obenergy(1) [debian 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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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