obgrep1

Usage

Overview

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