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# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Output of PDB files."""
from Bio._py3k import basestring
from Bio.PDB.StructureBuilder import StructureBuilder # To allow saving of chains, residues, etc..
from Bio.Data.IUPACData import atom_weights # Allowed Elements
_ATOM_FORMAT_STRING = "%s%5i %-4s%c%3s %c%4i%c %8.3f%8.3f%8.3f%s%6.2f %4s%2s%2s\n"
class Select(object):
"""Select everything fo PDB output (for use as a bas class).
Default selection (everything) during writing - can be used as base class
to implement selective output. This selects which entities will be written out.
"""
def __repr__(self):
return "<Select all>"
def accept_model(self, model):
"""Overload this to reject models for output."""
return 1
def accept_chain(self, chain):
"""Overload this to reject chains for output."""
return 1
def accept_residue(self, residue):
"""Overload this to reject residues for output."""
return 1
def accept_atom(self, atom):
"""Overload this to reject atoms for output."""
return 1
class PDBIO(object):
"""Write a Structure object (or a subset of a Structure object) as a PDB file.
Example:
>>> p=PDBParser()
>>> s=p.get_structure("1fat", "1fat.pdb")
>>> io=PDBIO()
>>> io.set_structure(s)
>>> io.save("out.pdb")
"""
def __init__(self, use_model_flag=0):
"""Creat the PDBIO object.
@param use_model_flag: if 1, force use of the MODEL record in output.
@type use_model_flag: int
"""
self.use_model_flag = use_model_flag
# private mathods
def _get_atom_line(self, atom, hetfield, segid, atom_number, resname,
resseq, icode, chain_id, charge=" "):
"""Returns an ATOM PDB string (PRIVATE)."""
if hetfield != " ":
record_type = "HETATM"
else:
record_type = "ATOM "
if atom.element:
element = atom.element.strip().upper()
if element.capitalize() not in atom_weights:
raise ValueError("Unrecognised element %r" % atom.element)
element = element.rjust(2)
else:
element = " "
name = atom.get_fullname()
altloc = atom.get_altloc()
x, y, z = atom.get_coord()
bfactor = atom.get_bfactor()
occupancy = atom.get_occupancy()
try:
occupancy_str = "%6.2f" % occupancy
except TypeError:
if occupancy is None:
occupancy_str = " " * 6
import warnings
from Bio import BiopythonWarning
warnings.warn("Missing occupancy in atom %s written as blank" %
repr(atom.get_full_id()), BiopythonWarning)
else:
raise TypeError("Invalid occupancy %r in atom %r"
% (occupancy, atom.get_full_id()))
args = (record_type, atom_number, name, altloc, resname, chain_id,
resseq, icode, x, y, z, occupancy_str, bfactor, segid,
element, charge)
return _ATOM_FORMAT_STRING % args
# Public methods
def set_structure(self, pdb_object):
# Check what the user is providing and build a structure appropriately
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def save(self, file, select=Select(), write_end=True):
"""
@param file: output file
@type file: string or filehandle
@param select: selects which entities will be written.
@type select: object
Typically select is a subclass of L{Select}, it should
have the following methods:
- accept_model(model)
- accept_chain(chain)
- accept_residue(residue)
- accept_atom(atom)
These methods should return 1 if the entity is to be
written out, 0 otherwise.
Typically select is a subclass of L{Select}.
"""
get_atom_line = self._get_atom_line
if isinstance(file, basestring):
fp = open(file, "w")
close_file = 1
else:
# filehandle, I hope :-)
fp = file
close_file = 0
# multiple models?
if len(self.structure) > 1 or self.use_model_flag:
model_flag = 1
else:
model_flag = 0
for model in self.structure.get_list():
if not select.accept_model(model):
continue
# necessary for ENDMDL
# do not write ENDMDL if no residues were written
# for this model
model_residues_written = 0
atom_number = 1
if model_flag:
fp.write("MODEL %s\n" % model.serial_num)
for chain in model.get_list():
if not select.accept_chain(chain):
continue
chain_id = chain.get_id()
# necessary for TER
# do not write TER if no residues were written
# for this chain
chain_residues_written = 0
for residue in chain.get_unpacked_list():
if not select.accept_residue(residue):
continue
hetfield, resseq, icode = residue.get_id()
resname = residue.get_resname()
segid = residue.get_segid()
for atom in residue.get_unpacked_list():
if select.accept_atom(atom):
chain_residues_written = 1
model_residues_written = 1
s = get_atom_line(atom, hetfield, segid, atom_number, resname,
resseq, icode, chain_id)
fp.write(s)
atom_number = atom_number + 1
if chain_residues_written:
fp.write("TER\n")
if model_flag and model_residues_written:
fp.write("ENDMDL\n")
if write_end:
fp.write('END\n')
if close_file:
fp.close()
if __name__ == "__main__":
from Bio.PDB.PDBParser import PDBParser
import sys
p = PDBParser(PERMISSIVE=True)
s = p.get_structure("test", sys.argv[1])
io = PDBIO()
io.set_structure(s)
io.save("out1.pdb")
with open("out2.pdb", "w") as fp:
s1 = p.get_structure("test1", sys.argv[1])
s2 = p.get_structure("test2", sys.argv[2])
io = PDBIO(1)
io.set_structure(s1)
io.save(fp)
io.set_structure(s2)
io.save(fp, write_end=1)
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