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# Copyright (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be)
# 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.
# Python stuff
import sys
from string import split
from Numeric import array, Float0
# My stuff
from StructureBuilder import StructureBuilder
from PDBExceptions import PDBConstructionException
from parse_pdb_header import _parse_pdb_header_list
__doc__="Parser for PDB files."
# 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=1, get_header=0, structure_builder=None):
"""
The PDB parser call a number of standard methods in an aggregated
StructureBuilder object. Normally this object is instanciated 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.
"""
if structure_builder!=None:
self.structure_builder=structure_builder
else:
self.structure_builder=StructureBuilder()
self.header=None
self.trailer=None
self.line_counter=0
self.PERMISSIVE=PERMISSIVE
# Public methods
def get_structure(self, id, file):
"""Return the structure.
Arguments:
o id - string, the id that will be used for the structure
o file - name of the PDB file OR an open filehandle
"""
self.header=None
self.trailer=None
# Make a StructureBuilder instance (pass id of structure as parameter)
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file=open(file)
self._parse(file.readlines())
file.close()
self.structure_builder.set_header(self.header)
# Return the Structure instance
return self.structure_builder.get_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."
# 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."
structure_builder=self.structure_builder
for i in range(0, len(header_coords_trailer)):
structure_builder.set_line_counter(i+1)
line=header_coords_trailer[i]
record_type=line[0:6]
if(record_type=='ATOM ' or record_type=='HETATM' or record_type=='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."
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(0, 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
fullname=line[12:16]
# get rid of whitespace in atom names
split_list=split(fullname)
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[16:17]
resname=line[17:20]
chainid=line[21:22]
try:
serial_number=int(line[6:11])
except:
serial_number=0
resseq=int(split(line[22:26])[0]) # sequence identifier
icode=line[26:27] # 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
x=float(line[30:38])
y=float(line[38:46])
z=float(line[46:54])
coord=array((x, y, z), Float0)
# occupancy & B factor
occupancy=float(line[54:60])
bfactor=float(line[60:66])
segid=line[72:76]
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, 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, message:
self._handle_PDB_exception(message, global_line_counter)
# init atom
try:
structure_builder.init_atom(name, coord, bfactor, occupancy, altloc, fullname, serial_number)
except PDBConstructionException, message:
self._handle_PDB_exception(message, global_line_counter)
elif(record_type=='ANISOU'):
anisou=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
anisou_array=(array(anisou, Float0)/10000.0).astype(Float0)
structure_builder.set_anisou(anisou_array)
elif(record_type=='MODEL '):
structure_builder.init_model(current_model_id)
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=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=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
siguij_array=(array(siguij, Float0)/10000.0).astype(Float0)
structure_builder.set_siguij(siguij_array)
elif(record_type=='SIGATM'):
# standard deviation of atomic positions
sigatm=map(float, (line[30:38], line[38:45], line[46:54], line[54:60], line[60:66]))
sigatm_array=array(sigatm, Float0)
structure_builder.set_sigatm(sigatm_array)
local_line_counter=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):
"""
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 will be missing
print "PDBConstructionException: %s" % message
print "Exception ignored.\nSome atoms or residues will be missing in the data structure."
else:
# exceptions are fatal - raise again with new message (including line nr)
raise PDBConstructionException, message
if __name__=="__main__":
import sys
p=PDBParser(PERMISSIVE=1)
s=p.get_structure("scr", sys.argv[1])
for m in s:
p=m.get_parent()
assert(p is s)
for c in m:
p=c.get_parent()
assert(p is m)
for r in c:
print r
p=r.get_parent()
assert(p is c)
for a in r:
p=a.get_parent()
if not p is r:
print p, r
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