Navigation
index
next
|
The RDKit 2015.03.1 documentation
»
Table Of Contents
An overview of the RDKit
Installation
Getting Started with the RDKit in Python
The RDKit Book
RDKit Cookbook
The RDKit database cartridge
Next topic
An overview of the RDKit
This Page
Show Source
The RDKit Documentation
¶
An overview of the RDKit
What is it?
Functionality overview
The Contrib Directory
License
Installation
Linux and the Mac
Installation from repositories
Ubuntu 12.04 and later
Fedora, CentOS, and RHEL
MacOS
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)
Building the Code Using GUIs (not recommended)
Testing the Build (optional, but recommended)
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
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
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
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
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
Navigation
index
next
|
The RDKit 2015.03.1 documentation
»