Thursday, December 15, 2011

Selected GH17 results for 10^6 structures

GH17 substructure search speed

OpenBabel with binary+SMILES storage and FP2 fingerprint

QueryHitsno IndexHitswith Index
GH24840108807 ms484021164 ms
GH7260105050 ms2601934 ms
GH13580118978 ms58052416 ms
GH1626910109886 ms2691064742 ms

Indigo with binary storage and ext+sub fingerprint

QueryHitsno IndexHitswith Index
GH24840213075 ms484027887 ms
GH7410178963 ms4104451 ms
GH13580251938 ms58039134 ms
GH1627100172534 ms2710080523 ms

Bingo 1.7beta2 with molfiles as text storage

QueryHitsno IndexHitswith Index
GH24710647889 ms471021733 ms
GH7410538784 ms4106658 ms
GH13580675093 ms58012418 ms
GH1627100528891 ms2710028541 ms

Index build times

SystemIndex build time
pgchem with OpenBabel or Indigo352137 ms

Again, Bingo without it's index is apparently killed by the overhead of parsing text into the internal molecule format. With index it's a mixed bag, while it shines at GH13 and GH16, pgchem is about equal or faster at GH2 and GH7.

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