obgrep(1) User's Reference Manual obgrep(1)NAMEobgrep — an advanced molecular search program using SMARTS
SYNOPSISobgrep [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 for‐
mats
-n Only print the name of the molecules
-t # Print a molecule only if the pattern occurs # times inside the mol‐
ecule
-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 ALSObabel(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 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
