MolFromSmiles/MolToSmiles for SMILES Format

This section provides a tutorial example on how to use rdkit.Chem.rdmolfiles.MolFromSmiles(s) and rdkit.Chem.rdmolfiles.MolToSmiles(m) methods to handle molecules expressed in SMILES strings.

There are two main methods that handle molecules expressed in SMILES strings:

1. rdkit.Chem.rdmolfiles.MolFromSmiles(s) or rdkit.Chem.MolFromSmiles(s) - Constructs a molecule object from a given SMILES string.

2. rdkit.Chem.rdmolfiles.MolToSmiles(m) or rdkit.Chem.MolToSmiles(m) - Returns a SMILES string representing the molecule from a given molecule object.

Here is an example session of using these two methods:

>>> from rdkit import Chem

>>> m = Chem.MolFromSmiles('Cc1ccccc1')

>>> m.GetNumAtoms()
>>> m.GetNumBonds()

>>> s = Chem.MolToSmiles(m)
>>> print(s)

Table of Contents

 About This Book

 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

 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

 What Is rdkit.Chem.rdmolfiles Module

MolFromSmiles/MolToSmiles for SMILES Format

 MolFromMolBlock/MolToMolBlock for Mol Block

 SmilesMolSupplier/SDWriter for SMILES Files

 SDMolSupplier/SDWriter for SDF Files

 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

 Resources and Tools

 Cheminformatics Related Terminologies


 Full Version in PDF/EPUB