Basic Tutorial

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To run SEA we need, for both the query and the reference, three files with the same basename and different extensions:

  • smiles (.smi) : The separator between smiles and IDs is a semicolon. Make sure it has the same characteristics than the reference by running the following command:
  > sea-molecule-clean
  • fingerprints (.fp) : Separator is also a semicolon. Can be generated by the following command:
  > sea-molecule-fingerprint
  • sets (.set) : First element (separated by semicolon) is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a colon.

Additionally, we will need the model fit file generated from SEA.

The actual command to run SEA is:

 > sea-run -f model_fit_file model_set_file query_set_file

Export the results

 > sea-export -t 0.5 -o sea_output 9