obgrep (1) - Linux Manuals

obgrep: an advanced molecular search program using SMARTS


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
-i format
Specifies input and output format, see babel(1) for available formats
Only print the name of the molecules
-t file ...
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"


The obgrep program was contributed by An Fabien Fontaine

An -nosplit Open Babel is developed by a cast of many, including currrent maintainers An Geoff Hutchison , An Chris Morley , An 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), 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>