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UNIX for Dummies Questions & Answers
Need to cut a string from a file recursively.
Post 302343801 by happyrain on Thursday 13th of August 2009 04:12:16 PM
08-13-2009
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LEARN ABOUT DEBIAN
obprobe
obprobe(1) User's Reference Manual obprobe(1) NAME
obprobe -- create electrostatic probe grid SYNOPSIS
obprobe [OPTIONS] type pchg filename DESCRIPTION
The obprobe tool creates a grid around a molecule, placing a probe atom with a specified atom type and partial charge at each point to calcu- late the MMFF94 energy. This can be used for docking experiments to test hydrogen-bond affinity, electrostatic potential, etc. Output is sent to standard output using the Gaussian Cube format. OPTIONS
If no filename is given, obprobe will give all options including the example probes. -s stepsize Set the resolution of the grid (stepsize) -p padding Set the padding -- extra distance on each side of the box formed by the molecule. type MMFF94 atom type pchg MMFF94 partial charge EXAMPLES
Probe the file pyridines.sdf using a carbonyl oxygen -- a hydrogen bond acceptor with partial charge -0.57: obprobe 7 -0.57 pyridines.sdf Probe the file pyridines.sdf using a phenyl carbon atom -- a hydrophobic atom with no partial charge: obprobe 37 0.0 pyridines.sdf SEE ALSO
babel(1). The web pages for Open Babel can be found at: <http://openbabel.org/> AUTHORS
The obprobe 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) 2006-2008 by Tim Vandermeersch Some portions Copyright (C) 2004-2008 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