1obrms(1)                    User's Reference Manual                   obrms(1)
2

NAME

4     obrms — Calculate the heavy-atom RMSD between two chemically identical
5     structures
6

SYNOPSIS

8     obrms [-fmxso] filename1 filename2
9

DESCRIPTION

11     Computes the heavy-atom RMSD of identical compound structures.  Struc‐
12     tures in multi-structure files are compared one-by-one unless -firstonly
13     is passed, in which case only the first structure in the reference file
14     is used.
15

OPTIONS

17     -f, --firstonly
18           use only the first structure in the reference file (otherwise the
19           nth molecule in the reference file is compared to the nth molecule
20           in the test file)
21
22     -m, --minimize
23           Compute the minimum RMSD achievable by applying a rigid-body trans‐
24           formation to the test molecule
25
26     -x, --cross
27           Compute all n^2 RMSDs between molecules of the reference file.
28           Test file is ignored.
29
30     -s, --separate
31           Separate reference file into constituent molecules (disconnected
32           fragments) and report best RMSD
33
34     -o, --out
35           Re-oriented test structure output (used with -m)
36

EXAMPLES

38           obrms ref.sdf test.sdf
39
40     Calculate the RMSD between ref.sdf and test.sdf.  Both files should have
41     the same number of molecules.
42
43           obrms -f ref.sdf test.sdf
44
45     Calculate the RMSD between the first molecule in ref.sdf and each mole‐
46     cule in test.sdf.
47

SEE ALSO

49     obfit(1).
50
51     The web pages for Open Babel can be found at: <http://openbabel.org/>
52

AUTHORS

54     Open Babel is developed by a cast of many, including currrent maintainers
55     Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
56     have contributed fixes and additions.  For more contributors to Open Ba‐
57     bel, see <http://openbabel.org/wiki/THANKS>
58

60     Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
61     Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other
62     contributors.
63
64     This program is free software; you can redistribute it and/or modify it
65     under the terms of the GNU General Public License as published by the
66     Free Software Foundation version 2 of the License.
67
68     This program is distributed in the hope that it will be useful, but WITH‐
69     OUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
70     FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
71     more details.
72
73Open Babel 3.1                   Oct 10, 2019                   Open Babel 3.1
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