FreeBSD Manual Pages
OBGREP(1) User's Reference Manual 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 obabel(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 mole- cule -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 direc- tory (i.e., *.smi) obgrep 'c' *.smi SEE ALSO obabel(1), obfit(1), obrotate(1). The web pages for Open Babel can be found at: <https://openbabel.org/> A guide for constructing SMARTS patterns can be found at: <https://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 current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see <https://openbabel.org/docs/Introduction/thanks.html> 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 un- der 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 FIT- NESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Open Babel 3.2 May 26, 2026 OBGREP(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | SEE ALSO | AUTHORS | COPYRIGHT
Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=obgrep&sektion=1&manpath=FreeBSD+Ports+15.1.quarterly>