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 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 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.