RF Diffusion Contigmap Config¶
Builds a contigmap configuration JSON for RF Diffusion runs. It parses and validates string ranges describing which residues or secondary-structure regions to mask/unmask, and optionally the overall sequence length or length range.
Usage¶
Use this node to define advanced sequence/structure masking for RF Diffusion. Connect its output to the contigmap_config input of the RF Diffusion node. For unconditional generation, only set length and leave other fields empty. For conditional or inpainting workflows, specify inpaint_* and/or provide_seq ranges that align with your input structure.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| inpaint_seq | True | STRING | Residue ranges whose sequence should be masked for inpainting. Use the same contig format (chains and ranges). | A10-25,B5-12 |
| inpaint_str | True | STRING | Residue indices to mask in 3D structure space. Include chain IDs when applicable. | B165-178 |
| inpaint_str_helix | True | STRING | Residue ranges to mask specifically for helix secondary structure. | 10-20,30-40 |
| inpaint_str_strand | True | STRING | Residue ranges to mask specifically for beta strand secondary structure. | 50-60,70-80 |
| inpaint_str_loop | True | STRING | Residue ranges to mask specifically for loop secondary structure. | 25-29,65-69 |
| provide_seq | True | STRING | Residue ranges to unmask (i.e., keep fixed/provided sequence) during design. Use inclusive ranges; multiple ranges can be comma-separated. | 172-177,200-205 |
| length | True | STRING | Desired total sequence length or length range for unconditional generation. | 100 or 100-150 |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| contigmap_config | JSON | Validated contigmap configuration object to pass into the RF Diffusion node. | {"inpaint_seq": [["A",10,25],["B",5,12]], "inpaint_str": [["B",165,178]], "inpaint_str_helix": [[10,20],[30,40]], "inpaint_str_strand": [[50,60],[70,80]], "inpaint_str_loop": [[25,29],[65,69]], "provide_seq": [[172,177],[200,205]], "length": [100,150]} |
Important Notes¶
- Unconditional runs: Only set length; all other inpainting fields should be empty. The RF Diffusion node enforces this and will error if other fields are provided.
- Conditional/inpainting runs: Provide proper chain-labeled ranges (e.g., A10-25) that align with your input structure.
- Format validation: All fields except length are validated as contig/range lists; length is validated as a single length or a numeric range.
- Index consistency: Ranges must correspond to actual residues in your input PDB when used with conditional or partial diffusion workflows.
- Secondary structure masks: The helix/strand/loop masking fields target specific secondary structure classes and are optional.
Troubleshooting¶
- Invalid range format: Ensure ranges use inclusive numeric spans with optional chain IDs (e.g., A10-25, 50-60). Separate multiple ranges with commas.
- Error during unconditional generation: If you see errors about unexpected fields, clear inpaint_* and provide_seq, and only specify length.
- Misaligned indices: If diffusion fails or results look incorrect, verify that the provided ranges match residues and chain IDs in the input PDB.
- Empty configuration not applied: Leave fields blank (empty string) rather than placeholders; the node interprets empty as None.
- Unexpected behavior with secondary structure masks: Confirm the ranges target the intended regions and avoid overlaps that contradict provide_seq.