Guide

User Guide

This guide describes the BIOVIA® Pipeline Pilot Gadget, the Pipeline Pilot collection provided to interact with Schrodinger® LiveDesign, and explains how best to use it.

The BIOVIA® Pipeline Pilot Gadget gives you access to an application that uses the Discngine Connector technology to execute calculations from the Schrodinger® LiveDesign Report externally on a Pipeline Pilot server and integrate the results back into LiveDesign. More concretely, the Pipeline Pilot collection provided with the Connector package allows you to create protocols that can manipulate LiveDesign data and modify your LiveDesign instance. In the gadget, you will have access to these protocols and their settings for maximum flexibility.

This protocol example is available in the collection at the following location: Protocols/Discngine/LiveDesign Connector/Examples:

Cluster Molecules in BIOVIA® Pipeline Pilot

When you open the BIOVIA® Pipeline Pilot Gadget in LiveDesign, you are directed to the application’s home page and a menu is directly accessible, giving you access to some examples. If you click on the Examples item in this menu, then on “Cluster Molecules”, the application will generate a form with the protocol parameters:

Cluster Molecules in Schrodinger® LiveDesign

By clicking on the “Submit” button, the Pipeline Pilot protocol is launched on the Pipeline Pilot server, with the data from the LiveReport. This protocol groups the molecules into clusters and generate new columns with information about these clusters. These new columns are added to the LiveReport once the protocol is finished.

A complete User Guide on this application is available here.

The collection allows you to manipulate Live Design Projects, folders, LiveReports, their columns and data. They are organized by entities and roles:

Pipeline Pilot collection

You can manipulate your data, either from an existing LiveReport or from another data source such as a database, and create new LiveReports, modify existing ones adding columns or rows, and organize your reports by creating folders and nested folders.

This section describes the use of the components through different examples of protocols.

You can retrieve molecules from an external source with the usual Pipeline Pilot components, or retrieve them from an existing LiveReport using the “Get LiveReport Content” component:

Build Protocol - Data Source

The “Get LiveReport Content” component needs the identifier of the LiveReport to retrieve. When you are on your LiveReport in LiveDesign, this identifier is the number after the endpoint livereports in the URL, in the following example the LiveReport identifier is 2209:https://[LiveDesign server]/livedesign/#/projects/302/livereports/2209.

In the case of data retrieved from a LiveReport, the records passed are Molecules with the columns of the LiveReport and its identifier as properties.

You can then manipulate this data with the usual Pipeline Pilot components, for example by calculating properties on the molecules:

Build Protocol - Data Manipulation

Finally, you can add these new properties as new columns in an existing LiveReport:

Build Protocol - Data Writing in Pipeline Pilot

Build Protocol - New Columns in LiveDesign

You can also create a new LiveReport with the molecules and all the properties. In that case, the identifier of the new LiveReport is exposed as a property of the molecules passed by the “Create LiveReport” component:

Build Protocol - New LiveReport in Pipeline Pilot

If an error occurs in a component of the collection, when calling the LiveDesign API, then the error returned by the API is directed to the Fail Port of the component, in a LiveDesignError record. In the following example, a non-existing LiveReport identifier has been provided to the "Get LiveReport Content" component:

Error Record in Pipeline Pilot