Click on the New API button in the "Scoring APIs" tab.
Left side: API Details
Next, the user can specify:
- the API name,
- the URL for the API endpoint,
- and any additional parameters that are needed for the API.
Right side: Scores
Add a new score by clicking on Add Score.
The user can specify:
- the score name (of their choice),
- the index of the score in the API output (starting at 0),
- the thresholds for the score.
Thresholds
If the API is used as a reward during molecule generation, and not just for rescoring datasets, the generator needs to get the feedback of what a good or bad molecule, with respect to the API score, is. This information is given by the thresholds. In the Iktos ranking calculation, the API Score is transformed with a Gaussian transform, using the thresholds values.
If you set a MIN value, molecules with API Score ≥ MIN will be considered good ("API contribution to Iktos ranking" = 1).
If you set a MAX value, molecules with API Score ≤ MAX will be considered good ("API contribution to Iktos ranking" = 1).
If you set a MIN and MAX values, molecules with API Score in the range [MIN; MAX] will be considered good ("API contribution to Iktos ranking" = 1).
The STANDARD DEVIATION represents the flexibility margin to the range of good values. By default, it is set at MIN/10 (or MAX/10) if there is only a MIN (or MAX) value, and (MAX - MIN)/10 if both MIN and MAX values are set. If you are setting thresholds, we highly recommend choosing your own standard deviation instead of using the default value.
Remove "bad" molecules
Check the box to specify if the molecules not meeting the threshold should be eliminated. If it is not checked for any target, as long as other objectives are good, the agent will still propose them.
An example API scorer is shown in the following figure.