Use Molecule input

In this tutorial you will learn how to use the Molecule input type to send a molecule in CTAB format to a parameter.

The use case is the following: search molecules by substructures in datasets and add chosen ones to a data table in Spotfire.

Create protocol in Pipeline Pilot

For this tutorial the main protocol will be the example protocol "Substructure Search" located under Protocols/Discngine/Spotfire Enabled Protocols/Client Automation/SWAPP Examples/Substructure Search.

This protocol searches for molecules by substructure across one or several reference datasets and lets you add some matching molecules to a data table in Spotfire based on user selection. It takes three parameters:

• Substructure, the searched substructure, in CTAB format.
• Datasets, the list of datasets to search in.
• Maximum, the maximum number of molecules to read per dataset.

Register protocol in the SWAPP

• Open the registration form

  • Open Spotfire and the SWAPP.
  • Click on the icon in the SWAPP menu and click "+ Register new Protocol".
  • Browse the tree of Pipeline Pilot protocols and select the example protocol "Substructure Search" under Discngine/Spotfire Enabled Protocols/Client Automation/SWAPP Examples.

• Define the inputs

  • Keep the Molecule input type for the Substructure parameter (preconfigured because it is TextType and contains "structure" in its name).
  • Select Ketcher (the option is visible only if MarvinJS has been configured on the Pipeline Pilot server).
  • Optionally set a default value like a benzene ring.
  • When launching the protocol, the drawn structure will be sent as CTAB to the parameter.
  • Leave the other parameters (Datasets, Maximum) with their automatically guessed input types.
  • Click on "Next".

• Create the menu item

  • Select a folder in the menu.
  • Click on "Save Protocol".

See the Register a protocol tutorial for more details on the registration process.

Test protocol in the SWAPP

• Select the "Substructure Search" protocol in the SWAPP menu.
• Draw a substructure query in the Molecule field, for example an aniline.
• Select one or several datasets to search in.
• Click on "Submit".
• The matching molecules should be displayed, with the searched substructure highlighted on each one.
• Select the molecules you want to keep.
• Add them to a new data table in Spotfire.