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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

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
smilesYes
api_keyNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Schema Changelog

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