ChemEdit

ChemEdit

Bring chemistry to Obsidian.

ChemEdit is a fully-integrated chemical structure editor and viewer. Powered by Ketcher and SmilesDrawer, it allows you to natively draw reactions, edit .mol files, preview ChemDraw (.cdxml) files directly inside your vault, and keep simple electronic lab notebooks (ELNs).

Quick Demo

✨ Features

• Native File Support: Render and edit .cdxml and .mol files directly.
• Double-Click to Edit: Click any rendered molecule to open the visual drawing interface.
• Auto-Save: Hit "Save" in the editor to instantly overwrite the .mol/.cdxml file on your hard drive and update the preview.
• Smart Themes: Structures automatically adapt to your Obsidian Light/Dark mode.
• Reactions: Full support for drawing and rendering complex chemical reactions.

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🚀 How to Use

1. SMILES Strings

Write SMILES strings directly in your markdown using code blocks:

```smiles
CC(=O)OC1=CC=CC=C1C(=O)O

2. ChemDraw & Mol files (.cdxml, .mol)

Drop a chemistry file into your vault and embed it in your note:

```mol
![[caffeine.cdxml]]

![[aspirine.mol]]

ChemEdit replaces the generic file box with an SVG rendering. Double-click the image to open Ketcher, edit the molecule, and save!

⚠️ Disclaimer on .cdxml files: ChemEdit uses Ketcher's open-source conversion engine. While most standard structures and reactions work perfectly, highly complex formatting or proprietary ChemDraw-specific objects may not be 100% supported.

Double-click the structure to edit it visually. Saving will automatically update the text in your code block.

3. Draw from Scratch

Click the Hexagon Icon in your left-hand ribbon (or use the Command Palette: Draw new SMILES molecule) to open a blank canvas. Draw your structure, hit Save, and it will be inserted exactly where you are typing.

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🧪 (basic support) Electronic Lab Notebook (ELN)

ChemEdit includes an, automatic stoichiometry calculator and experimental logbook generator. Using a simple YAML code block, you can define your reaction, and ChemEdit will:

• Calculate stoichiometry (moles, mass, volume).
• Calculate theoretical yield and percentage yield.

Usage

Create an eln code block and define your experiment:

```eln
Code: RSA-007
title: Aspirin Synthesis
author: rsa
creation_date: Dec 16, 2018

duration: 20 min
solvent: none
temperature: 80 °C

reactants:

- name: Salicylic acid
  smiles: O=C(C1C(O)=CC=CC=1)O
  eq: 1
  mass: 1381

- name: Acetic anhydride
  smiles: CC(=O)OC(=O)C
  eq: 1.5
  density: 1.08


- name: Sulfuric acid (catalytic)
  smiles: OS(=O)(=O)O
  eq: 0.05
  density: 1.84


products:

- name: Aspirin
  smiles: CC(=O)OC1=CC=CC=C1C(=O)O
  eq: 1
  mass_isolated: 1600



procedure: |  
  Salicylic acid was mixed with acetic anhydride, followed by the addition of catalytic sulfuric acid. The reaction mixture was heated at 80 °C for 20 min, then cooled and poured into ice-water. The precipitated aspirin was collected by filtration, washed with cold water, and dried.

📥 Installation

From Obsidian Community Plugins (Recommended)

1. Open Settings → Community plugins.
2. Click Browse and search for ChemEdit.
3. Click Install and then Enable.

Manual Installation

1. Download main.js and manifest.json from the Releases page.
2. Place them in your vault at .obsidian/plugins/chemedit/.
3. Reload plugins and enable ChemEdit.

🐛 Feedback & Bugs

Found a bug or have a feature request? Please open an issue on GitHub.

🏆 Acknowledgements

• Ketcher by EPAM Systems
• SmilesDrawer by the Reymond Group

🔬 Related Chemistry Plugins

ChemEdit focuses on interactive molecular drawing, editing, and visualization. Depending on your workflow, you may also find these Obsidian plugins useful:

Why ChemEdit?

ChemEdit combines features that would otherwise require several plugins:

• Interactive Ketcher editor.
• Native editing of SMILES, MOL, and CDXML files.
• Double-click editing directly from rendered structures.
• Automatic synchronization with files in your vault.
• Online and fully offline modes.
• Experimental Electronic Lab Notebook (ELN) with stoichiometry calculations.

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