SMILES De-salter

Batch process chemical structure strings, removing salt ion portions and retaining only the active core (API). Uses RDKit to identify and strip counterions from SMILES notation.

Quick Check

python -m py_compile scripts/main.py

Audit-Ready Commands

python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py -s "CC(C)CN1C(=O)N(C)C(=O)C2=C1N=CN2C.[Na+]"
python scripts/main.py -i input.csv -o output.csv -c smiles

When to Use

• Remove salt ions from SMILES strings before cheminformatics analysis
• Standardize compound libraries by stripping counterions
• Batch-process CSV/TSV files containing SMILES columns
• Prepare clean SMILES for downstream ADMET or docking workflows

Workflow

1. Confirm input format (single SMILES string, CSV/TSV file, or pure SMILES file) and column name.
2. Validate that the request involves SMILES de-salting; stop early if not.
3. Run the appropriate command (single -s flag or batch -i/-o flags).
4. Return a structured result separating assumptions, deliverables, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the Fallback Template below.

Fallback Template

If scripts/main.py fails or required fields are missing, respond with:

FALLBACK REPORT
───────────────────────────────────────
Objective        : <de-salting goal>
Inputs Available : <list what was provided>
Missing Inputs   : <list exactly what is missing>
Partial Result   : <any SMILES that could be processed safely>
Blocked Steps    : <what could not be completed and why>
Next Steps       : <minimum info needed to complete>
───────────────────────────────────────

Salt Ion Identification Rules

• Multiple components identified via . separator in SMILES
• Salt ions are typically smaller fragments (Na⁺, Cl⁻, K⁺, Br⁻, etc.)
• Default: retain the component with the most heavy atoms
• Supports common inorganic salts and organic acid salts

Type	Examples
Inorganic salts	NaCl, KCl, HCl, H₂SO₄
Organic acid salts	Citrate, Tartrate, Maleate
Quaternary ammonium	Various quaternary ammonium compounds

CLI Usage

# Single SMILES string
python scripts/main.py -s "CC(C)CN1C(=O)N(C)C(=O)C2=C1N=CN2C.[Na+]"
# Output: CC(C)CN1C(=O)N(C)C(=O)C2=C1N=CN2C

# Batch CSV processing
python scripts/main.py -i input.csv -o output.csv -c smiles_column

# Keep largest fragment (default: True)
python scripts/main.py -i input.csv -o output.csv -k True

Parameters

Parameter	Short	Description	Default
--input	-i	Input file path (CSV/TSV/SMILES)	Required for batch
--output	-o	Output file path	desalted_output.csv
--column	-c	SMILES column name	smiles
--smiles	-s	Single SMILES string	—
--keep-largest	-k	Keep largest component by atom count	True

Input / Output Format

Input CSV:

id,smiles,name
1,CCO.[Na+],ethanol_sodium
2,c1ccccc1.[Cl-],benzene_hcl

Output CSV:

id,smiles,name,desalted_smiles,status
1,CCO.[Na+],ethanol_sodium,CCO,success
2,c1ccccc1.[Cl-],benzene_hcl,c1ccccc1,success

Examples

Input SMILES	Output SMILES	Note
CCO.[Na+]	CCO	Simple inorganic salt
CN1C=NC2=C1C(=O)N(C)C(=O)N2C.Cl	CN1C=NC2=C1C(=O)N(C)C(=O)N2C	HCl salt
CC(C)CN1C(=O)...C.C(C(=O)O)...O	CC(C)CN1C(=O)...C	Complex organic salt

Input Validation

This skill accepts: SMILES strings (single via -s) or CSV/TSV/SMILES files (batch via -i) containing chemical structure data for salt removal.

If the request does not involve SMILES de-salting — for example, asking to predict toxicity, perform docking, or analyze non-chemical data — do not proceed. Instead respond:

"smiles-de-salter is designed to remove salt ions from chemical SMILES strings. Your request appears to be outside this scope. Please provide a valid SMILES string or input file, or use a more appropriate tool."

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the --input path contains ../ or resolves outside the workspace, reject with a path traversal warning before opening the file.
• If the task goes outside documented scope, stop instead of guessing.
• If scripts/main.py fails (e.g., RDKit parse error, file not found), use the Fallback Template above.
• Do not fabricate SMILES outputs, file contents, or execution outcomes.

Output Requirements

Every final response must include:

1. Objective — what was de-salted and why
2. Inputs Received — SMILES strings or file path and column used
3. Assumptions — any inferred column names or defaults applied
4. Result — cleaned SMILES or output file path
5. Risks and Limits — co-crystals or multi-component drugs may need manual review
6. Next Checks — recommend sampling and verifying results

Notes

1. This tool assumes the core is the component with the most heavy atoms; co-crystals may need manual review.
2. Some hydrochloride salts may appear as [Cl-] or Cl — both are handled.
3. Recommend spot-checking a sample of results after batch processing.
4. --keep-largest bool parsing: argparse type=bool treats any non-empty string as True. Always pass True or False explicitly. The script should use lambda x: x.lower() == 'true' as the argparse type to fix this.

Dependencies

• Python >= 3.8
• rdkit >= 2022.03.1
• pandas