Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task in cheminformatics and a range of molecular modeling. Fast, accurate, and open implementation of structure prediction is necessary for reproducible cheminformatics research. We introduce fragment-based coordinate generation for Open Babel, a widely accepted open source toolkit for cheminformatics. The new implementation significant improves speed and stereochemical accuracy, while retaining or improving accuracy of bond lengths, bond angles, and dihedral torsions. We first separate an input molecule into fragments by cutting at rotatable bonds. Coordinates of fragments are set according to the fragment library, which is prepared from open crystallographic databases. Since coordinates of multiple atoms are decided at once, coordinate prediction is accelerated over the previous rules-based implementation or the widely-used distance geometry methods in RDKit. This new implementation will be beneficial for a wide range of applications, including computational property prediction in polymers, molecular materials and drug design.
Revised version (resubmit) with correct Figure 12