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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.
"""
Modifies the occupancy column of a PDB file (default 1.0).
Usage:
python pdb_occ.py -<occupancy> <pdb file>
Example:
python pdb_occ.py -1.0 1CTF.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 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
option = 1.0
fh = sys.stdin # file handle
if not len(args):
# Reading from pipe with default option
if sys.stdin.isatty():
sys.stderr.write(__doc__)
sys.exit(1)
elif len(args) == 1:
# One of two options: option & Pipe OR file & default option
if args[0].startswith('-'):
option = args[0][1:]
if sys.stdin.isatty(): # ensure the PDB data is streamed in
emsg = 'ERROR!! No data to process!\n'
sys.stderr.write(emsg)
sys.stderr.write(__doc__)
sys.exit(1)
else:
if not os.path.isfile(args[0]):
emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
sys.stderr.write(emsg.format(args[0]))
sys.stderr.write(__doc__)
sys.exit(1)
fh = open(args[0], 'r')
elif len(args) == 2:
# Two options: option & File
if not args[0].startswith('-'):
emsg = 'ERROR! First argument is not an option: \'{}\'\n'
sys.stderr.write(emsg.format(args[0]))
sys.stderr.write(__doc__)
sys.exit(1)
if not os.path.isfile(args[1]):
emsg = 'ERROR!! File not found or not readable: \'{}\'\n'
sys.stderr.write(emsg.format(args[1]))
sys.stderr.write(__doc__)
sys.exit(1)
option = args[0][1:]
fh = open(args[1], 'r')
else: # Whatever ...
sys.stderr.write(__doc__)
sys.exit(1)
# Validate option
try:
option = float(option)
except ValueError:
emsg = 'ERROR!! You provided an invalid occupancy value: \'{}\'\n'
sys.stderr.write(emsg.format(option))
sys.exit(1)
return (fh, option)
def run(fhandle, occupancy):
"""
Set the occupancy column in all ATOM/HETATM records to a given value.
Non-ATOM/HETATM lines are give as are. This function is a generator.
Parameters
----------
fhandle : a line-by-line iterator of the original PDB file.
occupancy : float
The desired occupancy value
Yields
------
str (line-by-line)
The modified (or not) PDB line.
"""
records = ('ATOM', 'HETATM')
occupancy = "{0:>6.2f}".format(occupancy)
for line in fhandle:
if line.startswith(records):
yield line[:54] + occupancy + line[60:]
else:
yield line
alter_occupancy = run
def main():
# Check Input
pdbfh, occupancy = check_input(sys.argv[1:])
# Do the job
new_pdb = run(pdbfh, occupancy)
# Output results
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
# last line of the script
# Close file handle even if it is sys.stdin, no problem here.
pdbfh.close()
sys.exit(0)
if __name__ == '__main__':
main()
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