cheminformatics - SKILL.md Agent Skill

name: cheminformatics description: Chemical informatics and modeling license: MIT compatibility: opencode metadata: audience: cheminformaticians, computational chemists, researchers category: chemistry

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