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Table 1 Comparison between implementations

From: Fast, efficient fragment-based coordinate generation for Open Babel

Software

Time (s)

RMSD (Å)

Bond (Å)

Angle (\(^\circ\))

Torsion (\(^\circ\))

TFD

Success (%)

Open Babel

93.7

1.75

0.055

2.40

48.8

0.27

76.3

RDKit (ETKDG)

274.6

1.59

0.060

2.87

43.9

0.21

99.5

This work

54.8

1.75

0.049

2.49

44.1

0.27

93.9

  1. The performance on 4548 molecules in the Platinum dataset is shown. Time column shows the total time to process all molecules in second. RMSD column shows mean RMSD. Bond, Angle, Torsion columns show mean error of each. TFD column shows mean of the torsion fingerprint deviation [34]. Success indicates the percent of predicted molecules whose InChIKey match that of the original molecule. RMSD and mean error are calculated over successful molecules
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Journal of Cheminformatics

ISSN: 1758-2946

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