The new fragment-based coordinate generation requires several steps: (1) break the input molecule into fragments, (2) look up fragments from the library, and (3) generate a 3D structure by stitching fragments together. Figure shows an overview of the method. Since fragments include multiple atoms, placement of fragments improves both speed and accuracy over the rule-based method, in which the position of heavy atoms were determined one-by-one. All figures are produced by Avogadro version 1.2 from the corresponding SDF files .