Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Disconnected Structures in SMILES
This section provides a quick introduction on disconnected structures in SMILES. Disconnected structures are separated by the '.' symbol.
How Disconnected Structures Are Represented in SMILES? - Disconnected structures are represented in SMILES according to one single rule:
1. Disconnected structures are separated by the "." symbol. For example, "[Na].Cl", "[Na].Oc1ccccc1", etc.
Note that disconnected structures can be represented in branches too. For example, "c1cc(O.[Na])ccc1" is the same as "[Na].Oc1ccccc1".
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