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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
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Journal of Cheminformatics

ISSN: 1758-2946

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