Inference JSON Format

OpenDDE input is a JSON file whose top-level value is a non-empty list of jobs. It uses AlphaFold Server-style entity keys (proteinChain, dnaSequence, rnaSequence, ligand, ion), not the single-job alphafold3 dialect.

Minimal job:

[
  {
    "name": "example_job",
    "modelSeeds": [101],
    "sequences": [
      {
        "proteinChain": {
          "sequence": "ACDEFGHIKLMNPQRSTVWY",
          "count": 1
        }
      }
    ]
  }
]

covalent_bonds is optional and is omitted here; see the section below for when to add it.

Job fields:

Field	Required	Meaning
`name`	Yes	Job name used in output paths.
`sequences`	Yes	List of entities. Each item has exactly one entity key.
`modelSeeds`	No	Default seeds for the job. Overridden by `--seeds`; if neither is set, a random seed is sampled.
`covalent_bonds`	No	Explicit covalent links between entities.

Every entity has count. Optional id is a list of chain IDs; its length must match count.

`proteinChain`

{
  "proteinChain": {
    "sequence": "ACDEFGHIKLMNPQRSTVWY",
    "count": 1,
    "id": ["A"],
    "modifications": [
      {"ptmType": "CCD_MSE", "ptmPosition": 1}
    ],
    "pairedMsaPath": "/absolute/path/to/pairing.a3m",
    "unpairedMsaPath": "/absolute/path/to/non_pairing.a3m",
    "templatesPath": "/absolute/path/to/hmmsearch.a3m"
  }
}

sequence: 20 standard amino-acid letters plus X.
ptmType: CCD code prefixed with CCD_; ptmPosition is 1-based.
pairedMsaPath, unpairedMsaPath: optional protein A3M files.
templatesPath: optional template hits file (.a3m or .hhr), used only with --use_template true.

`dnaSequence`

{
  "dnaSequence": {
    "sequence": "GATTACA",
    "count": 1,
    "id": ["D"],
    "modifications": [
      {"modificationType": "CCD_6MA", "basePosition": 2}
    ]
  }
}

Supported documented letters: A, T, G, C, N, X.
DNA is single-stranded; add another dnaSequence for the other strand.
basePosition is 1-based.

`rnaSequence`

{
  "rnaSequence": {
    "sequence": "GUAC",
    "count": 1,
    "id": ["R"],
    "modifications": [
      {"modificationType": "CCD_5MC", "basePosition": 4}
    ],
    "unpairedMsaPath": "/absolute/path/to/rna_msa.a3m"
  }
}

Supported documented letters: A, U, G, C, N, X.
unpairedMsaPath is optional and used only with --use_rna_msa true.

`ligand`

{
  "ligand": {
    "ligand": "CCD_ATP",
    "count": 1,
    "id": ["L"]
  }
}

ligand can be:

A CCD code prefixed with CCD_, e.g. CCD_ATP.
Multiple CCD codes joined by underscores, e.g. CCD_NAG_BMA_BGC.
A 3D ligand file prefixed with FILE_ (.pdb, .sdf, .mol, .mol2).
A SMILES string.

`ion`

{
  "ion": {
    "ion": "MG",
    "count": 2,
    "id": ["M", "N"]
  }
}

Ion codes are CCD component names without the CCD_ prefix.

`covalent_bonds`

"covalent_bonds": [
  {
    "entity1": "1",
    "copy1": 1,
    "position1": "2",
    "atom1": "SG",
    "entity2": "2",
    "copy2": 1,
    "position2": "1",
    "atom2": "C1"
  }
]

Fields:

entity1, entity2: 1-based indices in sequences.
copy1, copy2: optional 1-based copy indices.
position1, position2: 1-based residue/ligand-part positions.
atom1, atom2: atom names. Integer references are also accepted for mapped SMILES or file ligands.

Use entity1/entity2 for new inputs. The old left_entity/right_entity style is accepted for compatibility.

Unsupported `constraint`

The inference-only build ignores legacy constraint fields. Use covalent_bonds for supported covalent links.

Output layout

opendde pred writes:

<out_dir>/<job_name>/seed_<seed>/predictions/
├── <job_name>_sample_<rank>.cif
├── <job_name>_summary_confidence_sample_<rank>.json
└── <job_name>_full_data_sample_<rank>.json   # only when --need_atom_confidence true

The summary JSON includes confidence metrics such as plddt, gpde, ptm, iptm, clash flags, and ranking_score when available.

Inference JSON Format

proteinChain

dnaSequence

rnaSequence

ligand

ion

covalent_bonds

Unsupported constraint