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Table 2 Conversion Time

From: jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

Encoding paramb molecules/s mean f.a max f.a median f.a complex. Mem.c
DFS d = 8, a = EN 68.6 396 3,554 362 O(d)
ASP d = 8, a = EN 112.1 216 1,198 204 O(d)
AP2D d = 8, a = EN 339.8 95 256 96 O(n2)
AT2D d = 5, a = EN 91.6 1,848 7,922 1,811 O(n3)
CATS2D d = 9, a = PPP 6.9 150 150 150 O(1)
PHAP2PT2D d = 8, a = PPP 6.8 35 132 34 O(p2)
PHAP3PT2D d = 5, a = PPP 6.7 300 1,664 277 O(p3)
SHED d = 8, a = PPP 8.0 15 15 15 O(1)
ECFP d = 4, a = DIR 181.0 77 349 77 O(d)
RAD2D d = 3, a = EN 232.5 55 192 55 O(nd)
LSTAR d = 6, a = EN 136.6 144 884 143 O(nd)
AP3D d = 10, a = EN 332.5 112 336 113 O(n2)
AT3D d = 6, a = EN 71.4 3,450 27,774 3,188 O(n3)
CATS3D d = 9, a = PPP 6.6 150 150 150 O(1)
PHAP2PT3D d = 10, a = PPP 7.2 41 189 40 O(p2)
PHAP3PT3D d = 6, a = PPP 7.1 660 5,844 601 O(p3)
RAD3D d = 4, a = EN 227.1 85 611 85 O(nd)
  1. Computation time on a random ChemDB [29] background data set consisting of about 175,000 compounds. This includes reading, typing, and generation of the feature map objects. Empirical computation time was obtained on a dual core AMD Opteron(tm) Processor 280, 2.4 GHz, 2 GByte RAM, Java Runtime Environment 1.6, Linux kernel 2.6.18, using a single core.
  2. aunique features, EN: element neighbor, PPP: possible pharmacophore points, DIR: Daylight Invariants plus ring flag b standard parameters of the implemented encodings c d: search depth, p: number of possible pharmacophore points