ImmunoGraph MCP

calculate_molecular_descriptors

Read-onlyIdempotent

Calculates molecular descriptor values from a supplied SMILES using RDKit or a lightweight method, providing chemistry features after compound validation.

Instructions

Calculate molecular descriptor values for a supplied SMILES using the selected RDKit or lightweight method. Use after validate_compound for chemistry features; this does not predict binding or prepare 3D ligand coordinates. RDKit mode requires its runtime, while lightweight estimates are explicitly identified as such.

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.
`smiles`	Yes	Chemical structure encoded as a SMILES string.
`compoundId`	Yes	Stable identifier for the supplied compound within this run.

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.

Changed5 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / compoundId / description

Added value: +"Stable identifier for the supplied compound within this run."

addedInput schema / properties / method / description

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

addedInput schema / properties / runId / description

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

addedInput schema / properties / smiles / description

Added value: +"Chemical structure encoded as a SMILES string."

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

A4.3/5.0

Behavior4/5

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

Annotations already cover read-only and idempotent semantics, and the description adds real context beyond them: RDKit mode has a runtime dependency, and lightweight mode produces estimates that are explicitly labeled as such (a quality/provenance disclosure). It does not say what happens if the RDKit runtime is absent, which is the one 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?

Three sentences, front-loaded with the action and followed by placement and exclusions; every clause carries information. Slight density in the second sentence ('does not predict binding or prepare 3D ligand coordinates') bundles two distinct exclusions, but nothing is wasted.

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, return values needn't be described, and the description covers prerequisites, method trade-offs, and scope exclusions. What's missing is modest: whether descriptor coverage varies by method, and the failure mode when RDKit is unavailable.

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 the baseline is 3, but the description adds meaning the schema does not: 'method' selects between RDKit and lightweight algorithms with different fidelity, and 'smiles' is the sole structure input to the calculation. It still doesn't enumerate allowed method values or explain how runId/compoundId scope the result.

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 (calculate) plus a specific resource (molecular descriptor values) with the input medium (SMILES) and the two method families (RDKit vs lightweight). It draws clear boundaries against siblings such as predict_synthetic_binding and prepare_ligand by saying it does not predict binding or prepare 3D coordinates.

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?

Explicitly positions the call in the workflow ('Use after validate_compound') and adds two negative conditions (no binding prediction, no 3D ligand prep). It stops short of naming the specific sibling tools to use for those excluded jobs, so routing is implied rather than spelled out.

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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