AI Chat

How the AI sees your molecule

The AI chat panel runs alongside the structure editor. When you have a molecule on the canvas, the AI receives its SMILES representation automatically with every message. You do not need to copy, paste, or describe your structure — the AI sees it in real time.

A molecule context badge in the chat panel confirms what the AI is working with. In reaction mode, this badge shows reactant and product counts instead.

Property prediction

Ask the AI about your molecule’s properties. It calls RDKit via a backend tool to compute:

• • Molecular weight (MW)
• • logP (Wildman-Crippen partition coefficient)
• • Hydrogen bond donors (HBD) and acceptors (HBA)
• • Topological polar surface area (TPSA)
• • Rotatable bonds
• • Drug-likeness — Lipinski Rule of Five pass/fail evaluation

Results display in a two-tier card: a summary with key values, and an expandable detailed view with range bars. Each value carries a confidence indicator — Computed (green, deterministic via RDKit) or AI Suggested (yellow, verify experimentally).

Reaction prediction

Draw reactants on the canvas and ask the AI about expected products with specific reagents. The AI suggests probable reaction products based on your structure and conditions.

Reaction predictions carry the AI Suggested confidence level. Always verify predicted products experimentally or against literature.

Retrosynthesis

Draw a target molecule and ask the AI for synthetic routes. It suggests retrosynthetic disconnections — working backward from the target to commercially available starting materials.

Routes are displayed as step-by-step sequences. Each step shows the transformation and intermediate structures. Retrosynthesis suggestions carry the AI Suggested confidence level.

IUPAC naming

Ask the AI to name your molecule. ChemStitch uses a py-opsin backend (Open Parser for Systematic IUPAC Nomenclature) for structure-to-name resolution.

Naming result cards show the method used: "IUPAC Name (OPSIN)" for OPSIN-resolved names, or "IUPAC Name (Common Name Lookup)" for fallback resolution. If OPSIN cannot determine the name, the card displays an explicit message suggesting manual verification.

You can also go from name to structure: type a chemical name and the AI generates the corresponding structure on the canvas.

Confidence indicators

Every AI result in ChemStitch carries a visible confidence level:

• • Computed (green badge) — Deterministic calculation via RDKit. These values are reproducible and exact for the given structure.
• • AI Suggested (yellow badge) — AI-generated prediction. Useful for exploration, but should be verified experimentally or against literature before making decisions.

This distinction matters in research contexts where the difference between a computed property and an AI guess can affect experimental planning.

Chat persistence

Conversations are saved per document and survive page refresh. Tool result cards — properties, structures, reactions — persist with full fidelity.

Long conversations are paginated: the most recent 50 messages load initially, with a "Load earlier messages" button for longer histories. Scroll position is maintained when loading older messages.