Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Branch Represenations in SMILES
This section provides a quick introduction on branch represenations in SMILES. An extra bond and its connected branch of atoms is represented in round brackets (...) inserted after the bonding atom and before any existing bonds.
How Branches Are Represented in SMILES? - Branches are represented in SMILES according to one single rule:
1. An extra bond and its connected branch of atoms is represented in round brackets (...) inserted after the bonding atom and before any existing bonds.
For example, the first C in C-F has 1 existing explicit bond of "-F". We can insert an extra bond to the first C before the existing bond, like C(-O)-F. Now the first C has 2 existing explicit bonds. We can insert another extra bond to the first C, like C(-N)(-O)-F. Of course, C(-N)(-O)-F can be simplified as C(N)(O)F.
Or we can start with a single C with no explicit bond. Then add an extra bond as C(-F). Then add another extra bond as C(-O)(-F). Then add another extra bond as C(-N)(-O)(-F).
Inside a branch, additional atoms and bonds can be added. For example, CCN(CC)CC, CC(C)C(=NCO)O, etc.
Inside a branch, additional branches can also be added. For example, C=CC(CCC)C(C(C)C)CC, c1c(N(O)O)cccc1, etc.
Table of Contents
►SMILES (Simplified Molecular-Input Line-Entry System)
►Branch Represenations in SMILES
Disconnected Structures in SMILES
Charge Represenations in SMILES
Isotope Represenations in SMILES
Chirality Representations in SMILES
Hydrogen Representations in SMILES
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
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