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.