foundry/models/rfd3/docs/input.md

RFdiffusion3 — Input specification (dialect 2)

TL;DR
Inputs are now defined with a single InputSpecification class.
Selections like “what’s fixed?”, “what’s sequence-free?”, “which atoms are donors/acceptors?” are all expressed with the same InputSelection mini-language.
Everything is reproducibly logged back out alongside your generation.

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• What changed (high level)
• Quick start
• The InputSelection mini-language
• Full schema: InputSpecification
• Common recipes (cookbook)
• Partial diffusion
• Symmetry
• Origin (ori_token) and initialization
• Validation & error messages
• Metadata & logging
• Legacy configs (dialect=1) & migration guide
• Multi-example files
• FAQ / gotchas

---

What changed (high level)

• Unified selections. All per-residue/atom choices now use InputSelection:
  • You can pass true/false, a contig string ("A1-10,B5-8"), or a dictionary ({"A1-10": "ALL", "B5": "N,CA,C,O"}).
  • New selection fields include: select_fixed_atoms, select_unfixed_sequence, select_buried, select_partially_buried, select_exposed, select_hbond_donor, select_hbond_acceptor, select_hotspots.
• Clearer unindexing. For unindexed motifs you typically either fix "ALL" atoms or explicitly choose subsets such as "TIP"/"BKBN"/explicit atom lists via a dictionary (see examples).
  When using unindex, only the atoms you mark as fixed are carried over from the input.
• Reproducibility. The exact specification and the sampled contig are logged back into the output JSON. We also log useful counts (atoms, residues, chains).
• Safer parsing. You’ll now get early, informative errors if:
  • You pass unknown keys,
  • A selection doesn’t match any atoms,
  • Indexed and unindexed motifs overlap,
  • Mutually exclusive selections overlap (e.g., two RASA bins for the same atom).
• Backwards compatible. Add "dialect": 1 to keep your old configs running while you migrate. (Deprecated.)

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InputSpecification

Field	Type	Description
input	str?	Path to input PDB/CIF. Required if you provide contig+length.
atom_array_input	internal	Pre-loaded AtomArray (not recommended).
contig	InputSelection?	Indexed motif specification, e.g., "A1-80,10,\0,B5-12".
unindex	InputSelection?	Unindexed motif components (unknown sequence placement).
length	str?	Total design length constraint; "min-max" or int.
ligand	str?	Ligand(s) by resname or index.
cif_parser_args	dict?	Optional args to CIF loader.
extra	dict	Extra metadata (e.g., logs).
dialect	int	2=new (default), 1=legacy.
select_fixed_atoms	InputSelection?	Atoms with fixed coordinates.
select_unfixed_sequence	InputSelection?	Where sequence can change.
select_buried / select_partially_buried / select_exposed	InputSelection?	RASA bins 0/1/2 (mutually exclusive).
select_hbond_donor / select_hbond_acceptor	InputSelection?	Atom-wise donor/acceptor flags.
select_hotspots	InputSelection?	Atom-level or token-level hotspots.
redesign_motif_sidechains	bool	Fixed backbone, redesigned sidechains for motifs.
symmetry	SymmetryConfig?	See docs/symmetry.md.
ori_token	list[float]?	[x,y,z] origin override to control COM placement
infer_ori_strategy	str?	"com" or "hotspots".
plddt_enhanced	bool	Default true.
is_non_loopy	bool	Default true.
partial_t	float?	Noise (Å) for partial diffusion, enables partial diffusion

Quick start

Minimal JSON example

{
    "": {
    "input": "path/to/template.pdb",
    "contig": "A1-80",
    "length": "150-180",
    "select_fixed_atoms": true,
    "select_unfixed_sequence": "A20-35",
    "ligand": "HAX,OAA",
    "dialect": 2
    }   
}

Mininmal YAML example

input: path/to/template.pdb
contig: A1-80
length: 150-180
select_fixed_atoms: true
select_unfixed_sequence: A20-35
ligand: HAX,OAA
dialect: 2

Python API

from projects.aa_design.inference.input_parsing import create_atom_array_from_design_specification

atom_array, metadata = create_atom_array_from_design_specification(
    input="path/to/template.pdb",
    contig="A1-80",
    length="150-180",
    select_fixed_atoms=True,
    select_unfixed_sequence="A20-35",
    dialect=2,
)

Demo examples

Enzyme

TODO

Symmetry

TODO. See symmetry.md for more details

Partial diffusion

TODO

Binder design

TODO

The InputSelection mini-language

Fields which are specified as InputSelection are fields which can take either: Bool, List, Dict. Dictionaries are the most expressive and can also take special :

select_fixed_atoms:
  A1-2: BKBN
  A3: N,CA,C,O,CB  # specific atoms by atom name
  B5-7: ALL # Selects all atoms within B5,B6 and B7
  B10: TIP  # selects common tipatom for residue (constants.py)
  LIG: ''  # selects no atoms (i.e. unfixes the atoms for ligands named `LIG`)

[Diagram]

Unindexing specifics

unindex marks motif tokens whose relative sequence placement is unknown to the model (useful for scaffolding around active sites, etc.). Use a string to list the unindexed components and where breaks occur. Use a dictionary if you want to fix specific atoms of those residues; atoms not fixed are not copied from the input (they will be diffused). Breaks between unindexed components follow the contig conventions you’re used to. For example:

"A244,A274,A320,A329,A375"

lists multiple unindexed components; internal “breakpoints” are inferred and logged. (Offset syntax like A11-12 or A11,0,A12 still ties residues.)

Appendix

FAQ / gotchas

Q: Do I need select_fixed_atoms & select_unfixed_sequence every time? A: No. Defaults apply when input present.

Q: What does "ALL" vs "TIP" in unindex mean? A: "ALL" → copy full residue; "TIP" → fix only sidechain tip atoms.

Q: Can selections overlap? A: Only certain ones (fixed vs unfixed) may; RASA & donor/acceptor cannot.

Q: How to fix backbone but redesign sidechains? A: redesign_motif_sidechains: true.

Q: Why “Input provided but unused”? A: You gave input but no contig, unindex, or partial_t.

Shorthand atoms

Keyword Expands to BKBN N, CA, C, O TIP Residue-specific “tip” atoms ALL All atoms of each residue