NAME

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

SYNOPSIS

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 n-th molecule in the reference file is compared to the n-th 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

-t t, --timeout t

Give up on matching after specified number of seconds

-o file, --out file

Re-oriented test structure output (used with -m)

EXAMPLES

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

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: <https://openbabel.org/>

AUTHORS

Open Babel is developed by a cast of many, including current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <https://openbabel.org/docs/Introduction/thanks.html>

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.