Fast, efficient fragment-based coordinate generation for Open Babel

Table 2 Effect of implementation

Difference from final	Time (s)	RMSD (Å)	Bond (Å)	Angle (\(^\circ\))	Torsion (\(^\circ\))	TFD	Success (%)
No index	140.9	1.78	0.056	2.77	45.5	0.30	92.8
No generic rings	20.6	2.01	0.103	4.75	51.5	0.51	89.4
Match generic rings before fragments	56.7	1.78	0.061	2.76	46.9	0.31	92.7
Final implementation	54.8	1.75	0.049	2.49	44.1	0.27	93.9

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 in Å. 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

ISSN: 1758-2946