obgrep (1) - Linux Man Pages
obgrep: an advanced molecular search program using SMARTS
NAMEobgrep - an advanced molecular search program using SMARTS
SYNOPSIS[OPTIONS ] 'SMARTS-pattern' filename
DESCRIPTIONThe obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.
OPTIONSIf 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
EXAMPLESNote 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"
AUTHORSThe 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>
COPYRIGHTCopyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and other contributors.
The web pages for Open Babel can be found at:
A guide for constructing SMARTS patterns can be found at:
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>