rfdiffusion.yaml

# RFdiffusion Model Configuration
# Backbone generation via diffusion

id: rfdiffusion
name: RFdiffusion (Foundry)
version: "1.1.0"
category: backbone_generation
description: >
  Diffusion-based protein backbone generation. Supports de novo design,
  fold conditioning, motif scaffolding, and partial diffusion modes for
  both monomers and binders.
container: dl_binder_design.sif

ui_icon: wand-magic-sparkles
ui_color: "#8B5CF6"

inputs:
  - pdb
outputs:
  - pdb
  - json

modes:
  - id: binder_denovo
    name: Binder De Novo
    description: Design a novel binder to a target protein (e.g., Antibody design, Viral inhibition)
    params:
      - rfd_input_pdb
      - rfd_contigs
      - rfd_hotspots
      - rfd_num_designs
      - seqs_per_design

  - id: binder_foldcond
    name: Binder Fold-Conditioned
    description: Design a binder with secondary structure constraints from scaffolds
    params:
      - rfd_input_pdb
      - rfd_contigs
      - rfd_scaffold_dir
      - rfd_num_designs
      - seqs_per_design

  - id: binder_motifscaff
    name: Binder Motif Scaffolding
    description: Scaffold a binding motif onto a new protein
    params:
      - rfd_input_pdb
      - rfd_contigs
      - rfd_length
      - rfd_num_designs
      - seqs_per_design

  - id: binder_partialdiff
    name: Binder Partial Diffusion
    description: Partially diffuse and redesign regions of an existing binder
    params:
      - rfd_input_pdb
      - rfd_contigs
      - rfd_inpaint_seq
      - rfd_partial_diffusion_timesteps
      - rfd_num_designs
      - seqs_per_design

  - id: monomer_denovo
    name: Monomer De Novo
    description: Design a novel protein monomer from scratch
    params:
      - rfd_contigs
      - rfd_num_designs
      - seqs_per_design

  - id: monomer_foldcond
    name: Monomer Fold-Conditioned
    description: Design a monomer with secondary structure constraints
    params:
      - rfd_contigs
      - rfd_target_ss
      - rfd_target_adj
      - rfd_num_designs
      - seqs_per_design

  - id: monomer_motifscaff
    name: Monomer Motif Scaffolding
    description: Scaffold a functional motif into a new protein
    params:
      - rfd_input_pdb
      - rfd_contigs
      - rfd_length
      - rfd_num_designs
      - seqs_per_design

  - id: monomer_partialdiff
    name: Monomer Partial Diffusion
    description: Partially diffuse and redesign regions of an existing protein
    params:
      - rfd_input_pdb
      - rfd_contigs
      - rfd_inpaint_seq
      - rfd_partial_diffusion_timesteps
      - rfd_num_designs
      - seqs_per_design

params:
  # Essential parameters
  - name: rfd_num_designs
    type: integer
    description: Number of backbone designs to generate
    required: true
    default: 8
    minimum: 1
    maximum: 1000

  - name: seqs_per_design
    type: integer
    description: Number of sequences to design per backbone
    required: true
    default: 8
    minimum: 1
    maximum: 100

  - name: rfd_input_pdb
    type: file
    description: Input PDB file (target for binders, template for modifications)
    required: false
    file_type: pdb
    preset_type: pdb
    pattern: \".*\\.pdb$\"

  - name: rfd_contigs
    type: string
    description: >
      Contig specification defining chain lengths and fixed regions.
      Example: '[A17-145/0 50-100]' means keep residues 17-145 of chain A,
      add a chainbreak, then generate 50-100 new residues.
    required: false
    pattern: "^\\[[A-Z0-9\\-\\/ \\[\\]]+\\]$"

  - name: rfd_hotspots
    type: string
    description: >
      Hotspot residues to bias binding toward. Format: '[A56,A115,A123]'
    required: false
    pattern: "^\\[[A-Z]\\d+(,[A-Z]\\d+)*\\]$"

  - name: rfd_scaffold_dir
    type: directory
    description: Directory containing scaffold PDB files for fold conditioning
    required: false

  - name: rfd_length
    type: string
    description: Length range for generated chain (e.g., '100-120')
    required: false
    pattern: "^\\d+-\\d+$"

  - name: rfd_inpaint_seq
    type: string
    description: Residues to mask for sequence inpainting
    required: false

  - name: rfd_partial_diffusion_timesteps
    type: integer
    description: Number of diffusion timesteps (higher = more change)
    required: false
    default: 20
    minimum: 1
    maximum: 200

  # Advanced parameters
  - name: rfd_ckpt_override
    type: string
    description: Override the model checkpoint for specialized tasks
    required: false
    enum:
      - active_site
      - base
      - base_epoch8
      - complex_base
      - complex_beta
      - complex_fold_base
      - inpaint_seq
      - inpaint_seq_fold

  - name: rfd_noise_scale
    type: number
    description: Noise scale (0=conservative, 1=diverse). Lower for binders.
    required: false
    minimum: 0
    maximum: 1

  - name: rfd_mask_loops
    type: boolean
    description: Ignore loop regions when applying scaffold constraints
    required: false
    default: true

  - name: rfd_extra_config
    type: string
    description: "Additional RFdiffusion config (e.g., 'contigmap.inpaint_str=[B165-178]')"
    required: false

enabled: true
experimental: false