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:
- fingerprints (.fp) : Separator is also a semicolon. Can be generated by the following command:
- 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