ImmunoGraph MCP

fetch_structure

Read-onlyIdempotent

Fetches PDB coordinates or AlphaFold models by known accession for coordinate-based analyses, with configurable live, cache, and fixture fallback.

Instructions

Retrieve PDB coordinates from RCSB or an AlphaFold model from the configured provider, or replay an exact fixture. Use when a structure accession is known and before coordinate-based analyses; this is not sequence prediction. LIVE_ONLY requires network access and returns source provenance plus coordinate artifact bytes.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`source`	Yes	Selected remote provider or exact fixture source.
`targetId`	Yes	Caller-chosen identifier for the target protein or structure.
`accession`	Yes	Provider accession, such as an RCSB PDB ID or AlphaFold accession, matching source.
`fallbackPolicy`	Yes	Allowed source order; LIVE_ONLY forbids cache and fixture substitution, FIXTURE_ONLY forbids live calls.

Output Schema

Name	Required	Description
`ok`	Yes	Whether execution completed successfully.
`data`	No	Tool-specific result fields on success.
`meta`	Yes	Run identifiers, timings, and input/output hashes.
`error`	No	Structured failure on unsuccessful execution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed6 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / accession / description

Added value: +"Provider accession, such as an RCSB PDB ID or AlphaFold accession, matching source."

addedInput schema / properties / fallbackPolicy / description

Added value: +"Allowed source order; LIVE_ONLY forbids cache and fixture substitution, FIXTURE_ONLY forbids live calls."

addedInput schema / properties / runId / description

Added value: +"Caller-chosen identifier linking this call to one research run."

addedInput schema / properties / source / description

Added value: +"Selected remote provider or exact fixture source."

addedInput schema / properties / targetId / description

Added value: +"Caller-chosen identifier for the target protein or structure."

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "additionalProperties": {},
+  "properties": {
+    "data": {
+      "additionalProperties": {},
+      "description": "Tool-specific result fields on success.",
+      "properties": {},
+      "type": "object"
+    },
+    "error": {
+      "additionalProperties": false,
+      "description": "Structured failure on unsuccessful execution.",
+      "properties": {
+        "category": {
+          "type": "string"
+        },
+        "code": {
+          "type": "string"
+        },
+        "details": {
+          "additionalProperties": {},
+          "properties": {},
+          "type": "object"
+        },
+        "message": {
+          "type": "string"
+        },
+        "retryable": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "code",
+        "category",
+        "message",
+        "retryable"
+      ],
+      "type": "object"
+    },
+    "meta": {
+      "additionalProperties": {},
+      "description": "Run identifiers, timings, and input/output hashes.",
+      "properties": {
+        "completedAt": {
+          "type": "string"
+        },
+        "durationMs": {
+          "type": "number"
+        },
+        "inputHash": {
+          "type": "string"
+        },
+        "outputHash": {
+          "type": "string"
+        },
+        "requestId": {
+          "type": "string"
+        },
+        "runId": {
+          "type": "string"
+        },
+        "startedAt": {
+          "type": "string"
+        },
+        "toolName": {
+          "type": "string"
+        },
+        "toolVersion": {
+          "type": "string"
+        }
+      },
+      "required": [
+        "requestId",
+        "runId",
+        "toolName",
+        "toolVersion",
+        "startedAt",
+        "inputHash"
+      ],
+      "type": "object"
+    },
+    "ok": {
+      "description": "Whether execution completed successfully.",
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "ok",
+    "meta"
+  ],
+  "type": "object"
+}

First observedv0.2.0Oct 31, 2026

TDQS

A4/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare read-only and idempotent behavior, and the description adds useful context that LIVE_ONLY requires network access. It also notes that results include source provenance and coordinate artifact bytes, though it does not elaborate on cache or fixture failure behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is three tight sentences with the main action and source options front-loaded. Every sentence contributes useful routing or behavioral context.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the output schema and complete parameter descriptions, the description supplies enough usage and behavior context to call the tool correctly. It does not fully explain the cache-oriented fallback policies, but the schema carries that detail.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so all five parameters are already well documented in the schema. The description reinforces source and accession concepts and mentions LIVE_ONLY network access, but adds limited meaning beyond the structured parameter definitions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource: retrieve PDB coordinates, AlphaFold models, or exact fixtures. It distinguishes the tool from sequence prediction, though it does not explicitly contrast with nearby siblings such as validate_structure.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It clearly says to use this when a structure accession is known and before coordinate-based analyses, and it excludes sequence prediction. It stops short of naming the alternative structure-related tools, but the context is strong.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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