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obfit(1) [debian man page]

obfit(1)						      User's Reference Manual							  obfit(1)

NAME

     obfit -- superimpose two molecules based on a pattern

SYNOPSIS

     obfit SMARTS-pattern fixed-file outfile

DESCRIPTION

     Superimpose two molecules using a quaternion fit. The atoms used to fit the two molecules are defined by the 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.

     Any molecules matching the supplied SMARTS pattern will be rotated and translated to provide the smallest possible RMSD between the matching
     regions. If a molecule does not match the SMARTS pattern, it will be output with no transformation.

EXAMPLES

     Align all the molecules in 'testmv.sdf' on a single molecule of 'testref.sdf' by superimposing them on its N-methylpiperidyl portion (and
     outputting a new SD file to the standard output):

	   obfit '[nh]1c2c(=O)n(C)c(=O)n(C)c2cc1' testref.sdf testmv.sdf

SEE ALSO

     babel(1), obchiral(1), obfit(1), obgrep(1), obrotate(1).

     The web pages for Open Babel can be found at: <http://openbabel.org/>

     A guide for constructing SMARTS patterns can be found at: <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>

AUTHORS

     The obfit program was contributed by Fabien Fontaine

     Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable oth-
     ers who have contributed fixes and additions.  For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

COPYRIGHT

     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 MERCHANTABIL-
     ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Open Babel 2.2							   July 4, 2008 						    Open Babel 2.2

Check Out this Related Man Page

obenergy(1)						      User's Reference Manual						       obenergy(1)

NAME

     obenergy -- calculate the energy for a molecule

SYNOPSIS

     obenergy [OPTIONS] filename

DESCRIPTION

     The obenergy tool can be used to calculate the energy for molecules inside (multi-)molecule files (e.g., MOL2, etc.)

OPTIONS

     If no filename is given, obenergy will give all options including the available forcefields.

     -v    Verbose: print out all individual energy interactions

     -ff forcefield
	   Select the forcefield

EXAMPLES

     View the possible options, including available forcefields:
	   obenergy

     Calculate the energy for the molecule(s) in file test.mol2:
	   obenergy test.mol2

     Calculate the energy for the molecule(s) in file test.mol2 using the Ghemical forcefield:
	   obenergy -ff Ghemical test.mol2

     Calculate the energy for the molecule(s) in file test.mol2 and print out all individual energy interactions:
	   obenergy -v test.mol2

SEE ALSO

     babel(1), obminimize(1), obrotamer(1).

     The web pages for Open Babel can be found at: <http://openbabel.org/>

     The web pages for Open Babel Molecular Mechanics can be found at: <http://openbabel.org/wiki/Molecular_mechanics>

AUTHORS

     The obenergy program was contributed by Tim Vandermeersch.

     Open Babel is developed by a cast of many, including currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable oth-
     ers who have contributed fixes and additions.  For more contributors to Open Babel, see <http://openbabel.org/wiki/THANKS>

COPYRIGHT

     Copyright (C) 2007 by Tim Vandermeersch.

      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 MERCHANTABIL-
     ITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

Open Babel 2.2							   July 4, 2008 						    Open Babel 2.2
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