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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

--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)
--minimize
Compute the minimum RMSD achievable by applying a rigid-body transformation to the test molecule
--cross
Compute all n^2 RMSDs between molecules of the reference file. Test file is ignored.
--separate
Separate reference file into constituent molecules (disconnected fragments) and report best RMSD
--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.

October 10, 2019 Open Babel 3.1