NAME

     obrms — Calculate the heavy-atom RMSD between two chemically identical structures

SYNOPSIS

     obrms [-fmxso] filename1 filename2

DESCRIPTION

     Computes the heavy-atom RMSD of identical compound structures.  Structures in multi-
     structure files are compared one-by-one unless -firstonly is passed, in which case only the
     first structure in the reference file is used.

OPTIONS

     -f, --firstonly
           use only the first structure in the reference file (otherwise the nth molecule in the
           reference file is compared to the nth molecule in the test file)

     -m, --minimize
           Compute the minimum RMSD achievable by applying a rigid-body transformation to the
           test molecule

     -x, --cross
           Compute all n^2 RMSDs between molecules of the reference file.  Test file is ignored.

     -s, --separate
           Separate reference file into constituent molecules (disconnected fragments) and report
           best RMSD

     -o, --out
           Re-oriented test structure output (used with -m)

EXAMPLES

           obrms ref.sdf test.sdf

     Calculate the RMSD between ref.sdf and test.sdf.  Both files should have the same number of
     molecules.

           obrms -f ref.sdf test.sdf

     Calculate the RMSD between the first molecule in ref.sdf and each molecule in test.sdf.

SEE ALSO

     obfit(1).

     The web pages for Open Babel can be found at: <http://openbabel.org/>

AUTHORS

     Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison,
     Chris Morley, Michael Banck, and innumerable others who have contributed fixes and
     additions.  For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

COPYRIGHT

     Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
     Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other contributors.

     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 version 2 of the
     License.

     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.