RF Diffusion Potentials Config¶
Builds a configuration object for guiding potentials used by the RF Diffusion node. It parses a semicolon-separated set of potential definitions, applies global scaling/decay settings, and optionally configures oligomer contact behaviors and a target substrate ligand. Empty or missing fields are normalized so downstream nodes receive a clean, consistent config.
Usage¶
Use this node to define and bundle all potential-related controls for an RF Diffusion run. Typically, you will: (1) specify one or more guiding potentials, (2) set guide scale and decay behavior, (3) configure oligomer-wide contact preferences or custom contacts, and (4) optionally target a ligand residue as a substrate. Connect the resulting potentials_config output into the RF Diffusion node alongside other configs (e.g., symmetry, contigmap, denoiser).
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| guiding_potentials | True | STRING | Semicolon-separated list of potentials. Each potential is defined as key:value pairs separated by commas. Required key: type. Other keys are potential-specific (e.g., weight, r_0, d_0). Supported examples include monomer_ROG, binder_ROG, dimer_ROG, binder_ncontacts, interface_ncontacts, monomer_contacts, olig_contacts, substrate_contacts. If left empty, no potentials are applied. | type:monomer_ROG,weight:1,min_dist:15;type:olig_contacts,weight_intra:1,weight_inter:0.1 |
| guide_scale | True | INT | Global scale factor applied to guiding potentials. | 10 |
| guide_decay | True | STRING | Decay schedule for applying guiding potentials over steps. Allowed values: constant, linear, quadratic, cubic. | constant |
| olig_inter_all | True | BOOLEAN | If true, applies contact potential to all off-diagonal (inter-chain) pairs in an oligomer. | false |
| olig_intra_all | True | BOOLEAN | If true, applies contact potential to all on-diagonal (intra-chain) regions within an oligomer. | false |
| olig_custom_contact | True | STRING | Comma-separated custom contacts between chain pairs. Use '!' for repulsive and '&' for attractive interactions. Leave empty if not used. | A!B,B&C |
| substrate | True | STRING | Ligand residue name in the input PDB to target with substrate-based potentials. Must exist as a ligand (HETATM). Leave empty to disable. | LLK |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| potentials_config | JSON | Configuration dictionary to pass into the RF Diffusion node that contains guiding potentials, scaling/decay, oligomer contact options, and optional substrate targeting. | {"guiding_potentials": ["type:monomer_ROG,weight:1,min_dist:15"], "guide_scale": 10, "guide_decay": "constant", "olig_inter_all": false, "olig_intra_all": false, "olig_custom_contact": "A!B", "substrate": "LLK"} |
Important Notes¶
- Guiding potentials format: Use semicolons to separate potentials and commas to separate key:value pairs within a potential. At minimum, include 'type:...' for each potential.
- Normalization: If guiding_potentials is empty, it is treated as None; if olig_custom_contact or substrate are empty strings, they are also treated as None.
- Allowed decay values: guide_decay must be one of constant, linear, quadratic, cubic.
- Substrate requirement: The substrate residue must exist in the provided PDB as a ligand (HETATM). Examples: LLK, HEM, ATP.
- Oligomer contacts: olig_inter_all and olig_intra_all enable global inter-chain or intra-chain contacts; use olig_custom_contact to specify fine-grained contacts by chain IDs.
Troubleshooting¶
- Invalid guiding_potentials syntax: Ensure each potential follows 'type:...,arg1:val1,...' and potentials are separated by semicolons. Remove stray spaces or trailing separators.
- Unsupported potential type or arg: Verify 'type' and its arguments match supported potentials. Typos or unknown keys may cause downstream errors.
- Decay value rejected: Set guide_decay to one of: constant, linear, quadratic, cubic.
- No such substrate in PDB: Confirm the substrate residue name exists as a HETATM ligand in the input structure. If not, clear the substrate field or correct the residue code.
- Unexpected oligomer behavior: If contacts are too widespread or too sparse, review olig_inter_all/olig_intra_all flags and adjust or use olig_custom_contact to target specific chain pairs.
- Over-strong guidance: If designs collapse or diverge, try lowering guide_scale or using a softer guide_decay (e.g., linear) to reduce guidance intensity over steps.