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Example data set

  • fragments.sqlite - Fragments sqlite database containing a small number of fragments with their smiles string and molblock.
  • fingerprints.sqlite - Fingerprints sqlite database with fingerprint stored as fastdumped intbitset
  • similarities.h5 - HDF5 file with similarities matrix of fingerprints using modified tanimoto similarity index

Creating tiny data set

  1. Create fingerprints db with 1000 fingerprints
gunzip -c fingerprint01.fp.gz | head -1001 | kripodb fingerprints import - fingerprints.sqlite
  1. Shrink fragments db to only contain fragments which have a fingerprint
cat | sqlite3 fragments.sqlite <<EOF
ATTACH DATABASE 'fingerprints.sqlite' AS fp;
DELETE FROM molecules WHERE frag_id NOT IN (SELECT frag_id FROM fp.bitsets);
DELETE FROM fragments WHERE frag_id NOT IN (SELECT frag_id FROM fp.bitsets);
DELETE FROM pdbs WHERE pdb_code || prot_chain NOT IN (SELECT pdb_code || prot_chain FROM fragments);
VACUUM;
EOF

  1. Create similarity matrix
kripodb fingerprints similarities --fragmentsdbfn fragments.sqlite fingerprints.sqlite fingerprints.sqlite similarities.h5
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