The Free Software Foundation version 2 of the License. Modify it under the terms of the GNU General Public License as published by This program is free software you can redistribute it and/or Some portions Copyright (C) 2001-2007 by Geoffrey R. For more contributors to OpenĬopyright (C) 1998-2001 by OpenEye Scientific Software, Inc. Who have contributed fixes and additions. Morley, Michael Banck, and innumerable others The web pages for Open Babel can be foundĪ cast of many, including the currrent maintainers xnįor further specific information and options, use Output format options are preceded by 'x', e.g. Input format options are preceded by 'a', e.g. Individual file formats may have additional formatting xyz - XYZ cartesian coordinates format.pqs - Parallel Quantum Solutions format.mpqcin - MPQC simplified input format.molreport - Open Babel molecule report.fs - Open Babel FastSearching database.fck - Gaussian formatted checkpoint file format.fchk - Gaussian formatted checkpoint file format.fch - Gaussian formatted checkpoint file format.crk3d - Chemical Resource Kit 3D format.crk2d - Chemical Resource Kit 2D diagram format.cif - Crystallographic Information File.car - Accelrys/MSI Biosym/Insight II CAR format.arc - Accelrys/MSI Biosym/Insight II CAR format.The following formats are currently supported by Open Babel: See -H format-ID for options allowed by a particularįormat -v SMARTS Convert only molecules NOT matching SMARTS pattern specified -V Output version number and exit -z Compress the output with gzip FILE FORMATS ¶ 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. l # For multiple entry input, stop import with molecule # as the lastĮntry -o format-ID Specifies output format, see below for the available formats -O outfile Specify the output file. Batch conversion - convert each of multiple input files into a.Splitting one input file - put each molecule into consecutively.Gaussian) -m Produce multiple output files, to allow: See -H format-ID for options allowed by a particularįormat -addtotitle Append text to the current molecule title -addformula Append the molecular formula after the current molecule title -b Convert dative bonds: e.g., ()=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:Ĥ = include "audit log" messages of changes to dataĥ = include debugging messages too -f # For multiple entry input, start import with molecule # as the firstĮntry -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 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 a options Format-specific input options. More than one can be used,Īnd a molecule title can be included if enclosed in quotes. String should be enclosed in quotation marks. " SMILES-string" Enter SMILES string and use it in place of an input file. The file type from the filename extension. If only input and output files are given, Open Babel will guess For more information, se the Open Babel web pages Open Babel is also a complete programmers toolkit for developingĬhemistry software. Modeling and computational chemistry and related areas. Converter for chemistry and molecular modeling data files SYNOPSIS ¶ obabelĭesigned to interconvert between many file formats used in molecular
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