obrms(1)                 General Commands Manual (urm)                obrms(1)

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.

Open Babel 3.1                 October 10, 2019                 Open Babel 3.1