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obgrep: an advanced molecular search program using SMARTS


obgrep - an advanced molecular search program using SMARTS


obgrep [OPTIONS] 'SMARTS-pattern' filename


The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.


If only a filename is given, obgrep will attempt to guess the file type from the filename extension. -c Print the number of matches -f Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern -i format Specifies input and output format, see babel(1) for available formats -n Only print the name of the molecules -t # Print a molecule only if the pattern occurs # times inside the molecule -v Invert the matching, print non-matching molecules
Note that in all examples, the SMARTS pattern is enclosed in single quotes '...' to ensure it is not changed by the shell. Print all the molecules with a methylamine group: obgrep 'CN' database.smi Print all the molecules without a methylamine group: obgrep -v 'CN' database.smi Print the number of molecules without a methylamine group: obgrep -v -c 'CN' database.smi Print methylamine (if it exists in the file): obgrep -f 'CN' database.smi Print methylamine and/or methanol (if they exist): obgrep -f 'C[N,O]' database.smi Print all molecules with aromatic carbon in all SMILES files in the directory (i.e., *.smi) obgrep 'c' *.smi
babel(1), obfit(1), obrotate(1). The web pages for Open Babel can be found at: <//openbabel.org/> A guide for constructing SMARTS patterns can be found at: <//www.daylight.com/dayhtml/doc/theory/theory.smarts.html>


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 others who have contributed fixes and additions. For more contributors to Open Babel, see <//openbabel.org/wiki/THANKS>


Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. Some portions Copyright (C) 2001-2007 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 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. OBGREP(1)

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