obrotate(1) [debian man page]
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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babel(1) User's Reference Manual babel(1) NAME
babel, obabel -- a converter for chemistry and molecular modeling data files SYNOPSIS
babel, [-H help-options] babel, [OPTIONS] [-i input-type] infile [-o output-type] outfile obabel [-H help-options] obabel [OPTIONS] [-i input-type | -: "SMILES-string"] infile [-o output-type] -O outfile DESCRIPTION
babel, is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas. obabel and babel, are slightly different. The first is closer to the normal Unix convention for commandline programs and more flexible when the user needs to specify parameter values on options. With babel this only works when the option is the last on the line; with obabel no such restriction applies. It further has a shortcut for entering SMILES strings, which can be used in place of an input file. Open Babel is also a complete programmers toolkit for developing chemistry software. For more information, se the Open Babel web pages <http://openbabel.org/>. OPTIONS
If only input and ouput files are given, Open Babel will guess the file type from the filename extension. -: "SMILES-string" Enter SMILES string and use it in place of an input file. The SMILES string should be enclosed in quotation marks. More than one can be used, and a molecule title can be included if enclosed in quotes. -a options Format-specific input options. See -H format-ID for options allowed by a particular format --addtotitle Append text to the current molecule title --addformula Append the molecular formula after the current molecule title -b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O -c Center atomic coordinates at (0,0,0) -C Combine molecules in first file with others having the same name -e Continue after errors -d Delete Hydrogens ---errorlevel 2 Filter the level of errors and warnings displayed: 1 = critical errors only 2 = include warnings too (default) 3 = include informational messages too 4 = include "audit log" messages of changes to data 5 = include debugging messages too -f # For multiple entry input, start import with molecule # as the first entry -F Output the available fingerprint types -h Add hydrogens -H Output usage information -H format-ID Output formatting information and options for format specified -Hall Output formatting information and options for all formats -i<format-ID> Specifies input format, see below for the available formats -j --join Join all input molecules into a single output molecule entry -k Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian) -m Produce multiple output files, to allow: - Splitting one input file - put each molecule into consecutively numbered output files - Batch conversion - convert each of multiple input files into a specified output format -l # For multiple entry input, stop import with molecule # as the last entry -o format-ID Specifies output format, see below for the available formats -O outfile Specify the output file. This option applies to obabel only. -p Add Hydrogens appropriate for pH (use transforms in phmodel.txt) --property Add or replace a property (e.g., in an MDL SD file) -s SMARTS Convert only molecules matching the SMARTS pattern specified --separate Separate disconnected fragments into individual molecular records -t All input files describe a single molecule --title title Add or replace molecular title -x options Format-specific output options. See -H format-ID for options allowed by a particular format -v SMARTS Convert only molecules NOT matching SMARTS pattern specified -V Output version number and exit -z Compress the output with gzip FILE FORMATS
The following formats are currently supported by Open Babel: acr -- Carine ASCI Crystal alc -- Alchemy format arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] bgf -- MSI BGF format box -- Dock 3.5 Box format bs -- Ball and Stick format c3d1 -- Chem3D Cartesian 1 format c3d2 -- Chem3D Cartesian 2 format caccrt -- Cacao Cartesian format cache -- CAChe MolStruct format [Write-only] cacint -- Cacao Internal format [Write-only] can -- Canonical SMILES format car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only] ccc -- CCC format [Read-only] cdx -- ChemDraw binary format [Read-only] cdxml -- ChemDraw CDXML format cht -- Chemtool format [Write-only] cif -- Crystallographic Information File cml -- Chemical Markup Language cmlr -- CML Reaction format com -- Gaussian 98/03 Cartesian Input [Write-only] copy -- Copies raw text [Write-only] crk2d -- Chemical Resource Kit 2D diagram format crk3d -- Chemical Resource Kit 3D format csr -- Accelrys/MSI Quanta CSR format [Write-only] cssr -- CSD CSSR format [Write-only] ct -- ChemDraw Connection Table format dmol -- DMol3 coordinates format ent -- Protein Data Bank format fa -- FASTA format [Write-only] fasta -- FASTA format [Write-only] fch -- Gaussian formatted checkpoint file format [Read-only] fchk -- Gaussian formatted checkpoint file format [Read-only] fck -- Gaussian formatted checkpoint file format [Read-only] feat -- Feature format fh -- Fenske-Hall Z-Matrix format [Write-only] fix -- SMILES FIX format [Write-only] fpt -- Fingerprint format [Write-only] fract -- Free Form Fractional format fs -- Open Babel FastSearching database fsa -- FASTA format [Write-only] g03 -- Gaussian 98/03 Output [Read-only] g98 -- Gaussian 98/03 Output [Read-only] gam -- GAMESS Output [Read-only] gamin -- GAMESS Input [Write-only] gamout -- GAMESS Output [Read-only] gau -- Gaussian 98/03 Cartesian Input [Write-only] gjc -- Gaussian 98/03 Cartesian Input [Write-only] gjf -- Gaussian 98/03 Cartesian Input [Write-only] gpr -- Ghemical format gr96 -- GROMOS96 format [Write-only] hin -- HyperChem HIN format inchi -- IUPAC InChI [Write-only] inp -- GAMESS Input [Write-only] ins -- ShelX format [Read-only] jin -- Jaguar input format [Write-only] jout -- Jaguar output format [Read-only] mdl -- MDL MOL format mmd -- MacroModel format mmod -- MacroModel format mol -- MDL MOL format mol2 -- Sybyl Mol2 format molreport -- Open Babel molecule report [Write-only] moo -- MOPAC Output format [Read-only] mop -- MOPAC Cartesian format mopcrt -- MOPAC Cartesian format mopin -- MOPAC Internal mopout -- MOPAC Output format [Read-only] mpc -- MOPAC Cartesian format mpd -- Sybyl descriptor format [Write-only] mpqc -- MPQC output format [Read-only] mpqcin -- MPQC simplified input format [Write-only] nw -- NWChem input format [Write-only] nwo -- NWChem output format [Read-only] pc -- PubChem format [Read-only] pcm -- PCModel format pdb -- Protein Data Bank format pov -- POV-Ray input format [Write-only] pqs -- Parallel Quantum Solutions format prep -- Amber Prep format [Read-only] qcin -- Q-Chem input format [Write-only] qcout -- Q-Chem output format [Read-only] report -- Open Babel report format [Write-only] res -- ShelX format [Read-only] rxn -- MDL RXN format sd -- MDL MOL format sdf -- MDL MOL format smi -- SMILES format sy2 -- Sybyl Mol2 format tdd -- Thermo format test -- Test format [Write-only] therm -- Thermo format tmol -- TurboMole Coordinate format txyz -- Tinker MM2 format [Write-only] unixyz -- UniChem XYZ format vmol -- ViewMol format xed -- XED format [Write-only] xml -- General XML format [Read-only] xyz -- XYZ cartesian coordinates format yob -- YASARA.org YOB format zin -- ZINDO input format [Write-only] FORMAT OPTIONS
Individual file formats may have additional formatting options. Input format options are preceded by 'a', e.g. -as Output format options are preceded by 'x', e.g. -xn For further specific information and options, use -H<format-type> e.g., -Hcml EXAMPLES
Standard conversion: babel -ixyz ethanol.xyz -opdb ethanol.pdb Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT: babel -ismi -omol2 Split a multi-molecule file into new1.smi, new2.smi, etc.: babel infile.mol new.smi -m SEE ALSO
obenergy(1), obfit(1), obgrep(1), obminimize(1), obprop(1), obrotate(1), obrotamer(1). The web pages for Open Babel can be found at: <http://openbabel.org/> AUTHORS
A cast of many, including the currrent maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others 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 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