Using the Schrödinger Python API

This document can be accessed from the Schrödinger website at www.schrodinger.com/pythonapi.

The full API documentation generated from the Python documentation strings can be accessed here.

Contents

• Introduction
  • General Python Information
  • Getting Started
  • Upgrading from Python 2 to Python 3
  • Accessing Your Own Modules
  • Setting Up Your Code Editor
• Core Concepts
  • Structures
• Interacting with Maestro
  • Basic Concepts
  • Running Scripts from Maestro
  • Adding Your Script to the Maestro Scripts Menu
  • The Maestro Module
  • Interacting with the Project Table
  • Registering Functions to be Called By Maestro
  • Displaying a GUI Within Maestro Using Python
  • Other Maestro Interactions
• Working With Trajectories
  • Atom indexing
  • Trajectory frames
  • Trajectory analysis
  • Utility scripts
  • Extracting trajectories from .fmp and .fmpdb files
• Jaguar
  • Example 1: Setting up jobs
  • Example 2: Launching jobs and parsing the output
  • Example 3: Chaining jobs using the restart file
  • Example 4: Setting up a constrained geometry optimization
  • Example 5: Running Jaguar jobs in parallel batches
• Enrichment
  • Calculate Enrichment from Virtual Screening
• Product Specific Modules
  • MacroModel
  • Prime
• Jobcontrol
  • Running a Job
  • Ordinary scripts
  • Add jobcontrol API
  • Register input and output files
  • Using a jobname
  • Maestro Incorporation
  • Using $SCHRODINGER/run -FROM <product>
  • Integration with an Argument Parser
  • Introduction to JobDJ
  • Basic Usage
  • Workflow Basics
  • Working With The Workflow Graph
  • Failure Tolerance
• Cookbook
  • IO
  • Structures
  • Properties
  • Ligands
  • Atom Specification Language (ASL)
  • Measurement
  • Structure Comparison
  • Modifying and Building Structures
  • Data Conversions

Search

• Index

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