ImmunoGraph MCP

validate_structure

Read-onlyIdempotent

Checks supplied structure metadata and parses PDB atoms, chains, and residues to catch mismatches before mapping, accessibility, or docking preparation.

Instructions

Check supplied structure metadata and, when PDB bytes are provided, parse actual atoms, chains, and residues. Use before mapping, accessibility, or docking preparation; this does not evaluate model confidence or binding. Mismatched metadata returns a structured failure.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`format`	Yes	Requested structure or export format, as enumerated by this tool.
`chainIds`	Yes	Protein chain identifiers selected from the supplied structure.
`structureId`	Yes	Stable identifier of the supplied or retrieved structure.
`residueCount`	Yes	Expected protein residue count for metadata consistency checks.
`sourceStatus`	Yes	Provenance label for the supplied structure or compound.
`structurePdbBase64`	No	Base64-encoded protein PDB coordinate bytes for direct computation.

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.

Changed8 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / chainIds / description

Added value: +"Protein chain identifiers selected from the supplied structure."

addedInput schema / properties / format / description

Added value: +"Requested structure or export format, as enumerated by this tool."

addedInput schema / properties / residueCount / description

Added value: +"Expected protein residue count for metadata consistency checks."

addedInput schema / properties / runId / description

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

addedInput schema / properties / sourceStatus / description

Added value: +"Provenance label for the supplied structure or compound."

addedInput schema / properties / structureId / description

Added value: +"Stable identifier of the supplied or retrieved structure."

addedInput schema / properties / structurePdbBase64 / description

Added value: +"Base64-encoded protein PDB coordinate bytes for direct computation."

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

A4.1/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint; the description adds value beyond them by disclosing the conditional parse path when structurePdbBase64 is supplied and the failure contract ('Mismatched metadata returns a structured failure'). It does not specify what exactly is compared or how format variants (PAE_JSON, FIXTURE_JSON) are handled.

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?

Three sentences, each earning its place: behavior first, placement/exclusions second, failure contract last. No filler and no repetition of the schema.

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?

With an output schema present and 100% parameter coverage, the description needn't explain returns; purpose, preconditions, conditional behavior, and failure mode are all covered. The remaining gap is that the mixed format enum (PDB vs MMCIF vs PAE_JSON vs FIXTURE_JSON) is never explained, leaving unclear what 'structure metadata' means for non-coordinate formats.

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

Parameters4/5

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

Schema coverage is 100%, so baseline would be 3, but the description adds real semantics for the optional PDB-bytes parameter (it triggers atom/chain/residue parsing) and frames residueCount/sourceStatus as consistency checks. It doesn't explain how validation differs across the four format enum values.

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?

Specific verb+resource: check structure metadata and, conditionally, parse atoms/chains/residues from PDB bytes. The resource (structure) is clearly distinct from siblings like validate_sequence and validate_compound, though it never names an alternative tool explicitly.

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?

'Use before mapping, accessibility, or docking preparation' pins the pipeline position against named sibling workflows, and 'does not evaluate model confidence or binding' carves out a scope boundary. No exclusion is expressed as a 'use X instead' routing, so it stops short of a full 5.

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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