---
title: Compare Molecules plugin
url: https://www.moldraw.com/docs/plugins/compare-molecules-plugin-tanimoto-similarity/
section: Plugins
updated: 2026-10-11
publisher: LabCanvas
---

# Compare Molecules plugin

> Install Compare molecules, open the Compare tab, press Add canvas for the reference, paste other SMILES and press Add SMILES.

![MolDraw Compare molecules plugin comparing chloramphenicol with salicylic acid and paracetamol, showing structure and functional similarity percentages](https://www.moldraw.com/docs/img/plugin-compare-molecules-annotated-screenshot.webp)
*Chloramphenicol as the reference, next to salicylic acid and paracetamol. You see two similarity scores and a list of changes.*

1. Compare tab.
2. Add canvas adds the current drawing (the first molecule is the reference).
3. SMILES box: one SMILES per line, optional name after a space.
4. Add SMILES adds them all to the table.
5. CSV exports the comparison table.

## What it does

Pick one molecule as the reference. Add others to compare.

- **Structure similarity** is a Tanimoto score from fingerprints.
- **Functional similarity** compares the groups each molecule has.
- **Changes** lists groups gained, lost or changed.
- Export the table as CSV.

## Who it is for

Medicinal chemists who look at analogues. Students who compare isomers or drug series.

## How to use it

1. Open the [MolDraw editor](https://www.moldraw.com/) and sign in. Click **Settings**, then **Plugins**, then **Install** next to Compare Molecules.
2. Draw the reference molecule.
3. Open the **Compare** tab (callout 1) and press **Add canvas** (callout 2).
4. Paste more structures as SMILES, one per line (callout 3), then press **Add SMILES** (callout 4).
5. Click a row to see reference and selected structures side by side with the shared core highlighted.
6. Sort by similarity, and press **CSV** (callout 5) to export.

## Tips

- Tanimoto 1.00 can still hide stereo differences; check the stereo flag column.
- Use the ChEMBL plugin's Send to Compare to add database hits directly.
- To get SMILES, convert names with [name to SMILES](https://www.moldraw.com/tools/free-chem-tools/iupac-name-to-smiles-converter.html).

## Questions and answers

**What is Tanimoto similarity?**
The number of fingerprint bits two molecules share divided by the number set in either. 1 means identical fingerprints; above about 0.7 is usually considered similar.

**How many molecules can I compare?**
You can add many rows at once by pasting a list of SMILES; the first molecule added is the reference.

**Does it detect stereoisomers?**
Yes, stereocentre differences are reported separately because fingerprints ignore stereochemistry.