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OBRMS(1) User's Reference Manual 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 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 trans- formation 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 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 un- der 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 FIT- NESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 3.2 May 26, 2026 OBRMS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT
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