obrms - Man Page

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.

-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)

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.

obfit(1).

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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 (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.