obrms - Man Page
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
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
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.