nonmem-mcp-server

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read_ext_file

Extract parameter estimates, standard errors, OFV, eigenvalues, and condition number from NONMEM .ext files for pharmacometric analysis.

Instructions

Parse a NONMEM .ext file to extract parameter estimates, standard errors, OFV, eigenvalues, and condition number.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "file_path": "<file_path>"
    },
    "name": "read_ext_file"
  }
}

Input Schema

Name	Required	Description	Default
`file_path`	Yes	Path to the .ext file

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Mar 30, 2026

TDQS

A3.8/5.0

Behavior3/5

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

With no annotations provided, the description carries the full burden. It transparently discloses what data is extracted (parameter estimates, standard errors, OFV, eigenvalues, condition number), but omits safety profile (read-only status), error handling for malformed files, or performance characteristics.

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?

Single sentence with zero waste. Front-loaded with the action ('Parse'), immediately identifies the domain-specific file type ('NONMEM .ext file'), and efficiently lists the five categories of extracted data. Every clause earns its place.

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 lack of output schema, the description compensates well by enumerating the specific data elements returned (parameter estimates through condition number). For a single-parameter read tool, this is sufficient, though explicit mention of return structure format would elevate it further.

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 coverage is 100% with the file_path parameter fully documented as 'Path to the .ext file'. The description reinforces the expected file type but adds no additional semantic details about valid path formats or constraints beyond the schema, warranting the baseline score.

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?

The description uses specific action verbs ('Parse', 'extract') and identifies the exact resource ('NONMEM .ext file'). It clearly distinguishes from siblings like read_lst_file and read_nm_tables by specifying the .ext extension and listing unique outputs (parameter estimates, OFV, eigenvalues) typical of this file format.

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

Usage Guidelines3/5

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

The description implies usage through the file extension '.ext' and lists specific extracted content, helping agents select this when needing parameter estimates or OFV values. However, it lacks explicit guidance on when to prefer this over siblings like read_lst_file or get_run_results, or prerequisites like file existence.

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