obgrep man page
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 extension.
Print the number of matches
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
Only print the name of the molecules
- -t #
Print a molecule only if the pattern occurs # times inside the molecule
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: < http://openbabel.org/>
A guide for constructing SMARTS patterns can be found at: < http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>
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 (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.
babel(1), obchiral(1), obconformer(1), obfit(1), obprop(1), obrotamer(1), obrotate(1).