def __init__(self, PERMISSIVE=1):
"""
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 own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
self.structure_builder = StructureBuilder()
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = PERMISSIVE
def __init__(self, PERMISSIVE=1):
"""
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 own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
self.structure_builder=StructureBuilder()
self.trailer=None
self.line_counter=0
self.PERMISSIVE=PERMISSIVE
class PDBCoordsParser:
"""
Parse a PDB file and return a Structure object.
"""
def __init__(self, PERMISSIVE=1):
"""
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 own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
self.structure_builder = StructureBuilder()
self.trailer = None
self.line_counter = 0
self.PERMISSIVE = PERMISSIVE
# Public methods
def get_models(self, filename):
"""
Return the models.
Arguments:
o file - name of the PDB file
"""
self.trailer = None
# Make a StructureBuilder instance (pass id of structure as parameter)
file = open(filename)
self._parse(file.readlines())
return self.structure_builder.all_models_generated
def get_trailer(self):
"Return the trailer."
return self.trailer
# Private methods
def _parse(self, header_coords_trailer):
"Parse the PDB file."
# Filters the header, parses the atomic data in the coords, then return the rest of the file (PDB file trailer)
self.trailer = self._parse_coordinates(
self._skip_header(header_coords_trailer))
def _skip_header(self, header_coords_trailer):
"Skip the header of the PDB file and return the rest."
for i in range(len(header_coords_trailer)):
self.structure_builder.set_line_counter(i + 1)
record_type = header_coords_trailer[i][0:6]
if record_type == 'ATOM ' or record_type == 'HETATM' or record_type == 'MODEL ':
break
# Return the rest of the coords+trailer for further processing
self.line_counter = i
return header_coords_trailer[i:]
def _parse_coordinates(self, coords_trailer):
"Parse the atomic data in the PDB file."
structure_builder = self.structure_builder
# Flag we have an open model
local_line_counter = current_model_id = model_open = 0
current_chain_id = current_segid = current_residue_id = current_resname = None
for i in range(len(coords_trailer)):
line = coords_trailer[i]
record_type = line[0:6]
global_line_counter = self.line_counter + local_line_counter + 1
structure_builder.set_line_counter(global_line_counter)
if 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
# Extract all data for one atom
serial_number = self._get_serial_number(line)
fullname, name = self._get_name(line)
altloc, resname = self._get_altloc_and_resname(line)
chainid = self._get_chainid(line)
resseq = self._get_residue_sequence_number(line)
icode = self._get_insertion_code(line)
coord = self._get_coordinates(line, global_line_counter)
occupancy, bfactor = self._get_occupancy_and_bfactor(
line, global_line_counter)
segid = self._get_segid(line)
element = self._get_element(line)
hetero_flag = self._get_hetero_flag(record_type, resname)
residue_id = (hetero_flag, resseq, icode)
if current_segid != segid:
current_segid = segid
structure_builder.init_seg(current_segid)
# Build new chain AND residue first
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)
# Build new residue first (still on same chain)
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)
# Build atom
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 record_type == 'MODEL ':
structure_builder.init_model(current_model_id,
self._get_model_serial_num(line))
current_model_id += 1
model_open = 1
current_chain_id = current_residue_id = None
elif record_type == 'ENDMDL':
model_open = 0
current_chain_id = current_residue_id = None
elif record_type == 'ANISOU':
structure_builder.set_anisou(self._get_anisou_array(line))
elif record_type == 'SIGUIJ':
structure_builder.set_siguij(self._get_siguij_array(line))
elif record_type == 'SIGATM':
structure_builder.set_sigatm(self._get_sigatm_array(line))
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:]
local_line_counter += 1
# EOF (does not end in END or CONECT)
self.line_counter += local_line_counter
return []
def _handle_PDB_exception(self, message, line_counter):
"""
This method catches an exception that occurs in the StructureBuilder
object (if PERMISSIVE==1), 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)
def _get_serial_number(self, line):
try:
return int(line[6:11])
except:
return 0
def _get_model_serial_num(self, line):
try:
return int(line[10:14])
except:
self._handle_PDB_exception(
"Invalid or missing model serial number", global_line_counter)
return 0
def _get_name(self, line):
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]
return fullname, name
def _get_altloc_and_resname(self, line):
return line[16:17], line[17:20]
def _get_chainid(self, line):
return line[21:22]
def _get_residue_sequence_number(self, line):
return int(line[22:26].split()[0]) # sequence identifier
def _get_insertion_code(self, line):
return line[26:27] # insertion code
def _get_coordinates(self, line, global_line_counter):
# atomic coordinates
try:
x, y, z = list(map(float, (line[30:38], line[38:46], line[46:54])))
except:
#Should we allow parsing to continue in permissive mode?
#If so what coordindates should we default to? Easier to abort!
raise PDBConstructionException(\
"Invalid or missing coordinate(s) at line %i." \
% global_line_counter)
return numpy.array((x, y, z), 'f')
def _get_occupancy_and_bfactor(self, line, global_line_counter):
# occupancy & B factor
try:
occupancy = float(line[54:60])
except:
self._handle_PDB_exception("Invalid or missing occupancy",
global_line_counter)
occupancy = 0.0 #Is one or zero a good default?
try:
bfactor = float(line[60:66])
except:
self._handle_PDB_exception("Invalid or missing B factor",
global_line_counter)
bfactor = 0.0 #The PDB use a default of zero if the data is missing
return occupancy, bfactor
def _get_segid(self, line):
return line[72:76]
def _get_element(self, line):
return line[76:78].strip()
def _get_hetero_flag(self, record_type, resname):
if record_type == 'HETATM': # hetero atom flag
if resname == "HOH" or resname == "WAT":
return "W"
else:
return "H"
else:
return " "
def _get_anisou_array(self, line):
anisou = list(
map(float, (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 on the PDB file, so this scales back
return (numpy.array(anisou, 'f') / 10000.0).astype('f')
def _get_siguij_array(self, line):
# standard deviation of anisotropic B factor
siguij = list(
map(float, (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
return (numpy.array(siguij, 'f') / 10000.0).astype('f')
def _get_sigatm_array(self, line):
# standard deviation of atomic positions
sigatm = list(
map(float, (line[30:38], line[38:45], line[46:54], line[54:60],
line[60:66])))
return numpy.array(sigatm, 'f')
class PDBCoordsParser:
"""
Parse a PDB file and return a Structure object.
"""
def __init__(self, PERMISSIVE=1):
"""
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 own StructureBuilder
object, the latter is used instead.
Arguments:
o PERMISSIVE - int, if this is 0 exceptions in constructing the
SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are
caught, but some residues or atoms will be missing. THESE EXCEPTIONS
ARE DUE TO PROBLEMS IN THE PDB FILE!.
o structure_builder - an optional user implemented StructureBuilder class.
"""
self.structure_builder=StructureBuilder()
self.trailer=None
self.line_counter=0
self.PERMISSIVE=PERMISSIVE
# Public methods
def get_models(self, filename):
"""
Return the models.
Arguments:
o file - name of the PDB file
"""
self.trailer=None
# Make a StructureBuilder instance (pass id of structure as parameter)
file = open(filename)
self._parse(file.readlines())
return self.structure_builder.all_models_generated
def get_trailer(self):
"Return the trailer."
return self.trailer
# Private methods
def _parse(self, header_coords_trailer):
"Parse the PDB file."
# Filters the header, parses the atomic data in the coords, then return the rest of the file (PDB file trailer)
self.trailer = self._parse_coordinates(self._skip_header(header_coords_trailer))
def _skip_header(self, header_coords_trailer):
"Skip the header of the PDB file and return the rest."
for i in range(len(header_coords_trailer)):
self.structure_builder.set_line_counter(i+1)
record_type = header_coords_trailer[i][0:6]
if record_type == 'ATOM ' or record_type == 'HETATM' or record_type == 'MODEL ':
break
# Return the rest of the coords+trailer for further processing
self.line_counter = i
return header_coords_trailer[i:]
def _parse_coordinates(self, coords_trailer):
"Parse the atomic data in the PDB file."
structure_builder = self.structure_builder
# Flag we have an open model
local_line_counter = current_model_id = model_open = 0
current_chain_id = current_segid = current_residue_id = current_resname = None
for i in range(len(coords_trailer)):
line = coords_trailer[i]
record_type = line[0:6]
global_line_counter = self.line_counter + local_line_counter + 1
structure_builder.set_line_counter(global_line_counter)
if 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
# Extract all data for one atom
serial_number = self._get_serial_number(line)
fullname, name = self._get_name(line)
altloc, resname = self._get_altloc_and_resname(line)
chainid = self._get_chainid(line)
resseq = self._get_residue_sequence_number(line)
icode = self._get_insertion_code(line)
coord = self._get_coordinates(line, global_line_counter)
occupancy, bfactor = self._get_occupancy_and_bfactor(line, global_line_counter)
segid = self._get_segid(line)
element = self._get_element(line)
hetero_flag = self._get_hetero_flag(record_type, resname)
residue_id=(hetero_flag, resseq, icode)
if current_segid != segid:
current_segid = segid
structure_builder.init_seg(current_segid)
# Build new chain AND residue first
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)
# Build new residue first (still on same chain)
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)
# Build atom
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 record_type == 'MODEL ':
structure_builder.init_model(current_model_id, self._get_model_serial_num(line))
current_model_id += 1
model_open = 1
current_chain_id = current_residue_id = None
elif record_type == 'ENDMDL':
model_open = 0
current_chain_id = current_residue_id = None
elif record_type == 'ANISOU':
structure_builder.set_anisou(self._get_anisou_array(line))
elif record_type == 'SIGUIJ' :
structure_builder.set_siguij(self._get_siguij_array(line))
elif record_type == 'SIGATM':
structure_builder.set_sigatm(self._get_sigatm_array(line))
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:]
local_line_counter += 1
# EOF (does not end in END or CONECT)
self.line_counter += local_line_counter
return []
def _handle_PDB_exception(self, message, line_counter):
"""
This method catches an exception that occurs in the StructureBuilder
object (if PERMISSIVE==1), 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)
def _get_serial_number(self, line):
try:
return int(line[6:11])
except:
return 0
def _get_model_serial_num(self, line):
try:
return int(line[10:14])
except:
self._handle_PDB_exception("Invalid or missing model serial number",
global_line_counter)
return 0
def _get_name(self, line):
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]
return fullname, name
def _get_altloc_and_resname(self, line):
return line[16:17], line[17:20]
def _get_chainid(self, line):
return line[21:22]
def _get_residue_sequence_number(self, line):
return int(line[22:26].split()[0]) # sequence identifier
def _get_insertion_code(self, line):
return line[26:27] # insertion code
def _get_coordinates(self, line, global_line_counter):
# atomic coordinates
try:
x, y, z = list(map(float, (line[30:38], line[38:46], line[46:54])))
except:
#Should we allow parsing to continue in permissive mode?
#If so what coordindates should we default to? Easier to abort!
raise PDBConstructionException(\
"Invalid or missing coordinate(s) at line %i." \
% global_line_counter)
return numpy.array((x, y, z), 'f')
def _get_occupancy_and_bfactor(self, line, global_line_counter):
# occupancy & B factor
try:
occupancy = float(line[54:60])
except:
self._handle_PDB_exception("Invalid or missing occupancy",
global_line_counter)
occupancy = 0.0 #Is one or zero a good default?
try:
bfactor = float(line[60:66])
except:
self._handle_PDB_exception("Invalid or missing B factor",
global_line_counter)
bfactor = 0.0 #The PDB use a default of zero if the data is missing
return occupancy, bfactor
def _get_segid(self, line):
return line[72:76]
def _get_element(self, line):
return line[76:78].strip()
def _get_hetero_flag(self, record_type, resname):
if record_type == 'HETATM': # hetero atom flag
if resname == "HOH" or resname == "WAT":
return "W"
else:
return "H"
else:
return " "
def _get_anisou_array(self, line):
anisou = list(map(float, (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 on the PDB file, so this scales back
return (numpy.array(anisou, 'f')/10000.0).astype('f')
def _get_siguij_array(self, line):
# standard deviation of anisotropic B factor
siguij = list(map(float, (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
return (numpy.array(siguij, 'f')/10000.0).astype('f')
def _get_sigatm_array(self, line):
# standard deviation of atomic positions
sigatm = list(map(float, (line[30:38], line[38:45], line[46:54], line[54:60], line[60:66])))
return numpy.array(sigatm, 'f')