# ChemSpec
An interactive, offline viewer for NMR, FT-IR, and analytical chemistry spectra directly inside your electronic lab notebook. **Fully supported on both Desktop and Mobile.**

## Quick demo:

<img width="800" height="759" alt="ChemSpeck qdemo" src="https://github.com/user-attachments/assets/63ef2ed3-6bb9-4804-acd6-c313f3450138" />

**Bring analytical chemistry to Obsidian.**

ChemSpec is an offline, interactive viewer for NMR, FT-IR, and analytical chemistry spectra inside your electronic lab notebook.

Created to use it alongside **ChemEdit** ELN to process raw analytical data, integrate peaks, and simulate spectra natively in your vault.

### What's New (v1.1.0)
*   **NMR Stacking:** Drag & drop multiple spectra onto the standalone viewer to stack/overlay them.
*NMR stacking screenshot:*
<img width="1003" height="567" alt="image" src="https://github.com/user-attachments/assets/bdf3a027-16aa-446f-b208-23f55cf38626" />

*NMR Overlay:*
<img width="1486" height="276" alt="image" src="https://github.com/user-attachments/assets/c2480476-ba68-491f-9161-57fc6987b622" />

*   **Fixed CV Plotting:** CV rendering with a full bounding box, inward-facing ticks, bold serif fonts, and high-res trace rendering.

<img width="1566" height="848" alt="image" src="https://github.com/user-attachments/assets/f50ef34e-a771-42b3-9f28-3efe96608cf0" />

*   **Electrochemistry Tools:** Added one-click **"Auto Fc Calc"** (E<sub>1/2</sub> and &Delta;E shifting) and **"Find Peaks"** (E<sub>pa</sub>, E<sub>pc</sub> detection and labeling) directly on the CV canvas.
*   **Smart NMR Labels:** Peak labels now dynamically hide when overlapping to prevent unreadable "walls of text" on zoom-out.
*   **SVG Export Fixes:** Publication SVG exports now mirror the canvas, including collision-aware peaks, multiplets, and integrals.

*Settings preview:*

<img width="804" height="658" alt="image" src="https://github.com/user-attachments/assets/315f6672-568b-4a73-a717-01850c585eb2" />


## Features

* **Native Embeds:** Render `.nmr`, `.jdx`, `.jcamp`, `.csv`, and `.txt` files directly via standard Obsidian embeds (`![[spectrum.jdx]]`).
* **NMR Processing:** Load raw Bruker `acqus`/`1r` datasets. Features include integration, multiplet brackets, J-coupling calculations, and peak picking.
* **FT-IR & Cyclic Voltammetry (CV):** Plot standard spectroscopy and electrochemistry trace files directly in your notes.
* **PubNMR Simulation:** Paste ACS NMR strings into a `pubnmr` code block to render a simulated, interactive spectrum.
* **Export & Draft:** Copy ACS multi-proton strings to your clipboard, or export `.svg` publication figures and `.jdx` files from the canvas.
* **Themes:** Spectra automatically adapt to Obsidian's Light/Dark mode.

---

## Usage

### 1. File Embeds

Drop a spectrum file into your vault and embed it using Obsidian's standard syntax:

```markdown
![[compound_1.nmr]]
![[ir_spectrum.jcamp]]
![[cv_trace.csv]]
```

### 2. Standalone Workspace

Click the **Activity Icon** in the left ribbon to open the ChemSpec application. Drag and drop raw Bruker folders or files directly into the workspace to process them.

### 3. Spectra Grids

Compare multiple spectra using a code block:

````markdown
```nmr
pdata/1/processed.nmr
reference_spectrum.jdx
```
````

### 4. Text-to-Spectrum (PubNMR)

Simulate a spectrum from experimental text:

````markdown
```pubnmr
1H NMR (400 MHz, CDCl3) δ 7.95 (d, J = 8.1 Hz, 2H), 7.42 (d, J = 8.1 Hz, 2H), 2.45 (s, 3H)
```
````

---

## Installation

**From Obsidian Community Plugins**

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

**Manual Installation**

1. Download `main.js` and `manifest.json` from the [Releases page](https://github.com/ruzx/chemspec/releases).
2. Place them in your vault at `.obsidian/plugins/chemspec/`.
3. Reload plugins and enable ChemSpec.

---

## Feedback & Bugs

Found a bug or have a feature request? Please [open an issue on GitHub](https://github.com/ruzx/chemspec/issues).

---

## Acknowledgements

ChemSpec was built to complement **ChemEdit**, providing a dedicated Electronic Lab Notebook (ELN) experience in Obsidian.

Thanks to the open-source cheminformatics community:

* [nmr-parser](https://github.com/cheminfo/nmr-parser) & [nmr-processing](https://github.com/cheminfo/nmr-processing) by Cheminfo / Zakodium.
* [jcampconverter](https://github.com/cheminfo/jcampconverter) for spectroscopy parsing.

## Related Plugins

| Plugin | Description |
| --- | --- |
| **[ChemEdit](https://github.com/ruzx/obsidian-chemedit)** | Natively draw reactions, calculate stoichiometry, and manage ELN entries. |
| [Chem](https://github.com/Acylation/obsidian-chem) | Render **SMILES** structures locally using SmilesDrawer and RDKit.js |
| [LaTeX Suite](https://github.com/artisticat1/obsidian-latex-suite) | Write chemistry equations easily with LaTeX packages such as `mhchem` and `chemfig`. |