Substructure Search - Usage Guide

Overview

Search molecular libraries for specific structural patterns using SMARTS. Filter compounds by functional groups, pharmacophores, or scaffold features.

Prerequisites

pip install rdkit

Quick Start

Tell your AI agent what you want to do: - "Find all compounds with a carboxylic acid group" - "Filter out molecules containing reactive groups" - "Search for benzimidazole scaffold in my library" - "Highlight the matched atoms in my molecule"

Example Prompts

Pattern Searching

"Find all molecules containing a primary amine."

"Search for compounds with both hydroxyl and carbonyl groups."

Library Filtering

"Remove compounds with nitro groups or Michael acceptors."

"Keep only molecules with aromatic rings."

Visualization

"Show me the carboxylic acid group highlighted in this molecule."

"Mark the matched substructure in red."

What the Agent Will Do

1. Parse SMARTS pattern
2. Search molecules for substructure matches
3. Return atom indices of matches
4. Filter library by inclusion/exclusion criteria
5. Generate visualizations with highlighting

Tips

• SMARTS uses square brackets for atom properties: [OX2H], [NH2], [CX3]; atom-only queries such as [NH2] do not define the neighboring functional-group context
• Aromatic atoms are lowercase: c for aromatic carbon, C for aliphatic
• Use recursive SMARTS for complex patterns: $(...) notation
• Common patterns: [OX2H] neutral hydroxyl, [NX3;H2;$(N-[#6]);!$(N-[C,S,P]=[O,S,N])] carbon-substituted primary amine excluding common amide-like N, and c1ccccc1 an aromatic six-cycle (including cycles embedded in fused systems)
• HasSubstructMatch is faster than GetSubstructMatches for presence check

Related Skills

• molecular-io - Load molecules for searching
• similarity-searching - Fingerprint-based searching
• admet-prediction - Filter before ADMET analysis