/usr/share/pyshared/Bio/PDB/Dice.py is in python-biopython 1.58-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | # 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.
import re
import warnings
from Bio.PDB.PDBIO import PDBIO
_hydrogen=re.compile("[123 ]*H.*")
class ChainSelector(object):
"""
Only accepts residues with right chainid
and between start and end. Remove hydrogens, waters and ligands.
Only use model 0 by default.
"""
def __init__(self, chain_id, start, end, model_id=0):
self.chain_id=chain_id
self.start=start
self.end=end
self.model_id=0
def accept_model(self, model):
# model - only keep model 0
if model.get_id()==self.model_id:
return 1
return 0
def accept_chain(self, chain):
if chain.get_id()==self.chain_id:
return 1
return 0
def accept_residue(self, residue):
# residue - between start and end
hetatm_flag, resseq, icode=residue.get_id()
if hetatm_flag!=" ":
# skip HETATMS
return 0
if icode!=" ":
warnings.warn("WARNING: Icode at %s" % residue.get_id(),
RuntimeWarning)
if self.start<=resseq<=self.end:
return 1
return 0
def accept_atom(self, atom):
# atoms - get rid of hydrogens
name=atom.get_id()
if _hydrogen.match(name):
return 0
else:
return 1
def extract(structure, chain_id, start, end, filename):
"""
Write out selected portion to filename.
"""
sel=ChainSelector(chain_id, start, end)
io=PDBIO()
io.set_structure(structure)
io.save(filename, sel)
if __name__=="__main__":
from Bio.PDB.PDBParser import PDBParser
import sys
p=PDBParser()
s=p.get_structure("scr", sys.argv[1])
extract(s, " ", 1, 100, "out.pdb")
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