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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
  1. The times reported are wallclock times from the best of three runs on a dual-core Intel Pentium 4 3.2 GHz machine with 1GB RAM.