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obgen(1) [debian man page]

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

NAME

     obgen -- generate 3D coordinates for a molecule

SYNOPSIS

     obgen [OPTIONS] filename

DESCRIPTION

     The obgen tool will generate 3D coordinates for molecules in a file (e.g. multi-molecule SMILES files). The resulting structure will be opti-
     mized using the given forcefield and checked for the lowest-energy conformer using a Monte Carlo search.  Output will be sent to standard
     output in the SDF file format.

OPTIONS

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

     -ff forcefield
	   Select the forcefield

EXAMPLES

     View the possible options, including available forcefields:
	   obgen

     Generate 3D coordinates for the molecule(s) in file test.smi:
	   obgen test.smi

     Generate 3D coordinates for the molecule(s) in file test.smi using the UFF forcefield:
	   obgen -ff UFF test.smi

SEE ALSO

     babel(1), obminimize(1), obconformer(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 obgen 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) 2007-2008 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

Check Out this Related Man Page

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

NAME

     obprop -- print standard molecular properties

SYNOPSIS

     obprop filename

DESCRIPTION

     The obprop program is a tool to print a set of standard molecular properties for all molecules in a file. It also serves as example code for
     using the Open Babel library (libopenbabel).

     Output format includes:
     name [Name]
     formula [Formula]
     mol_weight [Molecular Weight]
     exact_mass [Isotopic Mass]
     canonical_SMILES [String]
     num_atoms [Number]
     num_bonds [Number]
     num_residues [Number]
     sequence [Residue Sequence]
     num_rings [Number of Rings (by SSSR)]
     logP [Number (octanol-water partition)]
     PSA [Number (topological polar surface area)]
     MR [Number (molar refractivity)]
     $$$

     The "$$$" is the separator between multiple molecular entries in a file

EXAMPLES

	   obprop pyridines.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/>

AUTHORS

     The obprop 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) 2003 by Fabien Fontaine
     Some portions Copyright (C) 2004-2007 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
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