.Dd May 26, 2026
.Dt OBFIT 1 URM
.Os "Open Babel" 3.2
.Sh NAME
.Nm obfit
.Nd "superimpose two molecules based on a pattern"
.Sh SYNOPSIS
.Nm
.Ar SMARTS-pattern
.Ar fixed-file
.Ar outfile
.Sh DESCRIPTION
Superimpose two molecules using a quaternion fit.
The atoms used to fit the two molecules are defined by the
.Ar SMARTS-pattern
given by the user.
It is useful to align congeneric series of molecules on a common structural
scaffold for 3D\-QSAR studies.
It can also be useful for displaying the results of conformational
generation.
.Pp
Any molecules matching the supplied
.Ar SMARTS-pattern
will be rotated and translated to provide the smallest possible RMSD
between the matching regions.
If a molecule does not match the
.Ar SMARTS-pattern ,
it will be output with no transformation.
.Sh EXAMPLES
Align all the molecules in \(aqtestmv.sdf\(aq on a single molecule of
\(aqtestref.sdf\(aq by superimposing them on its N\-methylpiperidyl portion
(and outputting a new SD file to the standard output):
.Pp
.Dl "obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf"
.Sh SEE ALSO
.Xr obabel 1 ,
.Xr obchiral 1 ,
.Xr obgrep 1 ,
.Xr obrotate 1 .
.Pp
The web pages for Open Babel can be found at:
\%<\fBhttps://openbabel.org/\fR>
.Pp
A guide for constructing SMARTS patterns can be found at:
\%<\fBhttps://www.daylight.com/dayhtml/doc/theory/theory.smarts.html\fR>
.Sh AUTHORS
The obfit program was contributed by
.An Fabien Fontaine
.Pp
.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.