Cheminformatics (RDKit) — Pipeline Skill (Thin Scaffold)

Overview

Adds fingerprint selection logic, filter cascade ordering, and version-specific gotchas for RDKit workflows. The agent already knows RDKit syntax — this skill prevents parameter mismatches and deprecated API usage.

Usage

• Activate when filtering compound libraries (Lipinski/Veber/PAINS)
• Activate for fingerprint similarity search or clustering
• Activate for matched molecular pair (MMP) analysis with mmpdb

Core Concepts

Filter cascade order: Lipinski → Veber → PAINS → similarity (cheapest first, most expensive last).

Fingerprint API: Use rdFingerprintGenerator module exclusively (since RDKit 2024.03). The AllChem.GetMorganFingerprintAsBitVect() path is deprecated and will be removed.

SMILES validation: Always parse with sanitize=False then explicit SanitizeMol() in try/except. Default MolFromSmiles silently returns None on partial failures.