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 formats

       -n    Only print the name of the molecules

       -t #  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

SEE ALSO

       obabel(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>

AUTHORS

       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

       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.

Open Babel 3.1                                    Oct 10, 2019                                         obgrep(1)