internscience SMILES Functional Group Editor
Note:
- Local files are not directly accessible by the server. Please upload them to the server using
molclaw-file-transferbefore execution. - For PDB file inputs, it is recommended to preprocess them using
molclaw-pdbfixerbefore execution. - Please refer to skill
molclaw-scp-serverto complete tool invocation.
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"
}