size 3), atomic coordinates
o b_factor - float, B factor
o occupancy - float
o altloc - string, alternative location specifier
o fullname - string, atom name including spaces, e.g. " CA "
o element - string, upper case, e.g. "HG" for mercury
"""
residue = self.current_residue
# if residue is None, an exception was generated during
# the construction of the residue
if residue is None:
return
# First check if this atom is already present in the residue.
# If it is, it might be due to the fact that the two atoms have atom
# names that differ only in spaces (e.g. "CA.." and ".CA.",
# where the dots are spaces). If that is so, use all spaces
# in the atom name of the current atom.
if residue.has_atom_with_id(name):
duplicate_atom = residue.atoms(name)
# atom name with spaces of duplicate atom
duplicate_fullname = duplicate_atom.fullname()
if duplicate_fullname != fullname:
# name of current atom now includes spaces
name = fullname
warnings.warn("WARNING: atom names %s and %s differ "
"only in spaces at line %i."
% (duplicate_fullname, fullname,
self.line_counter),
PDBConstructionWarning)
atom = self.current_atom = Atom(serial_number, name, coord, element)
atom.pdb_atom_post_initialize(b_factor, occupancy, altloc, fullname)
if altloc!=" ":
# The atom is disordered
if residue.has_atom_with_id(name):
# Residue already contains this atom
duplicate_atom = residue.atoms(name)
if duplicate_atom.is_disordered() is 2:
duplicate_atom.add_atom(atom)
else:
# This is an error in the PDB file:
# a disordered atom is found with a blank altloc
# Detach the duplicate atom, and put it in a
# DisorderedAtom object together with the current
# atom.
residue.remove_atom_with_id(name)
disordered_atom = DisorderedAtom(name)
residue.add_atom(disordered_atom)
disordered_atom.add_atom(atom)
disordered_atom.add_atom(duplicate_atom)
residue.flag_disordered()
warnings.warn("WARNING: disordered atom found "
"with blank altloc before line %i.\n"
% self.line_counter,
PDBConstructionWarning)
else:
# The residue does not contain this disordered atom
# so we create a new one.
disordered_atom = DisorderedAtom(name)
residue.add_atom(disordered_atom)
# Add the real atom to the disordered atom, and the
# disordered atom to the residue
disordered_atom.add_atom(atom)
residue.flag_disordered()
else:
# The atom is not disordered
residue.add_atom(atom)
def set_anisou(self, anisou_array):
"Set anisotropic B factor of current Atom."
self.current_atom.set_anisou(anisou_array)
def set_siguij(self, siguij_array):
"Set standard deviation of anisotropic B factor of current Atom."
self.current_atom.set_siguij(siguij_array)
def set_sigatm(self, sigatm_array):
"Set standard deviation of atom position of current Atom."
self.current_atom.set_sigatm(sigatm_array)
