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 |