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                                    Oct 10, 2019                                          obrms(1)