The RDKit Documentation

• An overview of the RDKit
  • What is it?
    • Open source toolkit for cheminformatics
    • Operational:
    • History:
  • Functionality overview
  • Basics
    • 2D
    • 3D
    • Integration with other open-source projects
    • Usage by other open-source projects
  • The Contrib Directory
    • LEF: Local Environment Fingerprints
    • M_Kossner
    • PBF: Plane of best fit
    • mmpa: Matched molecular pairs
    • SA_Score: Synthetic assessibility score
    • fraggle: A fragment-based molecular similarity algorithm
    • pzc: Tools for building and validating classifiers
    • ConformerParser: parser for Amber trajectory files
    • NP_Score: Natural-product likeness score
    • AtomAtomSimilarity: atom-atom-path method for fragment similarity
  • Footnotes
  • License
• Installation
  • Cross-platform under anaconda python (fastest install)
    • Introduction to anaconda
    • How to get conda
    • How to install RDKit with Conda
    • How to build from source with Conda
      • macOS 10.12 (Sierra): 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
      • Prerequisites
      • 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
  • 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
    • 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 Fingerprints
  • Feature Definitions Used in the Morgan Fingerprints
  • License
• The RDKit Book
  • Misc Cheminformatics Topics
    • Aromaticity
    • 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
  • 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

Additional Information

• Python API Documentation
• C++ API Documentation