Workflow Example: Conditioned Generation¶

This workflow is for cases where you do not just want plausible molecules, but molecules that satisfy a more specific design objective. In MolCraftDiffusion, the conditioning can be either property-based or structure-based.

Two Main Modes¶

Mode	Question it answers	Typical method
Property-conditioned	“Can I bias generation toward a target value or regime?”	CFG, GG, or hybrid guidance
Structure-conditioned	“Can I preserve one part of the molecule while redesigning or extending another?”	Inpainting or outpainting

Conceptual Flow¶

                 [Base or adapted model]
                         |
          +--------------+--------------+
          |                             |
          v                             v
 [Property guidance]           [Structure guidance]
          |                             |
          v                             v
[Property-directed generation] [Structure-directed generation]

What Changes with Conditioning¶

This workflow adds a design constraint to generation. Rather than only sampling plausible molecules, you guide the model toward a target property profile or a target structural pattern.

Typical Outcome¶

This is often the right workflow when you want:

molecules around a known scaffold,
candidates with a target property profile,
a more directed search than unconditional generation can provide.

Where to Go Next¶