ImmunoGraph MCP

prepare_receptor

Read-onlyIdempotent

Converts selected protein PDB chains into receptor PDBQT with Meeko for docking, or returns a fixture reference; use before run_docking since validation does not prepare charges.

Instructions

Convert supplied protein PDB coordinates and selected chains into receptor PDBQT with Meeko, or return an exact fixture reference. Use before run_docking for the receptor; validate_structure checks coordinates but does not prepare charges or PDBQT. Live preparation requires the Meeko runtime and returns artifact bytes.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`chainIds`	Yes	Protein chain identifiers selected from the supplied structure.
`structureId`	Yes	Stable identifier of the supplied or retrieved structure.
`preparationMethod`	Yes	Preparation backend, such as configured Meeko or exact fixture mode.
`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.

Changed6 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 / preparationMethod / description

Added value: +"Preparation backend, such as configured Meeko or exact fixture mode."

addedInput schema / properties / runId / description

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

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

A4.4/5.0

Behavior4/5

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

Annotations already declare readOnlyHint and idempotentHint, so the safety profile is covered; the description then adds genuinely new context: a runtime dependency on Meeko for live preparation, and that the live path returns artifact bytes while the fixture path returns a reference. It does not spell out failure behavior if Meeko is unavailable, which keeps it below a 5.

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 doing distinct work: what it produces, when to call it relative to run_docking/validate_structure, and the runtime/output constraint. The primary operation is front-loaded with no filler.

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?

For a preparation tool with full schema coverage, annotations, and an output schema, the description supplies the pipeline ordering and the runtime dependency that structured fields cannot express. The dual output form (artifact bytes vs fixture reference) is only lightly explained, leaving a small residual gap.

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 (including structurePdbBase64 and chainIds) are documented in the schema itself. The description adds only thematic context — chains, coordinates, and the Meeko-vs-fixture backend — rather than per-parameter semantics, so the baseline 3 applies.

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

Purpose5/5

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

States a specific verb and transformation: convert protein PDB coordinates plus selected chains into receptor PDBQT via Meeko, with an explicit alternate mode (exact fixture reference). It distinguishes itself from validate_structure by naming what that sibling does not do (charges, PDBQT), so an agent can place it precisely in the pipeline.

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

Usage Guidelines5/5

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

"Use before run_docking for the receptor" gives explicit ordering, and "validate_structure checks coordinates but does not prepare charges or PDBQT" names the near-miss alternative and why it is insufficient. The only minor inference left is choosing fixture mode vs live mode, but the preparationMethod parameter and the 'live requires Meeko runtime' note point at that distinction.

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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