The RDKit Documentation

• An overview of the RDKit
  • What is it?
    • Open source toolkit for cheminformatics
    • Operational:
    • History:
  • Citing the RDKit
    • Powered by RDKit
  • Integration with other open-source projects
  • Usage by other open-source projects
  • The Contrib Directory
  • License
• Installation
  • Cross-platform using Conda
    • Introduction to Conda
    • How to get conda
    • How to install RDKit with Conda
    • 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
  • Cross-platform using PIP
  • 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 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, Drawing, 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
    • Metadata in Molecule Images
  • Substructure Searching
    • Stereochemistry in substructure matches
    • Atom Map Indices in SMARTS
    • Advanced substructure matching
  • Chemical Transformations
    • Substructure-based transformations
    • Murcko Decomposition
  • Maximum Common Substructure
    • FindMCS
    • RascalMCES
    • Clustering with Rascal
  • Fingerprinting and Molecular Similarity
    • RDKit (Topological) Fingerprints
    • Atom Pairs and Topological Torsions
    • Morgan Fingerprints (Circular Fingerprints)
    • MACCS Keys
    • Explaining bits from fingerprints
      • Morgan Fingerprints
      • RDKit Fingerprints
    • Generating images of fingerprint bits
    • Picking Diverse Molecules Using Fingerprints
    • Generating Similarity Maps Using Fingerprints
  • Descriptor Calculation
    • Calculating All Descriptors
    • Calculating Partial Charges
    • Visualization of Descriptors
  • Chemical Reactions
    • Drawing 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
  • R-Group Decomposition
  • 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
  • Filtering Molecular Datasets
    • Lipinski Rule of 5
    • Filtering Unwanted Substructures
  • 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
      • Ring closures
      • Specifying atoms by atomic number
      • Quadruple bonds
      • CXSMILES/CXSMARTS extensions
      • Reading molecule names
    • SMARTS Support and Extensions
      • Hybridization queries
      • Dative bonds
      • Heteroatom neighbor queries
      • Range queries
      • SMARTS Reference
    • Mol/SDF Support and Extensions
    • Ring Finding and SSSR
    • Stereochemistry
      • Types of stereochemistry supported
      • Identification of potential stereoatoms/stereobonds
      • Assignment of absolute stereochemistry
      • Stereogenic atoms/bonds
      • Brief description of the findPotentialStereo() algorithm
      • Sources of information about stereochemistry
    • Support for non-tetrahedral atomic stereochemistry
      • Status as of 2022.09.1 release
      • SMILES notation
  • Chemical Reaction Handling
    • Reaction SMARTS
      • Some features
      • Chirality
      • Rules and warnings
  • 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
  • Generic (“Markush”) queries in substructure matching
  • Molecular Sanitization
    • Valence calculation and allowed valences
  • JSON Support
    • rdkitjson format
      • Enhanced stereo
      • Substance groups
  • 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
    • Enhanced Stereochemistry and substructure search
  • Atropisomeric Bonds
    • Defining Atropisomers
    • Internal Representation of Atropisomers
    • Formats supporting atropisomers
    • Enhanced Stereochemistry
    • 3D Coordinates for Input of Atropisomers
    • Interpreting atropisomers without coordinates
    • Validation of Atropisomers
    • Searching and Canonicalization
  • Query Features in Molecule Drawings
    • Query Bonds
    • Query Atoms
  • Conformer Generation
    • Introduction
    • Parameters Controlling Conformer Generation
  • Additional Information About the Fingerprints
    • RDKit Fingerprints
      • Fingerprint-specific options
    • Pattern Fingerprints
    • Atom-Pair and Topological Torsion Fingerprints
    • Morgan and Feature Morgan Fingerprints
    • Layered Fingerprints
  • Feature Flags: global variables affecting RDKit behavior
  • License
• RDKit Cookbook
  • Introduction
    • What is this?
    • What gets included?
    • Feedback and Contributing
  • Drawing Molecules (Jupyter)
    • Include an Atom Index
    • Include a Bond Index
    • Include a Calculation
    • Include Stereo Annotations
    • Black and White Molecules
    • Highlight a Substructure in a Molecule
    • Highlight Molecule Differences
    • Highlight Entire Molecule
    • Highlight Molecule with Multiple Colors
    • Without Implicit Hydrogens
    • With Abbreviations
    • Using CoordGen Library
    • On a Plot
  • Bonds and Bonding
    • Hybridization Type and Count
  • Rings, Aromaticity, and Kekulization
    • Count Ring Systems
    • Identify Aromatic Rings
    • Identify Aromatic Atoms
  • Stereochemistry
    • Identifying Stereochemistry
  • Manipulating Molecules
    • Create Fragments
    • Largest Fragment
    • Sidechain-Core Enumeration
    • Neutralizing Molecules
  • Substructure Matching
    • Functional Group with SMARTS queries
    • Macrocycles with SMARTS queries
    • Returning Substructure Matches as SMILES
    • Within the Same Fragment
  • Descriptor Calculations
    • Molecule Hash Strings
    • Contiguous Rotatable Bonds
  • Writing Molecules
    • Kekule SMILES
    • Isomeric SMILES without isotopes
  • Reactions
    • Reversing Reactions
    • Reaction Fingerprints and Similarity
  • Error Messages
    • Explicit Valence Error - Partial Sanitization
    • Detect Chemistry Problems
  • Miscellaneous Topics
    • Explicit Valence and Number of Hydrogens
    • Wiener Index
    • Organometallics with Dative Bonds
    • Enumerate SMILES
    • Reorder Atoms
    • Conformer Generation with ETKDG
  • 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 2023.09
    • Changes in atomic stereochemistry perception
    • Changes in the MCS code
    • Changes to canonicalization
  • Release 2023.03
    • Changes to ring finding
    • Changes to canonicalization
  • Release 2022.09
    • Changes in canonicalization
    • Improvements to GetBestRMS() and CalcRMS()
  • Release 2022.03
    • Changes to the handling of dummy atoms and aromaticity
    • Tautomer enumeration improvements
  • Release 2021.03
    • Changes to conformer generation
    • Changes to R-Group Decomposition results
    • Reactions now produce STEREONONE instead of STEREOANY for unspecified double bonds
    • Moving MolToSVG()
  • Release 2020.09
    • Changes in the chemistry model [UPDATED for release 2020.09.2]
    • FindMCS can now return single atom MCSs
    • New return type for tautomer enumeration
    • Default precision for coordgen
    • Change in uncharge() behavior for inorganic acids
  • Release 2020.03
    • Use of chirality with @= in PostgreSQL cartridge
    • Handling of empty/invalid files in MolSuppliers
    • Renaming a cmake option
  • Release 2019.09
    • Updated van der Waals radii
    • “R” atoms in mol blocks are now converted into * queries
    • PandasTools.LoadSDF() uses isomeric SMILES
    • New fingerprinter defaults changed
  • Release 2019.03
  • 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
  • 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
  • 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
    • Module contents
      • VectIter
• Getting Started with the RDKit in C++
  • What is this?
  • Building and Running C++ RDKit Programs
  • Should You Use C++ or Python?
  • Memory Management
  • The Molecule Classes
  • 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
  • The SSSR Problem

Additional Information

• C++ API Documentation

Indices and tables

• Index

• Module Index

• Search Page