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MolTalk

MolTalk

by DomFico
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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Export Structure

export_structure
Read-onlyIdempotent

Export a chemical structure as a downloadable file in CDXML, MOL, SDF, PDB, XYZ, or SMILES, with 2D/3D coordinates and optional explicit hydrogens.

Instructions

Write the structure as a file the user can download: format "cdxml" (ChemDraw, default), "mol", "sdf", "pdb", "xyz" or "smiles". coordinates: "2d" (the drawing's layout; default for cdxml/mol/sdf) or "3d" (one calculated conformer with explicit hydrogens; required for pdb/xyz). name: compound name for the file name and title. hydrogens=true adds explicit hydrogens to a 2D file. The file holds the structure as given (charges, stereo, atom order), not drawing-only additions. Shown inline with a Download button.

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": {
      "smiles": "<smiles>"
    },
    "name": "export_structure"
  }
}

Input Schema

NameRequiredDescriptionDefault
nameNo
formatNocdxml
smilesYes
hydrogensNo
coordinatesNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.0.0

TDQS

A4.1/5.0
Behavior3/5

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

Annotations already declare readOnly, idempotent, non-destructive and closed-world, so the safety profile is settled. The description still adds real value: the file preserves the structure as given (charges, stereo, atom order) rather than drawing-only additions, 3d triggers one calculated conformer with explicit hydrogens, and the result is shown inline with a Download button. That goes beyond the annotations, though it doesn't cover overwrite behavior or failure modes.

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?

Dense and front-loaded, with the file-writing purpose first and options after; every clause carries format or constraint information. The semicolon-chained parameter list is efficient but reads as a run-on, slightly hurting scannability.

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 five-parameter export tool with no output schema, this covers formats, coordinate requirements, hydrogen control, naming, and how the file surfaces to the user. Only the smiles input and the source of the exported structure (current canvas vs. passed SMILES) are left ambiguous.

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 description coverage is 0%, so the description carries the load and does: it explains format values and default, the coordinates semantics and per-format requirement, name's dual role for filename and title, and hydrogens' effect on 2D files. The required smiles parameter is never described, leaving one of five inputs unexplained.

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 resource up front: "Write the structure as a file the user can download," then enumerates the exact formats produced. An agent can immediately separate this from drawing or analysis siblings because the output artifact (a downloadable file) is named 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?

Gives clear conditional guidance for options: default format cdxml, default coordinates per format, and the hard rule that 3d is required for pdb/xyz. It never says when to prefer this tool over siblings like draw_molecule, so it stops short of explicit alternatives or exclusions.

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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