{
"fields": [
{
"name": "job_name",
"label": "Job name",
"kind": "text",
"default": "opendde-job",
"required": false,
"help": "Names the single OpenDDE job generated from these parameters.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 80,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters"
},
{
"name": "sequence_molecules",
"label": "Molecules",
"kind": "molecule_builder",
"default": "[{\"type\": \"protein\", \"id\": \"A\", \"count\": 1, \"sequence\": \"ACDEFGHIKLMNPQRSTVWY\", \"modifications\": []}]",
"required": true,
"help": "Add one box per unique OpenDDE entity. Set count and an optional matching list of comma-separated IDs, plus the sequence/ligand/ion, type-specific modifications, and optional MSA or template paths.",
"options": [
{
"value": "protein",
"label": "Protein"
},
{
"value": "ligand",
"label": "Ligand"
},
{
"value": "dna",
"label": "DNA"
},
{
"value": "rna",
"label": "RNA"
},
{
"value": "ion",
"label": "Ion"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters",
"molecule_features": "id,count,modifications,protein_paired_msa,protein_unpaired_msa,protein_templates,rna_unpaired_msa"
},
{
"name": "covalent_bonds",
"label": "Covalent bonds (JSON, optional)",
"kind": "textarea",
"default": "",
"required": false,
"help": "Native OpenDDE covalent_bonds array. Entity references are 1-based sequence indexes; copy references are 1-based within count.",
"options": [],
"rows": 6,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 500000,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters"
},
{
"name": "input_json",
"label": "OpenDDE inference jobs (JSON)",
"kind": "textarea",
"default": "[\n {\n \"name\": \"opendde-demo\",\n \"modelSeeds\": [101],\n \"sequences\": [\n {\n \"proteinChain\": {\n \"sequence\": \"ACDEFGHIKLMNPQRSTVWY\",\n \"count\": 1,\n \"id\": [\"A\"]\n }\n }\n ]\n }\n]",
"required": true,
"help": "Complete native OpenDDE input: a non-empty top-level list of named jobs using proteinChain, dnaSequence, rnaSequence, ligand, or ion entities.",
"options": [],
"rows": 18,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 1000000,
"accept": "",
"task": "",
"group": "Input",
"help_note": "Bio Web writes this text to input.json. Any MSA, template, or ligand-file paths inside it must be absolute paths available to the runner.",
"input_modes": "text"
},
{
"name": "inputs_file",
"label": "Inference jobs file (JSON)",
"kind": "file",
"default": "",
"required": false,
"help": "The JSON file defining this run's jobs, in OpenDDE's own input format.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": ".json",
"task": "",
"group": "Input",
"input_modes": "upload",
"help_note": "Choose a file. Its contents are read here and sent as the input document."
},
{
"name": "seeds",
"label": "Override model seeds (optional)",
"kind": "text",
"default": "",
"required": false,
"help": "Comma-separated integers. When set, --seeds overrides every job's modelSeeds; otherwise OpenDDE uses modelSeeds from the JSON or samples a random seed.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 200,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "samples",
"label": "Samples",
"kind": "number",
"default": 5,
"required": false,
"help": "Number of structure samples per seed. The OpenDDE CLI default is 5.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 64,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "steps",
"label": "Diffusion steps",
"kind": "number",
"default": 200,
"required": false,
"help": "Number of diffusion steps. The OpenDDE CLI default is 200.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 1000,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "cycles",
"label": "Pairformer cycles",
"kind": "number",
"default": 10,
"required": false,
"help": "Number of Pairformer recycling cycles. The OpenDDE CLI default is 10.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 100,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "dtype",
"label": "Inference precision",
"kind": "select",
"default": "fp32",
"required": false,
"help": "OpenDDE defaults to FP32; BF16 can reduce memory use on supported devices.",
"options": [
{
"value": "fp32",
"label": "FP32"
},
{
"value": "bf16",
"label": "BF16"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Runtime"
},
{
"name": "device",
"label": "Device",
"kind": "select",
"default": "auto",
"required": false,
"help": "Auto selects CUDA when available and otherwise CPU.",
"options": [
{
"value": "auto",
"label": "Auto"
},
{
"value": "cuda",
"label": "CUDA"
},
{
"value": "cpu",
"label": "CPU"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Runtime"
},
{
"name": "use_msa",
"label": "Use or generate protein MSAs",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Enable protein MSA features. This may run OpenDDE's external feature-search pipeline unless precomputed paths are supplied.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Optional features"
},
{
"name": "use_template",
"label": "Use protein templates",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Use template features referenced by templatesPath in the input JSON.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Optional features"
},
{
"name": "use_rna_msa",
"label": "Use RNA MSAs",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Use RNA MSA features referenced by rnaSequence.unpairedMsaPath. OpenDDE requires protein MSA processing to be enabled too.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Optional features"
},
{
"name": "use_guidance",
"label": "Use training-free guidance",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Apply OpenDDE's geometry-based Training-Free Guidance to protein-ligand sampling.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Optional features"
},
{
"name": "need_atom_confidence",
"label": "Write atom-level confidence data",
"kind": "checkbox",
"default": true,
"required": false,
"help": "Write OpenDDE's full per-atom confidence JSON in addition to summary confidence.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Output"
},
{
"name": "deterministic",
"label": "Deterministic PyTorch algorithms",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Ask OpenDDE to use deterministic PyTorch algorithms for reproducible inference.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Runtime"
}
],
"input_modes": {
"name": "input_mode",
"label": "Input mode",
"default": "parameters",
"options": [
{
"value": "parameters",
"label": "Set parameters here"
},
{
"value": "text",
"label": "Enter YAML or JSON"
},
{
"value": "upload",
"label": "Upload YAML or JSON"
}
]
},
"tasks": []
}