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    Tools · Computational Biology

    OpenDDE

    Predict protein, nucleic acid, and small-molecule complex structures with OpenDDE
    On this page

    Prices, workflows, and method papersOpen in the app

    Run it from the API

    Submit with Submit a job and the job_type below. Price it first with Estimate job reservation cost: submitting reserves that amount from your wallet, and the charge settles at the actual runtime.

    OpenDDE opendde

    Job type
    opendde
    Hardware
    a10 (default)l40sa100-40gba100-80gbh100h200b200
    Typical runtime
    30 min on Nvidia A10

    Payload

    Shape 1: sequences
    FieldTypeDescription
    sequences[]requiredsequences

    Limits: min items 1

    covalent_bonds[]any[]
    modelSeeds[]integer[]
    job_namestring

    Limits: min length 1

    opendde_argsopendde_args
    opendde_args.model_variantstring

    Default: "opendde_v1"One of: "opendde_v1", "opendde_abag"

    opendde_args.seeds[]integer[] | null

    Limits: min items 1

    opendde_args.use_msaboolean

    Default: false

    opendde_args.use_templateboolean

    Default: false

    opendde_args.use_rna_msaboolean

    Default: false

    opendde_args.use_tfg_guidanceboolean

    Default: false

    opendde_args.sampleinteger

    Default: 1Limits: ≥ 1

    opendde_args.stepinteger

    Default: 200Limits: ≥ 1

    opendde_args.cycleinteger

    Default: 10Limits: ≥ 1

    opendde_args.dtypestring

    Default: "fp32"One of: "bf16", "fp16", "fp32"

    opendde_args.trimul_kernelstring

    Default: "auto"One of: "auto", "cuequivariance", "torch"

    opendde_args.triatt_kernelstring

    Default: "auto"One of: "auto", "cuequivariance", "torch"

    opendde_args.need_atom_confidenceboolean

    Default: false

    opendde_args.foldcp_modestring

    Default: "single"One of: "single", "distributed"

    opendde_args.foldcp_size_cpinteger

    Default: 1Limits: ≥ 1

    opendde_args.foldcp_size_dpinteger

    Default: 1Limits: ≥ 1

    opendde_args.foldcp_metrics_jsonlstring | null
    opendde_args.max_msa_seqsinteger

    Default: 8192Limits: ≥ 1

    opendde_args.num_subsampled_msainteger

    Default: 1024Limits: ≥ 1

    opendde_args.mmseqs_threadsinteger

    Default: 14Limits: ≥ 1

    Shape 2: opendde_input
    FieldTypeDescription
    opendde_input[]requiredobject[]

    Limits: min items 1

    opendde_input.namerequiredstring

    Limits: min length 1

    opendde_input.sequences[]requiredsequences

    Limits: min items 1

    opendde_input.modelSeeds[]integer[]
    opendde_input.covalent_bonds[]any[]
    opendde_argsopendde_args
    opendde_args.model_variantstring

    Default: "opendde_v1"One of: "opendde_v1", "opendde_abag"

    opendde_args.seeds[]integer[] | null

    Limits: min items 1

    opendde_args.use_msaboolean

    Default: false

    opendde_args.use_templateboolean

    Default: false

    opendde_args.use_rna_msaboolean

    Default: false

    opendde_args.use_tfg_guidanceboolean

    Default: false

    opendde_args.sampleinteger

    Default: 1Limits: ≥ 1

    opendde_args.stepinteger

    Default: 200Limits: ≥ 1

    opendde_args.cycleinteger

    Default: 10Limits: ≥ 1

    opendde_args.dtypestring

    Default: "fp32"One of: "bf16", "fp16", "fp32"

    opendde_args.trimul_kernelstring

    Default: "auto"One of: "auto", "cuequivariance", "torch"

    opendde_args.triatt_kernelstring

    Default: "auto"One of: "auto", "cuequivariance", "torch"

    opendde_args.need_atom_confidenceboolean

    Default: false

    opendde_args.foldcp_modestring

    Default: "single"One of: "single", "distributed"

    opendde_args.foldcp_size_cpinteger

    Default: 1Limits: ≥ 1

    opendde_args.foldcp_size_dpinteger

    Default: 1Limits: ≥ 1

    opendde_args.foldcp_metrics_jsonlstring | null
    opendde_args.max_msa_seqsinteger

    Default: 8192Limits: ≥ 1

    opendde_args.num_subsampled_msainteger

    Default: 1024Limits: ≥ 1

    opendde_args.mmseqs_threadsinteger

    Default: 14Limits: ≥ 1

    Example

    from cognichem_client import CogniChem
    
    client = CogniChem.from_env()  # reads COGNICHEM_API_KEY
    payload = {
        "sequences": [
            {
                "proteinChain": {"sequence": "ACDEFGHIK", "count": 1, "id": ["A"]},
            },
        ],
    }
    
    estimate = client.jobs.estimate(job_type="opendde", payload=payload, resource="a10")
    print(f"Reserves ${estimate.cost:.2f}")
    
    job = client.jobs.submit(
        job_name="my-opendde-run",
        job_type="opendde",
        payload=payload,
        resource="a10",
    )
    status = client.jobs.wait(job.process_id)
    if status.status == "completed":
        client.jobs.result(job.process_id, save_path=".")

    Sample data from the job catalog; long values are shortened here. Each job_name must be unique among your jobs.

    Workflow inputs

    None

    Workflow outputs

    • ArchiveZIP
    • StructuresPDB