.Dd May 26, 2026
.Dt OBRMS 1 URM
.Os "Open Babel" 3.2
.Sh NAME
.Nm obrms
.Nd "Calculate the heavy-atom RMSD between two chemically identical structures"
.Sh SYNOPSIS
.Nm
.Op -fmxso
.Ar filename1
.Ar filename2
.Sh DESCRIPTION
Computes the heavy\-atom RMSD of identical compound structures.
Structures in multi\-structure files are compared one\-by\-one unless
.Fl -firstonly
is passed, in which case only the first structure in the reference file is used.
.Sh OPTIONS
.Bl -tag -width flag
.It Fl 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)
.It Fl m ,  -minimize
Compute the minimum RMSD achievable by applying a rigid\-body transformation to
the test molecule
.It Fl x , -cross
Compute all n\(ha2 RMSDs between molecules of the reference file.
Test file is ignored.
.It Fl s , -separate
Separate reference file into constituent molecules (disconnected fragments)
and report best RMSD
.It Fl t Ar t , Fl -timeout Ar t
Give up on matching after specified number of seconds
.It Fl o Ar file , Fl -out Ar file
Re\-oriented test structure output (used with
.Fl m )
.El
.Sh EXAMPLES
.Dl "obrms ref.sdf test.sdf"
.Pp
Calculate the RMSD between ref.sdf and test.sdf.
Both files should have the same number of molecules.
.Dl "obrms -f ref.sdf test.sdf"
.Pp
Calculate the RMSD between the first molecule in ref.sdf and each molecule in
test.sdf.
.Sh SEE ALSO
.Xr obfit 1 .
.Pp
The web pages for Open Babel can be found at:
\%<\fBhttps://openbabel.org/\fR>
.Sh AUTHORS
.An -nosplit
Open Babel is developed by a cast of many, including current maintainers
.An Geoff Hutchison ,
.An Chris Morley ,
.An Michael Banck ,
and innumerable others who have contributed fixes and additions.
For more contributors to Open Babel, see
\%<\fBhttps://openbabel.org/docs/Introduction/thanks.html\fR>
.Sh COPYRIGHT
Copyright (C) 1998\-2001 by OpenEye Scientific Software, Inc.
.br
Some portions Copyright (C) 2001\-2007 by Geoffrey R. Hutchison and
other contributors.
.Pp
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.
.Pp
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.