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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2018 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""
Returns a new PDB file only with atoms in common to all input PDB files.
Atoms are judged equal is their name, altloc, res. name, res. num, insertion
code and chain fields are the same. Coordinates are taken from the first input
file. Keeps matching TER/ANISOU records.
Usage:
python pdb_intersect.py <pdb file> <pdb file>
Example:
python pdb_intersect.py 1XYZ.pdb 1ABC.pdb
This program is part of the `pdb-tools` suite of utilities and should not be
distributed isolatedly. The `pdb-tools` were created to quickly manipulate PDB
files using the terminal, and can be used sequentially, with one tool streaming
data to another. They are based on old FORTRAN77 code that was taking too much
effort to maintain and compile. RIP.
"""
import collections
import os
import sys
__author__ = "Joao Rodrigues"
__email__ = "j.p.g.l.m.rodrigues@gmail.com"
def check_input(args):
"""Checks whether to read from stdin/file and validates user input/options.
"""
# Defaults
fl = [] # file list
if len(args) >= 1:
for fn in args:
if not os.path.isfile(fn):
emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
sys.stderr.write(emsg.format(fn))
sys.stderr.write(__doc__)
sys.exit(1)
fh = open(fn, 'r')
fl.append(fh)
else: # no arguments
sys.stderr.write(__doc__)
sys.exit(1)
return fl
def run(flist):
"""
Returns atoms common to all input files.
This function is a generator.
Parameters
----------
flist : list of file-obj
The first item is the reference PBD files to which others will
be compared to. Items in this list should handle `.close()`
attribute.
Yields
------
str (line-by-line)
The modified (or not) PDB line.
"""
atom_data = collections.OrderedDict() # atom_uid: line
records = ('ATOM', 'HETATM', 'ANISOU', 'TER')
ref = flist[0]
for line in ref:
if line.startswith(records):
atom_uid = line[12:27]
atom_data[atom_uid] = line
ref.close()
common_atoms = set(atom_data.keys())
for fhandle in flist[1:]:
file_atoms = set()
for line in fhandle:
atom_uid = line[12:27]
file_atoms.add(atom_uid)
fhandle.close()
common_atoms = common_atoms & file_atoms
for atom in atom_data:
if atom in common_atoms:
yield atom_data[atom]
intersect_pdb_files = run
def main():
# Check Input
pdbflist = check_input(sys.argv[1:])
# Do the job
new_pdb = run(pdbflist)
try:
_buffer = []
_buffer_size = 5000 # write N lines at a time
for lineno, line in enumerate(new_pdb):
if not (lineno % _buffer_size):
sys.stdout.write(''.join(_buffer))
_buffer = []
_buffer.append(line)
sys.stdout.write(''.join(_buffer))
sys.stdout.flush()
except IOError:
# This is here to catch Broken Pipes
# for example to use 'head' or 'tail' without
# the error message showing up
pass
sys.exit(0)
if __name__ == '__main__':
main()
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