Table 3 Performance of Cinfony modules compared to a native Java or C++ implementation.
From: Cinfony – combining Open Source cheminformatics toolkits behind a common interface
Iterate over SDF | Iterate and calculate molecular weight | |||
|---|---|---|---|---|
CDK | Time (s) | Normalised | Time (s) | Normalised |
Native Java | 21.2 | 1.00 | 36.8 | 1.00 |
cdkjython | 23.1 | 1.09 | 41.6 | 1.13 |
cdkjpype | 33.0 | 1.57 | 69.5 | 1.89 |
OpenBabel | ||||
Native C++ | 31.9 | 1.00 | 43.0 | 1.00 |
pybel | 34.1 | 1.07 | 45.1 | 1.05 |
jybel | 38.0 | 1.19 | 49.6 | 1.15 |
RDKit | ||||
Native C++ | 99.7 | 1.00 | 100.7 | 1.00 |
rdkit | 99.9 | 1.00 | 101.0 | 1.00 |