ImmunoGraph MCP

extract_interactions

Read-onlyIdempotent

Identifies computed protein-ligand contacts by running PLIP on a supplied complex PDB or replaying a fixture, useful after docking pose export for structured interaction analysis.

Instructions

Run PLIP on a supplied protein-ligand complex PDB to identify computed contact geometry, or replay an exact fixture. Use after run_docking when a representative pose has been exported; this does not experimentally measure binding. Live mode requires PLIP and returns structured contacts plus the original XML artifact.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`method`	Yes	Algorithm or provider method selected for this operation; inspect allowed schema values.
`dockingRunId`	Yes	Identifier of the docking run whose poses or complex are analyzed.
`complexPdbBase64`	No	Base64-encoded protein-ligand complex PDB bytes from a representative pose.
`representativePoseIds`	Yes	Pose IDs whose complex should be examined for contacts.

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 / complexPdbBase64 / description

Added value: +"Base64-encoded protein-ligand complex PDB bytes from a representative pose."

addedInput schema / properties / dockingRunId / description

Added value: +"Identifier of the docking run whose poses or complex are analyzed."

addedInput schema / properties / method / description

Added value: +"Algorithm or provider method selected for this operation; inspect allowed schema values."

addedInput schema / properties / representativePoseIds / description

Added value: +"Pose IDs whose complex should be examined for contacts."

addedInput schema / properties / runId / description

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

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

A3.8/5.0

Behavior4/5

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

Annotations already establish readOnlyHint and idempotentHint, so the safety profile is covered. The description adds genuinely non-structured context: live mode has an external dependency on PLIP, and the call returns structured contacts plus the original XML artifact. It does not say what happens when PLIP is unavailable, which would be the remaining behavioral gap.

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

Conciseness4/5

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

Two sentences, front-loaded with the verb and engine, with no filler. The final clause is packed with three distinct facts (dependency, return shape, artifact) but each is load-bearing.

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

Completeness3/5

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

Output schema covers return values and annotations cover safety, and the description supplies the upstream sequencing and the PLIP dependency. However, with 4 required parameters and a required `method` whose accepted values are enumerated nowhere, the definition is not quite sufficient for an agent to invoke it without further guessing.

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 the parameter meanings are already documented, which sets the baseline at 3. The description hints that `method` selects live-vs-fixture execution and that `complexPdbBase64` comes from a representative pose, but since `method` has no enum values and the schema only says 'inspect allowed schema values', the agent still cannot determine valid values from either source.

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?

Names a specific engine (PLIP) and a specific resource (protein-ligand complex PDB contacts), and distinguishes the live computation path from a fixture-replay path. It is clearly not any of the docking, pocket-detection, or scoring siblings, though the brief 'or replay an exact fixture' clause leaves the second mode somewhat under-defined.

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 after run_docking when a representative pose has been exported' gives an explicit ordering constraint and precondition, and 'this does not experimentally measure binding' rules out a misuse (citing it as empirical evidence). It does not name an alternative sibling (e.g. detect_binding_pockets) for the case where no complex PDB exists yet, so it stops short of full when/when-not guidance.

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

Deploy Server