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xbgf.py
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/
xbgf.py
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import warnings
import numpy
from Bio.PDB.PDBExceptions import \
PDBConstructionException, PDBConstructionWarning
from Bio.PDB.StructureBuilder import StructureBuilder
from Bio.PDB.Polypeptide import is_aa
from Bio.PDB import Selection
from chain import Chain
ELEMENTS = { 1: 'H', 2: 'HE', 3: 'LI', 4: 'BE', 5: 'B',
6: 'C', 7: 'N', 8: 'O', 9: 'F', 10: 'NE',
11: 'NA', 12: 'MG', 13: 'AL', 14: 'SI', 15: 'P',
16: 'S', 17: 'CL', 18: 'AR', 19: 'K', 20: 'CA',
21: 'SC', 22: 'TI', 23: 'V', 24: 'CR', 25: 'MN',
26: 'FE', 27: 'CO', 28: 'NI', 29: 'CU', 30: 'ZN',
31: 'GA', 32: 'GE', 33: 'AS', 34: 'SE', 35: 'BR',
36: 'KR', 37: 'RB', 38: 'SR', 39: 'Y', 40: 'ZR',
41: 'NB', 42: 'MO', 43: 'TC', 44: 'RU', 45: 'RH',
46: 'PD', 47: 'AG', 48: 'CD', 49: 'IN', 50: 'SN',
51: 'SB', 52: 'TE', 53: 'I', 54: 'XE', 55: 'CS',
56: 'BA', 57: 'LA', 58: 'CE', 59: 'PR', 60: 'ND',
61: 'PM', 62: 'SM', 63: 'EU', 64: 'GD', 65: 'TB',
66: 'DY', 67: 'HO', 68: 'ER', 69: 'TM', 70: 'YB',
71: 'LU', 72: 'HF', 73: 'TA', 74: 'W', 75: 'RE',
76: 'OS', 77: 'IR', 78: 'PT', 79: 'AU', 80: 'HG',
81: 'TL', 82: 'PB', 83: 'BI', 84: 'PO', 85: 'AT',
86: 'RN', 87: 'FR', 88: 'RA', 89: 'AC', 90: 'TH',
91: 'PA', 92: 'U', 93: 'NP', 94: 'PU', 95: 'AM',
96: 'CM', 97: 'BK', 98: 'CF', 99: 'ES', 100: 'FM',
101: 'MD', 102: 'NO', 103: 'LR', 104: 'RF', 105: 'DB',
106: 'SG', 107: 'BH', 108: 'HS', 109: 'MT', 110: 'DS',
111: 'RG', 112: 'CN', 113: 'UUT', 114: 'UUQ', 115: 'UUP',
116: 'UUH', 117: 'UUS', 118: 'UUO' }
class XBGFParser:
def __init__(self, PERMISSIVE=1, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.PERMISSIVE = PERMISSIVE
# public interface
def parse(self, id, file):
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file=open(file)
self.charges = dict()
self.chain_suffix = 0
self._parse(file.readlines())
self.structure = self.structure_builder.get_structure()
return self._process_structure()
# private methods
def _parse(self, lines):
self.structure_builder.init_model(0)
self.structure_builder.init_seg("")
self.current_chain_id = None
self.current_residue_id = None
self.current_resname = None
for i in range(0, len(lines)):
self.line_counter = i + 1
self.structure_builder.set_line_counter(self.line_counter)
line = lines[i]
if line[0:6] == 'ATOM ':
self._update_atom(line)
def _update_chain(self, line):
chain_id = self._extract_chain(line)
if self.current_chain_id != chain_id:
try:
self.structure_builder.init_chain(chain_id)
self.current_chain_id = chain_id
self.current_residue_id = None
self.current_resname = None
except PDBConstructionException, message:
self._handle_PDB_exception(message)
def _update_residue(self, line):
resseq, resname, hetero_flag = self._extract_residue(line)
residue_id = (hetero_flag, resseq, " ")
if hetero_flag == 'W':
# ignore water residues
return False
if self.current_residue_id and hetero_flag != self.current_residue_id[0]:
# moving from protien to ligand or vice versa, reset chain
self.current_chain_id = None
self.chain_suffix += 1
self._update_chain(line)
if self.current_residue_id != residue_id or self.current_resname != resname:
try:
self.structure_builder.init_residue(resname, hetero_flag, resseq, " ")
self.current_residue_id = residue_id
self.current_resname = resname
except PDBConstructionException, message:
self._handle_PDB_exception(message)
return True
def _update_atom(self, line):
# _update_residue returns False for water residues, which we ignore
if not self._update_residue(line):
return
fullname, name = self._extract_name(line)
serial_number = self._extract_serial_number(line)
coord = self._extract_coord(line)
bfactor = self._extract_bfactor(line)
occupancy = self._extract_occupancy(line)
element = self._extract_element(line)
try:
self.structure_builder.init_atom(name, coord, bfactor, occupancy, " ",
fullname, serial_number, element)
except PDBConstructionException, message:
self._handle_PDB_exception(message)
return
self.charges[self.structure_builder.atom] = self._extract_charge(line,
self.structure_builder.atom)
def _extract_chain(self, line):
return "%s%d" % (line[25:26], self.chain_suffix)
def _extract_residue(self, line):
resseq = int(line[27:32].split()[0])
resname = line[20:24].split()[0]
if is_aa(resname):
hetero_flag = " "
elif resname == "HOH" or resname == "WAT":
hetero_flag = "W"
else:
hetero_flag = "H"
return resseq, resname, hetero_flag
def _extract_name(self, line):
fullname = line[14:19]
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 _extract_serial_number(self, line):
try:
return int(line[10:13])
except:
return 0
def _extract_coord(self, line):
try:
x = float(line[32:42])
y = float(line[42:52])
z = float(line[52:62])
return numpy.array((x, y, z), 'f')
except:
self._handle_PDB_exception("Invalid or missing coordinate(s)")
return numpy.array((0, 0, 0), 'f')
def _extract_bfactor(self, line):
try:
return float(line[83:90])
except:
self._handle_PDB_exception("Invalid or missing bfactor")
return 0
def _extract_occupancy(self, line):
try:
return float(line[90:97])
except:
self._handle_PDB_exception("Invalid or missing occupancy")
return 0
def _extract_element(self, line):
try:
return ELEMENTS[int(line[97:101])]
except:
self._handle_PDB_exception("Invalid or missing element")
return ""
def _extract_charge(self, line, atom):
try:
charge = float(line[74:82])
if charge == 0 and self.current_residue_id[0] == 'H':
if atom.element == 'O':
charge = -0.5
elif atom.element == 'C':
charge = +0.1
return charge
except:
self._handle_PDB_exception("Invalid or missing charge")
return 0
def _handle_PDB_exception(self, message):
"""
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, self.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 _process_structure(self):
return [Chain(chain, self.charges) for chain in
Selection.unfold_entities(self.structure, 'C')]