Forge Tools pdb_lookup

pdb_lookup read

scidex.forge.pdb_lookup

Fetch RCSB PDB metadata for a 4-character PDB ID. Returns the deposition title, experimental method, resolution, deposit and release year, author chain identifiers, deposition authors, and the canonical structure-file + viewer URLs.

HTTP: POST /api/scidex/forge/pdb_lookup

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.pdb_lookup``.",
  "properties": {
    "pdb_id": {
      "description": "Four-character PDB ID (e.g. ``1TUP`` for tumor-suppressor p53). Case-insensitive on input; the verb normalizes to upper-case before the upstream call. Must be alphanumeric.",
      "maxLength": 4,
      "minLength": 4,
      "title": "Pdb Id",
      "type": "string"
    }
  },
  "required": [
    "pdb_id"
  ],
  "title": "PdbLookupIn",
  "type": "object"
}
Output schema 
{
  "description": "Response shape for ``scidex.forge.pdb_lookup``.",
  "properties": {
    "pdb_id": {
      "title": "Pdb Id",
      "type": "string"
    },
    "title": {
      "default": "",
      "description": "Free-text deposition title.",
      "title": "Title",
      "type": "string"
    },
    "method": {
      "default": "",
      "description": "Primary experimental method (``X-RAY DIFFRACTION``, ``SOLUTION NMR``, ``ELECTRON MICROSCOPY``, etc.).",
      "title": "Method",
      "type": "string"
    },
    "resolution": {
      "anyOf": [
        {
          "type": "number"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Resolution in Ångströms; ``None`` for NMR.",
      "title": "Resolution"
    },
    "deposit_year": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Year of deposition (parsed from ``deposit_date``).",
      "title": "Deposit Year"
    },
    "release_year": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Year of initial public release.",
      "title": "Release Year"
    },
    "chains": {
      "description": "Sorted, de-duplicated author chain identifiers across all polymer entities, e.g. ``['A', 'B', 'C']``.",
      "items": {
        "type": "string"
      },
      "title": "Chains",
      "type": "array"
    },
    "authors": {
      "description": "Deposition authors in order.",
      "items": {
        "type": "string"
      },
      "title": "Authors",
      "type": "array"
    },
    "structure_url": {
      "default": "",
      "description": "Direct PDB-format coordinate file URL.",
      "title": "Structure Url",
      "type": "string"
    },
    "viewer_url": {
      "default": "",
      "description": "RCSB 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": [
    "pdb_id",
    "took_ms"
  ],
  "title": "PdbLookupOut",
  "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/pdb_lookup' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "pdb_id": ""
}'

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