obgrep (1) - Linux Manuals

obgrep: an advanced molecular search program using SMARTS

NAME

obgrep - an advanced molecular search program using SMARTS

SYNOPSIS

[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 babel(1) for available formats

-n

Only print the name of the molecules

-t file ...

Print a molecule only if the pattern occurs # times inside the molecule

-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 directory (i.e., *.smi)

"obgrep 'c' *.smi"

AUTHORS

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

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.