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
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | ||
| smiles | Yes | ||
| api_key | No |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |