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"obgrep" - Search Molecules using SMARTS
What Is "obgrep" command? How to use it to Search Molecules using SMARTS strings?
✍: FYIcenter.com
"obgrep" command is a command line tool provided in the Open Babel package
that allows you to Search Molecules using SMARTS strings.
"obgrep" command does the same job as the "babel ... -s ..." with more options.
Here is the user manual of the "obgrep" command.
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
⇒ "obminimize" - Optimize Geometry/Energy of Molecule
2020-11-11, 850🔥, 0💬
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