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Table 6 Summary of systematic benchmark comparing v1.4.19 to v2.0 without read times

From: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Benchmark Data set CDK v1.4.19 CDK v2.0 Improvement
Skip Time Per Min Skip Time Per min
countheavy ChEBI 149 smi 0 0s 0 0s  
sdf 0 0s 0 0s  
ChEMBL 22.1 smi 0 0s 0 0s  
sdf 0 0s 0 0s  
rings -mark ChEBI 149 smi 0 0.4s 6.1M 0 0.21s 11.6M 1.9
sdf 0 1.5s 1.7M 0 0.11s 23.3M 13.6
ChEMBL 22.1 smi 0 6.48s 15.5M 0 6.35s 15.9M 1
sdf 0 54.72s 1.8M 0 13.27s 7.6M 4.1
rings -sssr ChEBI 149 smi 0 4.89s 498.1K 0 0.58s 4.2M 8.4
sdf 0 4.63s 553.4K 0 0.78s 3.3M 5.9
ChEMBL 22.1 smi 0 3m25.32s 490.5K 0 16.42s 6.1M 12.5
sdf 0 3m52.29s 433.5K 0 14.9s 6.8M 15.6
rings -all ChEBI 149 smi 14 22.77s 107K 17 0.41s 5.9M 55.5
sdf 16 29.35s 87.3K 15 0.51s 5M 57.5
ChEMBL 22.1 smi 88 4m0.9s 418K 0 14.23s 7.1M 16.9
sdf 90 4m48.35s 349.2K 0 12.41s 8.1M 23.2
cansmi ChEBI 149 smi 0 14.07s 173.1K 0 1.06s 2.3M 13.3
sdf 35 13.94s 183.8K 1 1.37s 1.9M 10.2
ChEMBL 22.1 smi 14 5m54.56s 284K 0 30.1s 3.3M 11.8
sdf 0 5m42.53s 294K 0 36.06s 2.8M 9.5
convert -ofmt smi ChEBI 149 smi 0 13.12s 185.7K 7 0.62s 3.9M 21.2
sdf 35 13.7s 187K 0 1.55s 1.7M 8.8
ChEMBL 22.1 smi 14 5m46.72s 290.4K 28 15.46s 6.5M 22.4
sdf 0 5m42.09s 294.4K 1 19.22s 5.2M 17.8
convert -ofmt sdf ChEBI 149 smi 0 9.91s 245.8K 0 9.54s 255.3K 1
sdf 13 9.79s 261.7K 0 10.96s 233.8K 0.9
ChEMBL 22.1 smi 0 5m46.52s 290.6K 0 5m15.55s 319.1K 1.1
sdf 1 5m34.04s 301.5K 0 5m41.23s 295.1K 1
convert -gen2d -ofmt sdf ChEBI 149 smi 0 24m5.51s 1.7K 0 35.01s 69.6K 41.3
sdf 13 35m4.82s 1.2K 0 39.43s 65K 53.4
ChEMBL 22.1 smi 0 3h18m28s 8.5K 0 17m33.9s 95.6K 11.3
sdf 1 5h55m13s 4.7K 0 18m49.5s 89.2K 18.9
fpgen -type path ChEBI 149 smi 0 1m15.49s 32.3K 0 9.43s 258.3K 8
sdf 0 2m3.82s 20.7K 0 10.03s 255.5K 12.3
ChEMBL 22.1 smi 0 34m16.85s 49K 0 6m23.93s 262.3K 5.4
sdf 0 43m48.29s 38.3K 0 6m59.05s 240.3K 6.3
fpgen -type maccs ChEBI 149 smi 38 1h37m12s 418 0 18.66s 130.5K 312.6
sdf 48 1h44m10s 410 0 18.25s 140.4K 342.5
ChEMBL 22.1 smi 214 20h16m18s 1.4K 0 13m20.47s 125.8K 91.2
sdf 225 24h38m29s 1.1K 0 12m33.14s 133.7K 117.8
fpgen -type circ ChEBI 149 smi 0   0 3.52s 692K  
sdf 0   0 3.81s 672.5K  
ChEMBL 22.1 smi 0   0 2m32.71s 659.4K  
sdf 0   0 2m48.74s 596.8K  
  1. The number of records skipped and time to run the countheavy benchmark (Table 5) has been subtracted. The remaining results provides a relative comparison without accounting for the overhead of reading the input