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     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

     -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: <>

     A guide for constructing SMARTS patterns can be found at:


     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 <>


     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

      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.