The RDKit Documentation

• An overview of the RDKit
  • What is it?
    • Open source toolkit for cheminformatics
    • Operational:
    • History:
  • Integration with other open-source projects
  • Usage by other open-source projects
  • The Contrib Directory
  • Footnotes
  • License
• Installation
  • Cross-platform under anaconda python (fastest install)
    • Introduction to anaconda
    • How to get conda
    • How to install RDKit with Conda
      • conda-forge package
    • How to build from source with Conda
      • macOS 10.12 (Sierra): Python 3 environment
      • Linux x86_64: Python 3 environment
    • Installing and using PostgreSQL and the RDKit PostgreSQL cartridge from a conda environment
  • Linux and OS X
    • Installation from repositories
      • Ubuntu 12.04 and later
      • Fedora, CentOS, and RHEL
      • OS X
    • Building from Source
      • Installing prerequisites from source
      • Building the RDKit
      • Testing the build (optional, but recommended)
      • Advanced
      • Frequently Encountered Problems
  • Windows
    • Prerequisites
      • Recommended extras
    • Installation of RDKit binaries
    • Installation from source
      • Extra software to install
      • Setup and Preparation
      • Building from the command line (recommended)
      • Testing the Build (optional, but recommended)
  • License
• Getting Started with the RDKit in Python
  • Important note
  • What is this?
  • Reading and Writing Molecules
    • Reading single molecules
    • Reading sets of molecules
    • Writing molecules
    • Writing sets of molecules
  • Working with Molecules
    • Looping over Atoms and Bonds
    • Ring Information
    • Modifying molecules
    • Working with 2D molecules: Generating Depictions
    • Working with 3D Molecules
    • Preserving Molecules
    • Drawing Molecules
  • Substructure Searching
    • Stereochemistry in substructure matches
    • Atom Map Indices in SMARTS
  • Chemical Transformations
    • Substructure-based transformations
    • Murcko Decomposition
  • Maximum Common Substructure
  • Fingerprinting and Molecular Similarity
    • Topological Fingerprints
    • MACCS Keys
    • Atom Pairs and Topological Torsions
    • Morgan Fingerprints (Circular Fingerprints)
      • Explaining bits from Morgan Fingerprints
    • Generating images of fingerprint bits
    • Picking Diverse Molecules Using Fingerprints
    • Generating Similarity Maps Using Fingerprints
  • Descriptor Calculation
    • Visualization of Descriptors
  • Chemical Reactions
    • Advanced Reaction Functionality
      • Protecting Atoms
    • Recap Implementation
    • BRICS Implementation
    • Other fragmentation approaches
  • Chemical Features and Pharmacophores
    • Chemical Features
    • 2D Pharmacophore Fingerprints
  • Molecular Fragments
  • Non-Chemical Functionality
    • Bit vectors
    • Discrete value vectors
    • 3D grids
    • Points
  • Getting Help
  • Advanced Topics/Warnings
    • Editing Molecules
  • Miscellaneous Tips and Hints
    • Chem vs AllChem
    • The SSSR Problem
  • List of Available Descriptors
  • List of Available 3D Descriptors
  • List of Available Fingerprints
  • Feature Definitions Used in the Morgan Fingerprints
  • License
• The RDKit Book
  • Misc Cheminformatics Topics
    • Aromaticity
      • The RDKit Aromaticity Model
      • The Simple Aromaticity Model
      • The MDL Aromaticity Model
    • SMILES Support and Extensions
      • Aromaticity
      • Dative bonds
      • Specifying atoms by atomic number
      • CXSMILES extensions
    • SMARTS Support and Extensions
      • Hybridization queries
      • Dative bonds
      • Heteroatom neighbor queries
      • Range queries
    • Ring Finding and SSSR
  • Chemical Reaction Handling
    • Reaction SMARTS
      • Some features
      • Chirality
      • Rules and caveats
  • The Feature Definition File Format
    • Chemical Features
    • Syntax of the FDef file
      • AtomType definitions
      • Feature definitions
      • Additional syntax notes:
      • Atom weights and feature locations
    • Frequently Asked Question(s)
  • Representation of Pharmacophore Fingerprints
  • Atom-Atom Matching in Substructure Queries
  • Molecular Sanitization
  • Implementation Details
    • “Magic” Property Values
      • ROMol (Mol in Python)
      • Atom
    • Thread safety and the RDKit
      • What has been tested
      • Known Problems
    • Implementation of the TPSA Descriptor
  • Atom Properties and SDF files
  • Support for Enhanced Stereochemistry
    • Overview
    • Representation
    • Use cases
  • License
• RDKit Cookbook
  • What is this?
  • Miscellaneous Topics
    • Using a different aromaticity model
  • Manipulating Molecules
    • Cleaning up heterocycles
    • Parallel conformation generation
    • Neutralizing Charged Molecules
  • 3D functionality in the RDKit
  • Using scikit-learn with RDKit
  • Using custom MCS atom types
  • Clustering molecules
  • RMSD Calculation between N molecules
    • Introduction
    • Details
  • License
• The RDKit database cartridge
  • What is this?
  • Tutorial
    • Introduction
    • Creating databases
      • Configuration
      • Creating a database from a file
      • Loading ChEMBL
    • Substructure searches
      • SMARTS-based queries
      • Using Stereochemistry
      • Tuning queries
    • Similarity searches
      • Adjusting the similarity cutoff
    • Using the MCS code
  • Reference Guide
    • New Types
    • Parameters
    • Operators
      • Similarity search
      • Substructure and exact structure search
      • Molecule comparison
    • Functions
      • Fingerprint Related
      • Molecule Related
      • Other
  • Using the Cartridge from Python
  • License
• Backwards incompatible changes
  • Release 2018.03
    • MolToSmiles() generates isomeric SMILES by default
    • MolToMolBlock() generates a 2D conformation when the includeStereo flag is set
    • The conformation generation code now uses ETKDG by default
  • Release 2018.09
    • GetAtomSmiles() generates isomeric SMILES by default
    • Changes to ringMatchesRingOnly option in the MCS code
    • The conformation generation code now uses ETKDG by default when called from Python
  • License
• Python API Reference
  • rdkit package
    • Subpackages
      • rdkit.Avalon package
      • rdkit.Chem package
      • rdkit.DataManip package
      • rdkit.DataStructs package
      • rdkit.Dbase package
      • rdkit.DistanceGeometry package
      • rdkit.ForceField package
      • rdkit.Geometry package
      • rdkit.ML package
      • rdkit.Numerics package
      • rdkit.SimDivFilters package
      • rdkit.VLib package
      • rdkit.utils package
    • Submodules
      • rdkit.rdBase module
      • rdkit.RDConfig module
      • rdkit.RDLogger module
      • rdkit.RDPaths module
      • rdkit.RDRandom module
      • rdkit.TestRunner module
      • rdkit.six module
    • Module contents

Additional Information

• C++ API Documentation

Indices and tables

• Index
• Module Index
• Search Page