Table 1 |
|
Some features of toolkits which are not shared by all three toolkits. |
| 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 |
|
* Where the term "like" is used, it indicates that the implementation details differ. |
O'Boyle and Hutchison Chemistry Central Journal 2008 2:24 doi:10.1186/1752-153X-2-24 |
