3D Molecular Conformer Generator

A utility that generates three-dimensional coordinates for molecular structures from their SMILES representations.

Requirements

Generate 3D coordinates from SMILES

• Given a valid SMILES string "CCO" (ethanol), generate a 3D conformer and return the molecule with 3D coordinates @test
• Given a SMILES string "c1ccccc1" (benzene), generate a 3D conformer with proper aromatic ring geometry @test
• Given an invalid SMILES string "XYZ123", raise an appropriate error without generating coordinates @test
• Given a valid SMILES string for a chiral molecule "CC@HCC" (S-2-butanol), generate a 3D conformer that preserves the stereochemistry @test

Implementation

@generates

API

def generate_conformer(smiles: str) -> object:
    """
    Generate a single 3D conformer for a molecule from its SMILES representation.

    Args:
        smiles: A SMILES string representing the molecular structure

    Returns:
        A molecule object with 3D coordinates embedded

    Raises:
        ValueError: If the SMILES string is invalid or conformer generation fails
    """
    pass

Dependencies { .dependencies }

rdkit { .dependency }

Provides cheminformatics capabilities for molecular structure handling and 3D coordinate generation.

@satisfied-by