CovaSyn Chemistry Tools

covabasic_atom_indices

Return atom indices for a named structural query — replaces hand-written SMARTS.

Use this when you need atom positions for a structural feature
(e.g. "which atoms are in the aromatic ring?", "where are the stereocenters?",
"which carbon has the highest oxidation state?").

Returns: `{indices: [...], groups: [[...]], smarts_used: "..."}`. Plus:
  - `named_groups: [{name, atoms, smarts}]` for `functional_group_atoms`
  - `oxidation_states: [{atom, state}]` for `oxidation_state`

Supported query names (22):
  ring/topology    : aromatic_ring, aliphatic_ring, saturated_ring,
                     heterocycle, fused_ring, bridgehead
  atom-class       : halogen_atom, carbon_atom, heavy_atom, csp3_carbon
  stereo           : stereocenter, r_s_stereocenter, unspecified_stereocenter
  bonds & chains   : rotatable_bond, branch_point, chain_termini,
                     longest_carbon_chain
  derived          : murcko_scaffold_atoms, brics_break_atoms,
                     functional_group_atoms
  H-bonding / oxidation:
                     hba (Lipinski-style hydrogen-bond acceptors),
                     oxidation_state (per-carbon Pauling-EN ox-state,
                     with parallel `oxidation_states` field)

Examples:
  query="aromatic_ring" + smiles="c1ccccc1"  → indices [0..5], one group
  query="r_s_stereocenter" + smiles="C[C@H](O)C(=O)O" → stereo carbon indices
  query="hba" + smiles="CC(=O)O"  → carbonyl + hydroxyl O indices
  query="oxidation_state" + smiles="CC(=O)O" → carbon indices PLUS
    oxidation_states=[{atom:0, state:-3}, {atom:1, state:+3}]
  query="functional_group_atoms" + any SMILES → also returns named_groups list

Cost: 2 credits, available on Free tier.

Input Schema

Name	Required	Description	Default
`query`	Yes
`smiles`	Yes
`api_key`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 9, 2026

TDQS

A4.5/5.0

Behavior4/5

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

No annotations are provided, so the description carries the full burden. It discloses return shape, extra fields for specific queries, cost (2 credits), and Free-tier availability, but does not cover error behavior or authentication requirements beyond the api_key parameter.

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?

Despite its length, the description is tightly structured with clear sections (purpose, return shape, supported queries, examples, cost). It is front-loaded and every sentence adds useful information for selecting or invoking the tool.

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

Completeness5/5

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

An output schema exists, yet the description still helpfully documents return fields and query-specific extras. Combined with the full query-name list, examples, and cost note, it gives an agent everything needed to select and correctly invoke this tool.

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 0%, so the description must compensate. It thoroughly explains the 'query' parameter with all 22 supported values and binds query+smiles in worked examples. The 'api_key' parameter is left unexplained and the SMILES syntax is only implied.

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: 'Return atom indices for a named structural query.' The phrase 'replaces hand-written SMARTS' and the list of 22 supported query names make it clearly distinct from siblings like covabasic_substructure or covabasic_functional_groups.

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 states when to use it: 'Use this when you need atom positions for a structural feature,' with concrete examples. It does not name when NOT to use it or point to specific alternative tools, so it stops short of a 5.

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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