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

NAME
obrotate -- batch-rotate dihedral angles matching SMARTS patterns SYNOPSIS
obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle DESCRIPTION
The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it does the same as a user setting an angle in a molecular modelling package, but much faster and in batch mode (i.e. across multiple molecules in a file). The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0 (zero). The angle supplied is in degrees. The two atoms used to set the dihedral angle <atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3> in any way. The order of the atoms matters -- the portion of the molecule attached to <atom1> and <atom2> remain fixed, but the portion bonded to <atom3> and & <atom4> moves. EXAMPLES
Let's say that you want to define the conformation of a large number of molecules with a pyridyl scaffold and substituted with an aliphatic chain at the 3-position, for example for docking or 3D-QSAR purposes. To set the value of the first dihedral angle to 90 degrees: obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90 Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C and atoms 5 and 8 define the particular dihedral angle to rotate. Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used: obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90 Keep the pyridyl ring fixed and moves the aliphatic chain: obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90 Keep the aliphatic chain fixed and move the pyridyl ring: obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90 SEE ALSO
babel(1), obchiral(1), obfit(1), obgrep(1), obprop(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 obgrep 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) 2001-2005 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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obspectrophore(1)					      User's Reference Manual						 obspectrophore(1)

NAME
obspectrophore -- SPECTROPHORE calculator SYNOPSIS
obspectrophore [options] -i input_file obspectrophore [-u | -h] DESCRIPTION
obspectrophore can be used to generate Spectrophores, which are one-dimensional descriptors generated from the property fields surrounding the molecules. This technology allows the accurate description of molecules in terms of their surface properties or fields. Comparison of molecules property fields provides a robust structure-independent method of aligning actives from different chemical classes. When applied to molecules such as ligands and drugs, Spectrophores can be used as powerful molecular descriptors in the fields of chemoinformatics, virtual screening, and QSAR modeling. OPTIONS
-i file Specifies the molecular input file from which Spectrophores are to be calculated. The filetype is automatically detected from the file extension. -n value Specifies the kind of normalization that should be performed. Valid values are (without quotes): No (default), ZeroMean, UnitStd and ZeroMeanAndUnitStd. -a value Specifies the required accuracy expressed as the angular stepsize. Only the following discrete values are allowed: 1 | 2 | 5 | 10 | 15 | 20 (default) | 30 | 36 | 45 | 60 -s value Specifies the kind of cages that should be used in terms of the underlying pointgroup: P1 or P-1. Valid values are (without quotes): No (default), Unique, Mirror and All. -r value Specifies the required resolution expressed as a real positive number. The default value is 3.0 Angstrom. Negative values or a value equal to 0 generate an error message. -u Display implementation details. -h Display help message. SEE ALSO
babel(1). The web pages for Open Babel can be found at: <http://openbabel.org/> AUTHORS
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) 2005-2010 by Silicos NV 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. The algorithm in this software has been covered by patent WO2009146735. However, Silicos NV and the inventors of the above mentioned patent assure that no patent infringment claims will be issued against individuals or institutions that use this software under the GNU General Pub- lic 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 2.3 June 2, 2012 Open Babel 2.3
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