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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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bond

DestructiveIdempotent

Connect two selected atoms with a chemical linkage and set the order to single, double, triple, or aromatic.

Instructions

Creates a bond between two atoms

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": {
      "atom1": "<atom1>",
      "atom2": "<atom2>"
    },
    "name": "bond"
  }
}

Input Schema

NameRequiredDescriptionDefault
atom1YesFirst atom, as a selection matching exactly one atom.
atom2YesSecond atom, as a selection matching exactly one atom.
orderNoBond order: ``1`` single, ``2`` double, ``3`` triple, ``4`` aromatic.1

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.5.1
    • addedInput schema / properties / atom1 / description
      Added value: +"First atom, as a selection matching exactly one atom."
    • addedInput schema / properties / atom2 / description
      Added value: +"Second atom, as a selection matching exactly one atom."
    • addedInput schema / properties / order / description
      Added value: +"Bond order: ``1`` single, ``2`` double, ``3`` triple, ``4`` aromatic."
  2. First observedv1.2.1

TDQS

C2.9/5.0
Behavior2/5

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

Annotations already declare destructiveHint=true, idempotentHint=true, and readOnlyHint=false, so the mutation and repeat-safety profile is carried by structured data. The description adds nothing beyond that: it doesn't say what happens if a bond already exists between the atoms, whether it overwrites an existing bond order, or whether the change survives without a rebuild.

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?

A single front-loaded sentence with no filler or redundant wording. It is efficient, though extremely minimal for a structure-mutating tool.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With a full schema, an output schema, and complete annotations, the description only needs to add behavioral nuance — and it doesn't. The definition is adequate to call the tool correctly but leaves edge cases (duplicate bonds, overwriting order) undocumented.

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% and the schema already explains that atom1/atom2 each require a selection matching exactly one atom and that 'order' takes 1-4 with 4 meaning aromatic. The description adds no format, default, or constraint information beyond that, so the baseline 3 applies.

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

Purpose4/5

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

The description names a specific verb and resource ('Creates a bond between two atoms'), so the core action is unambiguous. It does not distinguish itself from the natural sibling 'unbond' or from related geometry tools like 'distance'/'angle', which is the only thing keeping it below a 5.

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

Usage Guidelines2/5

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

There is no guidance on when to use this versus 'unbond', 'rebuild', 'h_add', or 'alter', and no prerequisites such as needing atoms already loaded or selected. Usage is only inferred from the tool name and the word 'Creates'.

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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