Cheminformatics

What I do

• Apply computational methods to chemical data analysis
• Design and search chemical databases
• Predict molecular properties and reactivity
• Perform molecular similarity analysis
• Develop quantitative structure-activity relationships (QSAR)
• Visualize and analyze chemical structures

When to use me

• When searching chemical databases
• When predicting molecular properties
• When building QSAR/QSPR models
• When analyzing molecular similarity
• When virtual screening compounds
• When managing chemical data

Key Concepts

Molecular Descriptors

Constitutional Descriptors

• Molecular weight
• Atom counts (C, H, O, N, etc.)
• Number of rings
• LogP (lipophilicity)

Topological Descriptors

• Wiener index
• Balaban index
• Connectivity indices
• Hydrogen bond donors/acceptors

# Example: Simple molecular fingerprint
def morgan_fingerprint(molecule, radius=2):
    """Generate Morgan/ECFP fingerprint."""
    # Simplified representation
    return {
        'features': extract_substructures(molecule, radius),
        'bit_vector': encode_as_bits(features),
        'similarity': lambda other: tanimoto_coefficient(features, other)
    }

Chemical File Formats

• SMILES: String representation
• SDF: Structure-data file
• MOL: MOL file format
• PDB: 3D structure
• InChI: IUPAC identifier

Similarity Metrics

• Tanimoto coefficient (Jaccard)
• Dice similarity
• Cosine similarity
• Euclidean distance