obrms.1

.Dd Oct 10, 2019
.Os "Open Babel" 3.1
.Dt obrms 1 URM
.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 -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 nth molecule
in the reference file is compared to the nth 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^2 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 o, -out 
Re-oriented test structure output (used with -m) 
.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:
\%<\fBhttp://openbabel.org/\fR>
.Sh AUTHORS
.An -nosplit
Open Babel is developed by a cast of many, including currrent 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
\%<\fBhttp://openbabel.org/wiki/THANKS\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.