Skip to main content
Glama
Sign In
MolTalk

MolTalk

by DomFico
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

Enumerate Stereoisomers

enumerate_stereoisomers
Read-onlyIdempotent

Generate all stereoisomers for unspecified stereochemistry while preserving specified elements, including R/S, E/Z, axial, allene, helicene and spiro configurations with CIP labels.

Instructions

Enumerate unspecified stereochemistry (specified elements are preserved): R/S, E/Z, the twist of hindered biaryl and C–N axes, and the configuration of allenes, helicenes and Xabab spiro atoms. Shows the isomers inline as a grid. Each isomer has CIP labels (input atom indices), stereo_units with verified descriptors, an achiral/meso flag and its enantiomer's index. Isomers that plain SMILES cannot state are given as CXSMILES (with coordinates), which draw_molecule accepts unchanged.

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": "enumerate_stereoisomers"
  }
}

Input Schema

NameRequiredDescriptionDefault
limitNo
smilesYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.0.0

TDQS

A4.1/5.0
Behavior5/5

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

Annotations already cover readOnly/idempotent/non-destructive, and the description adds substantial behavior beyond them: results are shown as an inline grid, each isomer carries CIP labels keyed to input atom indices, stereo_units with verified descriptors, an achiral/meso flag and its enantiomer index, and isomers inexpressible in plain SMILES come back as CXSMILES with coordinates. This is exactly the output-shape disclosure a caller needs.

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 dense sentences with the scoping rule front-loaded, then the coverage list, then the return shape. Every clause carries information, though the enumeration of stereo element types is long and could be compressed without loss.

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 no output schema, the description does the heavy lifting on return values (grid, CIP labels, stereo_units, meso flag, enantiomer index, CXSMILES), which is what makes this callable. The remaining gap is the undocumented limit parameter and what happens when the isomer count exceeds it.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0% for two parameters, so the description must carry the load — and it never mentions 'limit' (default 16), which is the single most consequential knob for an enumeration tool that can explode combinatorially. The 'smiles' parameter is only indirectly illuminated by the note that CIP labels use input atom indices.

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 (enumerate) and the exact resource scope: unspecified stereochemistry only, with specified elements preserved, and names the stereo element classes covered (R/S, E/Z, biaryl and C–N axes, allenes, helicenes, Xabab spiro). An agent can tell immediately this is a stereoisomer generator rather than a drawer or analyzer.

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?

The parenthetical '(specified elements are preserved)' defines the operating condition: use it when the input has unspecified stereo. The pointer that CXSMILES output 'draw_molecule accepts unchanged' gives a concrete follow-up path. It stops short of explicit when-not conditions or a note about combinatorial explosion, so not a 5.

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

Deploy Server

Other Tools