Chemical Structure Converter

"Chemical Structure Converter is designed to interconvert chemical identifiers (names, SMILES, formulas). Please provide a compound name or SMILES string. For other cheminformatics tasks, use a more appropriate tool."

Quick Check

python -m py_compile scripts/main.py
python scripts/main.py --help

Workflow

1. Confirm the input identifier type (name, SMILES, IUPAC) and desired output format.
2. Validate that the request matches the documented scope; stop if the task requires unsupported assumptions.
3. Run the script or apply the documented conversion path with only the inputs available.
4. Return a structured result separating assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Fallback: If no identifier is provided, respond: "No chemical identifier provided. Please supply a compound name (--name), SMILES string (--smiles), or IUPAC name (--iupac). Cannot convert without an input identifier."

Core Capabilities

1. Multi-Format Conversion

from scripts.main import ChemicalStructureConverter
converter = ChemicalStructureConverter()
data = converter.name_to_identifiers("aspirin")
# → IUPAC: 2-acetoxybenzoic acid, SMILES: CC(=O)Oc1ccccc1C(=O)O, Formula: C9H8O4, MW: 180.16

2. SMILES Validation

is_valid, message = converter.validate_smiles("CC(=O)Oc1ccccc1C(=O)O")
# → True, "Valid SMILES syntax"

3. Batch Processing

for compound in compound_list:
    data = converter.name_to_identifiers(compound)
    if not data:
        print(f"Warning: '{compound}' not found in database")

CLI Usage

# Convert by compound name
python scripts/main.py --name aspirin

# Convert SMILES to IUPAC
python scripts/main.py --smiles "CC(=O)Oc1ccccc1C(=O)O"

# Validate SMILES
python scripts/main.py --smiles "CCO" --validate

# List all compounds
python scripts/main.py --list

Parameters

Output Requirements

Every final response must make these explicit:

• Objective or requested deliverable
• Inputs used (identifier type and value) and assumptions introduced
• Conversion method applied
• Core result: all available identifiers (SMILES, IUPAC, formula, MW)
• Constraints and risks (local database limited; novel compounds may not be found)
• Unresolved items and next-step checks (validate against PubChem for critical work)

Error Handling

• If no identifier is provided, list the required input options and request clarification.
• If a compound is not found in the local database, flag it and provide direct lookup URLs: https://pubchem.ncbi.nlm.nih.gov/compound/{compound_name} and https://www.chemspider.com/Search.aspx?q={compound_name}. For programmatic lookup, query the PubChem REST API: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{name}/JSON. The script should automatically query this endpoint when a compound is not found locally.
• If scripts/main.py fails, report the failure point and provide manual fallback guidance.
• Do not fabricate SMILES strings, molecular weights, or identifiers.
• Batch mode: Include a summary line: X/N compounds converted successfully, Y failed (list failed compound names).
• Database versioning: The local compound database version is tracked in DB_VERSION in scripts/main.py. To add compounds, update the COMPOUND_DB dict and increment DB_VERSION.

Common Pitfalls

• Ambiguous names: Use CAS numbers or specific synonyms for unambiguous lookup
• Stereochemistry omitted: Specify @/@@ in SMILES for chiral compounds
• Hydrates vs anhydrous: Always specify form (e.g., "caffeine anhydrous")
• Duplicate entries: Deduplicate by canonical SMILES when building databases
• Character encoding: Use UTF-8 for IUPAC names with special characters

SMILES Quick Reference

• C = aliphatic carbon, c = aromatic carbon
• = = double bond, # = triple bond
• () = branching, [] = explicit valence/charge
• @ = anticlockwise (S), @@ = clockwise (R)

References

• PubChem: https://pubchem.ncbi.nlm.nih.gov
• ChemSpider: http://www.chemspider.com
• SMILES Specification: http://opensmiles.org
• RDKit Documentation: https://www.rdkit.org/docs/

Known Limitation: Local database contains common compounds only. Integrate PubChem API for production use.