Mols2Bases

Molecule visualization for Obsidian Bases — render SMILES/MOL structures in a grid view, search by text or SMARTS substructure, and import SDF/CSV files.

Requires Obsidian 1.10.0+.

Features

• Molecule Grid View — Custom Bases view rendering molecular structures as SVG cards via RDKit.js
• Text & SMARTS Search — Filter molecules by name/properties or by substructure pattern with match highlighting
• SDF Import — Parse SDF files into one-note-per-molecule with YAML frontmatter
• CSV Import — Parse CSV files (with a smiles column) into notes with frontmatter
• Rendering Options — Configurable bond width, transparent background, comic mode, hydrogen removal, coordinate handling
• Lazy Rendering — IntersectionObserver-based deferred rendering for large datasets

See docs/features.md for the full list.

Usage

1. Import your data

Open the command palette (Ctrl/Cmd + P) and run one of the import commands:

• Mols2Bases: Import SDF file — each molecule becomes a note with SMILES (converted via RDKit), MOL block (optional), and all SDF properties stored as YAML frontmatter.
• Mols2Bases: Import CSV file — each row becomes a note. The plugin auto-detects the smiles column (case-insensitive) and adds all other columns as frontmatter properties.

Both commands create a folder of notes and a .base file that ties them together.

Note: The plugin works best with files under ~5,000 compounds. Larger datasets may degrade Obsidian's performance — test with your setup before importing very large files.

2. Browse the molecule grid

Open the generated .base file. Switch the view layout to Molecules — you'll see a grid of SVG-rendered structure cards with labels underneath.

Click any card to open the corresponding note. Hover to see a larger preview with additional properties.

3. Search

Use the search bar at the top of the grid:

• Text mode — case-insensitive filter across file names and all frontmatter properties.
• SMARTS mode — toggle to SMARTS to filter by substructure pattern. Matching atoms and bonds are highlighted directly in the SVGs. A counter shows how many molecules match (e.g. "6 of 642").

4. Configure the view

Click the view options button to adjust per-view settings:

• Molecule property — which frontmatter field to render (smiles by default). Change this if your CSV uses a different column name for molecular structures.
• Label property — which field to display as the card label.
• Card width / height — adjust card size with sliders.
• Tooltip — toggle hover previews and configure which properties to show.

5. Plugin settings

Global settings are available under Settings > Mols2Bases:

Setting	Default	Description
Remove hydrogens	off	Strip H atoms before rendering
Use original coordinates	on	Use input coords; off regenerates 2D layouts
Bond line width	1.0	Thickness of bonds in depictions
Transparent background	off	Remove white background (better for dark themes)
Comic mode	off	Hand-drawn style rendering
Lazy render	on	Only render molecules when scrolled into view
Highlight all SMARTS matches	off	Highlight every match, not just the first
Align on SMARTS search	off	Align molecules to matched substructure
Search delay	300ms	Debounce delay for search input
Store MOL block	on	Include full MOL block in frontmatter on SDF import

Installation

Note: Mols2Bases is currently under review for the Obsidian Community Plugins directory. In the meantime, install it manually using the steps below.

Manual install from release

1. Go to the latest release and download main.js, manifest.json, and styles.css.
2. In your vault, create the folder .obsidian/plugins/mols2bases/ if it doesn't exist.
3. Copy the three downloaded files into that folder.
4. Open Obsidian, go to Settings → Community plugins, and enable Mols2Bases.

Alternatively, you can use the BRAT plugin to install directly from this repository and receive automatic updates.

RDKit WASM

The plugin depends on RDKit.js for molecule rendering. On first use, it automatically downloads RDKit_minimal.js and RDKit_minimal.wasm (~7MB total) from the unpkg CDN and caches them in the plugin directory. Subsequent loads use the cached files with no network required.

Building from Source

npm install
npm run build   # production build
npm run dev     # development build with sourcemaps

Acknowledgments

Inspired by mols2grid by Cédric Bouysset — an interactive molecule viewer for Jupyter notebooks. The grid-based molecule browsing concept, feature ideas like SMARTS filtering with match highlighting, and several planned features in this plugin were directly influenced by mols2grid.

Molecule rendering is powered by RDKit.js.