Python API

At the highest level, the Schrödinger Python Application Programming Interface (API) provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. You can use it to automate workflows and extend the software’s core functionality.

NOTE: This documentation provides an overview of the API but does not provide the level of detail given in the class and function API documentation. It is aimed at a developer who already knows Python (or can pick it up on their own) and wants to use our API to complete a scientific project.

Getting Started

Find out how to get started using Schrödinger Python Scripts.

Core Concepts

Learn how to work with structures (the fundamental class in our modules), including reading, writing, querying and modifying them.

Interacting with Maestro

Interact with the Workspace and Project Table using Python, and install your own custom scripts as Maestro menu items.

Working with MD Simulation Data

The Desmond package contains modules for various operations such as reading, converting, and analyzing trajectories.


The Jaguar package has modules to help set up and run quantum-mechanical calculations using Jaguar and to parse the results.


The analysis enrichment helps to calculate enrichments based on known actives and the number of decoys in screen.

Product Specific Modules

MacroModel and Prime packages help set up and run associated tasks.


Information and instructions on how to run Jobcontrol (a tool for running tasks asynchronously and, optionally, on different machines) scripts.


This cookbook aims to give short, self-contained, runnable code samples to perform common tasks that would be assembled into a larger script.

Schrödinger Python API

Links to all the Schrodinger Python modules that can be used for scripting.

Examples of the Python API in use

See the scripts included with the release at $SCHRODINGER/mmshare-v*/python/common. $SCHRODINGER/mmshare-v*/python/scripts contains code for most of the panels inside of Maestro.

Additional Resources



An online resource with user manuals, panel descriptions, help topics and more.


Tutorials, videos, webinars and online courses for the Schrödinger platform.

Knowledge Base

Frequently asked questions with solutions and troubleshooting for technical issues.

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