pdb_linewidth.py

#!/usr/bin/env python

"""
Sets the width of all 'ATOM/HETATM' lines in the PDB to 80 characters (pads/trims whitespace).

usage: python pdb_linewidth.py <pdb file>
example: python pdb_linewidth.py 1CTF.pdb

Author: {0} ({1})

This program is part of the PDB tools distributed with HADDOCK
or with the HADDOCK tutorial. The utilities in this package
can be used to quickly manipulate PDB files, with the benefit
of 'piping' several different commands. This is a rewrite of old
FORTRAN77 code that was taking too much effort to compile. RIP.
"""

import os
import re
import sys

__author__ = "Joao Rodrigues"
__email__ = "j.p.g.l.m.rodrigues@gmail.com"

USAGE = __doc__.format(__author__, __email__)

def check_input(args):
    """Checks whether to read from stdin/file and validates user input/options."""

    if not len(args):
        # Read from pipe
        if not sys.stdin.isatty():
            pdbfh = sys.stdin
        else:
            sys.stderr.write(USAGE)
            sys.exit(1)
    elif len(args) == 1:
        # Read from file
        if not os.path.isfile(args[0]):
            sys.stderr.write('File not found: ' + args[0] + '\n')
            sys.stderr.write(USAGE)
            sys.exit(1)
        pdbfh = open(args[0], 'r')
    else:
        sys.stderr.write(USAGE)
        sys.exit(1)

    return pdbfh

def _fix_lines(fhandle):
    """Enclosing logic in a function to speed up a bit"""

    coord_re = re.compile('^(ATOM|HETATM)')
    fhandle = fhandle

    for line in fhandle:
        line = line.strip()
        if coord_re.match(line):
            size_of_line = len(line)
            # Pad short lines
            if size_of_line < 80:
                padding = 80 - size_of_line
                line = line + ' '*padding

            yield line[:80] + '\n'

if __name__ == '__main__':
    # Check Input
    pdbfh = check_input(sys.argv[1:])

    # Do the job
    new_pdb = _fix_lines(pdbfh)

    try:
        sys.stdout.write(''.join(new_pdb))
        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
    # We can close it even if it is sys.stdin
    pdbfh.close()
    sys.exit(0)