This is the command obgrep that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 babel(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
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