| name | molclaw-smiles-fg-editor |
| description | Edit molecular structures in SMILES notation by adding, deleting, or replacing functional groups. Use this skill whenever the user asks to modify a molecule's SMILES by manipulating functional groups (e.g., "delete hydroxyl", "add nitrile", "replace amine with carboxyl"). This skill prevents the most common error: treating the same atom pattern (like -OH) as one functional group when it actually represents different groups depending on chemical context. |
SMILES Functional Group Editor
Core Rule: Context Determines Identity
Never match functional groups by SMILES substring alone. The same pattern represents different
groups depending on what it's bonded to. Always classify from most-specific to least-specific —
first match wins.
Functional Group Hierarchy
Oxygen-containing (check top-down)
| Priority | Group | Pattern | Key Test |
|---|
| 1 | Carboxylic acid | C(=O)O (terminal OH) | C=O adjacent to OH |
| 2 | Ester | C(=O)OC | C=O adjacent to O-C |
| 3 | Phenol | c-O (aromatic carbon-OH) | Lowercase c bonded to O |
| 4 | Enol | C=C-O | Vinyl carbon bonded to OH |
| 5 | Ketone | CC(=O)C (non-terminal) | Internal C=O, no adjacent N or OC |
| 6 | Aldehyde | terminal C=O | Terminal C=O |
| 7 | Ether | C-O-C (aliphatic) | Not part of ester |
| 8 | Alcohol/Hydroxyl | C-O (aliphatic C-OH) | Aliphatic C — lowest priority |
Nitrogen-containing
| Priority | Group | Pattern | Key Test |
|---|
| 1 | Nitro | [N+](=O)[O-] | Charged N with two oxygens |
| 2 | Amide | C(=O)N | N adjacent to C=O |
| 3 | Nitrile | C#N | Triple bond |
| 4 | Imine | C=N | Double bond |
| 5 | Heterocyclic N | n in ring | Ring member — not an amine |
| 6 | Amine | C-N (aliphatic) | Not in amide/ring — lowest |
User Term → Target Mapping
| User says | Target only | Do NOT touch |
|---|
| "hydroxyl" | Alcohol (aliphatic C-OH) | Phenol, enol, carboxyl OH |
| "amine" | Aliphatic amine | Amide N, ring N |
| "carbonyl" | Ketone/Aldehyde C=O | Ester/amide/carboxyl C=O |
| "nitrile" | C≡N | Isocyanide |
| "carboxyl" | -COOH | Ester |
Workflow
- Inventory: list all candidate groups in the molecule
- Classify: walk the hierarchy top-down for each candidate, first match wins
- Filter: keep only groups matching the user's term per the mapping table above
- Modify: delete/add/replace at the matched positions; preserve
@/@@ stereochemistry
- Validate: check parentheses balanced, ring closures matched, stereo preserved
Output Format
{
"output": "Modified Molecule SMILES"
}
