pdb2filter_residues.py

################################################################################
#
#   MRC FGU Computational Genomics Group
#
#   $Id$
#
#   Copyright (C) 2009 Andreas Heger
#
#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
#################################################################################
'''
pdb2filter_residues.py - 
======================================================

:Author: Andreas Heger
:Release: $Id$
:Date: |today|
:Tags: Python

Purpose
-------

.. todo::
   
   describe purpose of the script.

Usage
-----

Example::

   python pdb2filter_residues.py --help

Type::

   python pdb2filter_residues.py --help

for command line help.

Documentation
-------------

Code
----

'''
USAGE = """filter out a list of residues from a
pdb file.
"""


import sys, re, os, string, getopt

import alignlib

param_master = 0
param_format = None
param_multiple_alignment = None

GAPCHARS=(".", "-")

if __name__ == '__main__':
     
    try:
        optlist, args = getopt.getopt(sys.argv[1:],
                                      "V:m:f:",
                                      ["Verbose=", "master=", 
                                       "format="])
    except getopt.error, msg:
        print USAGE, msg
        sys.exit(2)


    for o,a in optlist:
        if o in ("-f", "--format"):
            param_format = a
        elif o in ("-i", "--iterations"):
            param_max_iterations = string.atoi(a)
        

    if len(args) != 1:
        print "please specify file with residue number."
        print USAGE
        sys.exit(1)

    residues = map(lambda x: string.split(x[:-1], "\t")[0], filter(lambda x: not re.match("#",x), open(args[0], "r").readlines()))
    
    residues_map = {}
    for r in residues:
        residues_map[r] = 1

    for line in sys.stdin:
        
        if line[:6] not in ("ATOM  ", "HETATM"): continue

        chain   = line[21]
        number  = string.strip(line[22:26])
        aa      = line[17:20]
        atom    = string.strip(line[13:17])

        if not residues_map.has_key( number ):
            continue

        print line[:-1]