# Ohai Markdown Reader Documentation

> Native macOS Markdown reader for live AI workflows, source-aware documentation, chemistry and biology notes, and shareable export.

Ohai Markdown Reader turns Markdown into a live working surface. It is useful when an AI assistant is writing files over time, when documentation needs to stay connected to source code, when chemistry or biology notes need rendered scientific structures, and when a rendered document needs to become HTML, PDF, DOCX, or processed Markdown.

## Availability

| Field | Value |
|-------|-------|
| Platform | macOS 14.0 Sonoma or later |
| Distribution | Mac App Store |
| Price | $19.99 USD one-time purchase |
| Website | https://www.ohaimarkdown.com |
| Support | support@ohaimarkdown.com |

## Core Capabilities

- Instant Markdown reload with support for editors that use atomic saves.
- Source-aware transclusion with `![[file]]`, section, symbol, and data-path references.
- Syntax highlighting for 185+ languages.
- Scientific rendering for chemistry, biology, diagrams, charts, math, and media.
- Large document handling with virtualization for long files.
- Composer for drafting Markdown with live preview and AI handoff helpers.
- Finder QuickLook previews and thumbnails for Markdown files.
- Export to HTML, PDF, DOCX, and processed Markdown.
- CLI and AppleScript automation.
- Website and app-facing copy across 20 locale bundles.

## User Journeys

### AI Pairing and Progress Files

Open a Markdown file in Ohai while Claude Code, Codex, or another assistant writes to it. The user can watch sections appear, task lists complete, tables fill in, and generated charts load without manually refreshing.

Good fit:

- Multi-step engineering tasks.
- Code review packets.
- Data analysis reports.
- Migration checklists.
- Release readiness docs.
- Long-running agent work where the user needs a live status surface.

### Chemistry and Medchem Notes

Ohai supports chemistry-heavy Markdown where compounds and assay data should be read together.

Useful patterns:

- SMILES and reaction SMILES blocks.
- Inline `smi:` structures inside medchem SAR tables.
- Tables with potency, selectivity, ADME, liability, and notes columns.
- 3Dmol.js molecular views in fenced `3dmol` blocks.
- ELN-style attachments such as local images, generated plots, videos, and transcluded notes.

Example:

```markdown
| Compound | Structure | IC50 | Notes |
|----------|-----------|------|-------|
| A-101 | `smi:CC(=O)Oc1ccccc1C(=O)O` | 12 uM | reference |
| B-204 | `smi:CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O` | 8 uM | chiral center |
```

### Biology Notes

Ohai supports biological sequence and structure notes that combine prose, diagrams, data, and local attachments.

Useful patterns:

- Fenced `seqviz` blocks for plasmids and construct maps.
- Fenced `phylotree` or Newick blocks for phylogenetic trees.
- Fenced `3dmol` blocks for molecular structures.
- Ideogram visualizations for chromosome context.
- Chart.js, KaTeX, local images, videos, and generated plots.

### Source-Aware Documentation

Use transclusion to keep docs connected to source files.

```markdown
![[README.md#Install]]
![[src/auth.ts#validateToken]]
![[config.yaml#database.host]]
![[packages/api/CHANGELOG.md]]
```

This is useful for living API docs, architecture notes, monorepo dashboards, onboarding docs, and release checklists.

### Export and Sharing

Use Ohai when the rendered Markdown needs to leave the app:

- HTML for web publishing or portable previews.
- PDF for review packets and sharing.
- DOCX for editable Word workflows.
- Processed Markdown when transcluded content should be materialized.

## Markdown Support

| Family | Supported patterns |
|--------|--------------------|
| Core Markdown | headings, emphasis, lists, links, blockquotes, code, tables |
| GFM | task lists, strikethrough, tables |
| Obsidian-style syntax | `![[file]]` transclusion, `==highlight==`, `%%comments%%`, callouts |
| Code | syntax highlighting and source-aware symbol extraction |
| Chemistry | SMILES, reaction SMILES, inline SMILES, 3Dmol.js molecular views |
| Biology | SeqViz, phylotree/Newick, 3Dmol.js, Ideogram |
| Visuals | Mermaid, Graphviz DOT, Chart.js, KaTeX, ABC music, images, videos |

## CLI

```bash
open -a "Ohai Markdown Reader" report.md
echo "# Status" | ohaimarkdown
ohaimarkdown export html input.md -o output.html
ohaimarkdown export md input.md -o output.md
```

If `ohaimarkdown` is not found, install the command line tool from Ohai settings.

## Agent-Readable Site Resources

- `/llms.txt` - discovery index.
- `/llm.txt` - singular alias.
- `/llms-full.txt` - full guide.
- `/api/docs.md` - website API docs.
- `/api/docs` - extensionless API docs.
- `/claude-md-templates.txt` - reusable templates.