src/python/sample.py

   1 #!/usr/bin/python
   2 #  -*- mode: python; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
   3 #
   4 #  $Id$
   5 #
   6 #  Copyright (c) Erik Lindahl, David van der Spoel 2003-2007.
   7 #  Coordinate compression (c) by Frans van Hoesel.
   8 #  Python wrapper (c) by Roland Schulz
   9 #
  10 #  IN contrast to the rest of Gromacs, XDRFILE is distributed under the
  11 #  BSD license, so you can use it any way you wish, including closed source:
  12 #
  13 #  Permission is hereby granted, free of charge, to any person obtaining a
  14 #  copy of this software and associated documentation files (the "Software"),
  15 #  to deal in the Software without restriction, including without limitation
  16 #  the rights to use, copy, modify, merge, publish, distribute, sublicense,
  17 #  and/or sell copies of the Software, and to permit persons to whom the
  18 #  Software is furnished to do so, subject to the following conditions:
  19 #
  20 #  The above copyright notice and this permission notice shall be included in
  21 #  all copies or substantial portions of the Software.
  22 #
  23 #  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  24 #  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  25 #  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  26 #  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  27 #  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  28 #  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  29 #  DEALINGS IN THE SOFTWARE.
  30 #
  31 from xdrfile import *
  32 import sys
  33
  34 #you have to compile with --enable-shared
  35 #and have libxdrfile.so in the LD_LIBRARY_PATH
  36
  37 if len(sys.argv)!=2:
  38   print "Missing file argument\nUsage: sample.py FILE"
  39   sys.exit()
  40
  41
  42 x=xdrfile(sys.argv[1])
  43 for f in x:   #iterates frames
  44     print "%8s %8s %8s %8s   Step: %8d "%("Atom","X","Y","Z",f.step) #print header
  45     for i,a in enumerate(f.x):  #iterate atoms
  46       print "%8d %8.1f %8.1f %8.1f"%(i+1,a[0],a[1],a[2]) #print atom number, x, y, z