Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Substructure Search with Wildcard Atom "*"
This section provides a tutorial example on how to use '*' to represent a wildcard atom in SMARTS string to do substructure search using 'obabel ... -s ...' command with Open Babel.
You can use "*" in a SMARTS string as a wildcard atom to represent "ANY" atom in a substructure search using "obabel ... -s ..." commands with Open Babel.
Here are some examples of substructure matching with a wildcard atom "*" in the molecule pattern:
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=CO c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=CC c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=C* c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=C*N c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=C*C c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=C** c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=C**ccccO c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=C******O c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles -s O=*******O c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted
You can validate the above matching result by looking at the tyrosine molecule structure below:
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
►Substructure Search with Open Babel
"obabel -s ..." Command - Substructure Search
►Substructure Search with Wildcard Atom "*"
Substructure Search with Wildcard Bond "~"
Substructure Search with SMARTS Expressions
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction