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obgrep(1)           DragonFly General Commands Manual (urm)          obgrep(1)


NAME

     obgrep - an advanced molecular search program using SMARTS


SYNOPSIS

     obgrep [OPTIONS] 'SMARTS-pattern' filename


DESCRIPTION

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


OPTIONS

     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


EXAMPLES

     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


SEE ALSO

     babel(1), obfit(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 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 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.

Open Babel 2.2                   July 4, 2008                   Open Babel 2.2

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