molclaw-smiles-fg-editor

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

Note:

• Local files are not directly accessible by the server. Please upload them to the server using molclaw-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using molclaw-pdbfixer before execution.
• Please refer to skill molclaw-scp-server to 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

1. Inventory: list all candidate groups in the molecule
2. Classify: walk the hierarchy top-down for each candidate, first match wins
3. Filter: keep only groups matching the user's term per the mapping table above
4. Modify: delete/add/replace at the matched positions; preserve @/@@ stereochemistry
5. Validate: check parentheses balanced, ring closures matched, stereo preserved

Output Format

{
    "output": "Modified Molecule SMILES"
}