RF Diffusion Scaffold Guided Config

Builds a configuration object for scaffold-guided and fold-conditioned protein design. It lets you enable scaffold-guided mode, optionally condition on a target protein (binder design), and specify directories and files for secondary structure and adjacency guidance.

Usage

Use this node to prepare the scaffold-guided/fold-conditioning settings and connect its output to the 'scaffoldguided_config' input of the RF Diffusion node. Typical workflows: enabling scaffold-guided design with a scaffold directory, performing binder design by providing a target PDB (plus optional secondary-structure and adjacency files), or cropping specific residues from a scaffold to use as a starting template.

Inputs

Field	Required	Type	Description	Example
scaffoldguided	True	BOOLEAN	Enable scaffold-guided mode. When true, the model expects secondary structure guidance for the designed backbone.	True
target_pdb	True	BOOLEAN	Set true if conditioning on a target protein structure (binder/protein–protein interaction design). Requires a valid target_path.	True
target_path	True	STRING	Filesystem path to the target protein PDB file. Required when target_pdb is true.	/data/targets/1XYZ_target.pdb
scaffold_dir	True	STRING	Directory containing secondary structure (.pt) and block adjacency (.pt) files used for guided scaffolding.	/data/scaffolds/my_project_guidance/
sampled_insertion	False	INT	Max residues to insert into loops during inference. Only applied if > 0.	5
sampled_N	False	INT	Max additional residues to sample at the N-terminus. Only applied if > 0.	3
sampled_C	False	INT	Max additional residues to sample at the C-terminus. Only applied if > 0.	7
target_ss	False	STRING	Path to a secondary structure .pt file for the target protein. Optional; used with target_pdb.	/data/targets/1XYZ_target_ss.pt
target_adj	False	STRING	Path to an adjacency .pt file for the target protein. Optional; used with target_pdb.	/data/targets/1XYZ_target_adj.pt
scaffold_list	False	STRING	Path to a .txt file listing a subset of scaffold guidance files to use (when many are available).	/data/scaffolds/selection.txt
ss_mask	False	INT	Number of residues to mask at the end of a secondary structure block. Only applied if > 0.	2
systematic	False	BOOLEAN	If true, scaffolds are iterated systematically rather than randomly sampled.	False
mask_loops	False	BOOLEAN	Whether to mask loops. Set to false for protein–protein interaction design; when true, extra residues may be added without precise secondary structure.	True
contig_crop	False	STRING	Residue/chain selection to crop from a scaffold PDB as the starting template, using contig-like notation (e.g., 'A10-50', possibly multiple segments/chains).	A10-50/0 B1-25

Outputs

Field	Type	Description	Example
scaffoldguided_config	JSON	Configuration dictionary to plug into the RF Diffusion node's scaffold-guided/fold conditioning input.	{'scaffoldguided': True, 'target_pdb': True, 'target_path': '/data/targets/1XYZ_target.pdb', 'scaffold_dir': '/data/scaffolds/my_project_guidance/', 'sampled_insertion': 5, 'sampled_N': 3, 'mask_loops': False, 'contig_crop': [['A', 10, 50], ['/0'], ['B', 1, 25]]}

Important Notes

• Target conditioning: If target_pdb is true, target_path must be a non-empty valid path or the node will raise an error.
• Optional fields apply conditionally: sampled_insertion, sampled_N, sampled_C, and ss_mask are only included if their values are greater than 0. systematic is included only when true; mask_loops is included only when set to false (since true is the default).
• Scaffold directory: scaffold_dir should contain compatible .pt files (secondary structure and adjacency) produced by appropriate preprocessing tools.
• Contig cropping: contig_crop must follow valid contig-like syntax (e.g., A10-50). Invalid formats will be rejected.
• This node only configures: It does not perform generation; connect its output to the RF Diffusion node's scaffoldguided_config input.

Troubleshooting

• Error: 'target_path is required when target_pdb is True': Provide a valid path in target_path or set target_pdb to false.
• Invalid contig_crop format: Use chain-letter and inclusive index ranges like 'A10-50' and separate segments/chains appropriately. Correct the string and try again.
• No effect from sampled_* or ss_mask: These parameters are only included when > 0. Increase from 0 to activate.
• Unexpected behavior in PPI design: For protein–protein interactions, set mask_loops to false as recommended.
• Missing guidance files: Ensure scaffold_dir exists and contains the expected .pt files; if conditioning on a target, verify target_ss/target_adj paths if you intend to use them.