debian man page for obgrep

obgrep(1)						      User's Reference Manual							 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 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) 2001-2007 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 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