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Table 1 Some features of toolkits which are not shared by all three toolkits.

From: Cinfony – combining Open Source cheminformatics toolkits behind a common interface

CDK
A large number of descriptors (some overlap with RDKit)
Pharmacophore searching (like RDKit*)
Calculation of maximum common substructure
2D structure layout (like RDKit) and depiction
MACCS keys (also RDKit) and E-State fingerprints
Integration with the R statistical programming environment
Support for mass-spectrometry analysis (representations for cleavage reactions, structure generation from formulae)
Fragmentation schemes (ring fragments, Murcko)
3D structure generation using a template and heuristics (like OpenBabel)
3D similarity using ultrafast shape descriptors
Gasteiger π charge calculation
OpenBabel
Not just focused on cheminformatics
Supports a very large number of chemical file formats including quantum mechanics file formats, molecular mechanics trajectories, 2D sketchers
3D structure generation using a template method (like CDK)
Included in all major Linux distributions
Bindings available from several scripting languages apart from Python, as well as the Java and .NET platforms
Conformation generation and searching
InChI (also CDK) and InChIKey generation
Support for crystallographic space groups
Several forcefield implementations: UFF (also RDKit), MMFF94, MMFF94s, Ghemical
Ability to add custom data types to atoms, bonds, residues, molecules
RDKit
A large number of descriptors (some overlap with CDK)
Fragmentation using RECAP rules
2D coordinate generation (like CDK) and depiction
3D coordinate generation using geometry embedding
Calculation of Cahn-Ingold-Prelog stereochemistry codes (R/S)
Pharmacophore searching (like CDK)
Calculation of shape similarity (based on volume overlap)
Chemical reaction handling and transforms
Atom pairs and topological torsions fingerprints
Feature maps and feature-map vectors
Machine-learning algorithms
  1. * Where the term "like" is used, it indicates that the implementation details differ.