Forge Tools alphafold_structure

alphafold_structure read

scidex.forge.alphafold_structure

Fetch the AlphaFold DB prediction record for a UniProt accession. Returns structure-file URLs, mean pLDDT confidence, sequence length, model version, and a viewer link.

HTTP: POST /api/scidex/forge/alphafold_structure

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.alphafold_structure``.",
  "properties": {
    "uniprot_id": {
      "description": "UniProt accession (canonical form, e.g. ``P02649`` for APOE). Upper-case alphanumerics, 6–10 characters. Gene symbols are not accepted at this verb; use a future ``scidex.forge.uniprot_lookup`` to resolve them first.",
      "maxLength": 10,
      "minLength": 6,
      "title": "Uniprot Id",
      "type": "string"
    }
  },
  "required": [
    "uniprot_id"
  ],
  "title": "AlphafoldStructureIn",
  "type": "object"
}
Output schema 
{
  "description": "Response shape for ``scidex.forge.alphafold_structure``.",
  "properties": {
    "uniprot_id": {
      "title": "Uniprot Id",
      "type": "string"
    },
    "pdb_url": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Direct download URL for the predicted PDB file.",
      "title": "Pdb Url"
    },
    "cif_url": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Direct download URL for the predicted mmCIF file.",
      "title": "Cif Url"
    },
    "plddt_url": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "URL for the per-residue pLDDT track (JSON / PNG).",
      "title": "Plddt Url"
    },
    "mean_plddt": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Mean pLDDT across the structure (0..100).",
      "title": "Mean Plddt"
    },
    "sequence_length": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Number of residues in the predicted sequence.",
      "title": "Sequence Length"
    },
    "model_version": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "AlphaFold DB ``latestVersion`` string for the entry.",
      "title": "Model Version"
    },
    "viewer_url": {
      "default": "",
      "description": "AlphaFold 3D viewer URL for human inspection.",
      "title": "Viewer Url",
      "type": "string"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream call.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "uniprot_id",
    "took_ms"
  ],
  "title": "AlphafoldStructureOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/alphafold_structure' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "uniprot_id": ""
}'

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