Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Atom Represenations in SMILES
This section provides a quick introduction on atom represenations in SMILES. Each non-hydrogen atom is represented by its atomic symbol followed by H or Hn for bonded hydrogens in square brackets [].
How Atoms Are Represented in SMILES? - Atoms are represented in SMILES according to the following rules:
1. Each non-hydrogen atom, in a molecule is represented by its atomic symbol enclosed in square brackets []. For example, [C], [Na], [F], [Fe], etc.
2. Hydrogens bonded to each non-hydrogen atom are represented as H or Hn after the bonding atom inside the brackets. For example, [FH], [OH2], [NH3], [CH4], etc.
3. Hydrogen atom not bonded to any non-hydrogen atoms is represented as [H]. For example, [H] and [H][H].
4. Organic atoms, B, C, N, O, P, S, F, Cl, Br, and I, may be represented without brackets if the number of bonded hydrogens conforms to the lowest normal valence consistent with explicit bonds. For example, O is the same as [OH2]; C is the same as [CH4]; CC is the same as [CH3][CH3].
5. Atoms in aromatic rings may be represented by lower case letters. For example, c1ccccc1 is the benzene ring.
Table of Contents
►SMILES (Simplified Molecular-Input Line-Entry System)
►Atom Represenations in SMILES
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