---
title: "Use Molecule input"
slug: "connector-spo-pp-swapp-tutorials-molecule"
updated: 2026-09-25T16:29:15Z
published: 2026-09-25T16:29:15Z
canonical: "docs.discngine.com/connector-spo-pp-swapp-tutorials-molecule"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# 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.

![Substructure Search protocol](https://connector.discngine.com/images-doc360/spo_pp/swapp_tutorials/swapp_molecule/molecule_input_protocol.png)

## 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](/public/docs/connector-spo-pp-admin-references-global-properties) 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".

![Register Substructure Search protocol in the SWAPP](https://connector.discngine.com/images-doc360/spo_pp/swapp_tutorials/swapp_molecule/molecule_input_register.png)

See the [Register a protocol](/public/docs/connector-spo-pp-swapp-tutorials-register) 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.

![Test Substructure Search protocol in the SWAPP](https://connector.discngine.com/images-doc360/spo_pp/swapp_tutorials/swapp_molecule/molecule_input_test.png)