Applications

This section connects the core tutorials to concrete research workflows. Instead of introducing new configuration concepts, it shows how to combine the existing training, generation, and analysis modules for common molecular design objectives discussed in the MolCraftDiffusion manuscript.

Application Map

The current examples fall into three broad categories:

#	Application	Core mechanism	Entry point
1	Local chemical space exploration	Inpainting — vary a region while fixing the scaffold	Local Chemical Space
2	Library design	Outpainting — expand a scaffold into a diverse candidate set	Library Design
3	Inverse design	Property- or geometry-directed generation toward a design objective	Inverse Design

Before You Start

Important

These application notes assume you are already familiar with the following tutorials:

• Tutorial 6: Structure-Guided Generation

• Tutorial 7: Property-Directed Generation

• Tutorial 8: Property Prediction and Evaluation

• Tutorial 9: Analysis

You will also need:

• a trained or fine-tuned checkpoint in chkpt_directory,

• reference XYZ structures for structure-guided workflows,

• any required regressor or guidance checkpoints for property-directed workflows.

Pages

• Application: Local Chemical Space Exploration
• Application: Library Design with Structure-Directed Generation
• Application: Inverse Design