|obgrep(1)||General Commands Manual (urm)||obgrep(1)|
obgrep — an
advanced molecular search program using SMARTS
||[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
- Specifies input and output format, see obabel(1) for available formats
- Only print the name of the molecules
- 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
obgrep 'c' *.smi
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.
|October 10, 2019||Open Babel 3.1|