# Aminak Phase 14 — downloadable bundle

You unzipped a self-contained version of the project deck.

## Quick start

1. **Open the deck**: double-click `aminak_phase14_summary.pptx`.
2. **Click any deep-linked text** (deep-blue, monospace). The links open files
   that live next to the PPTX:
   - `cavity18_viewers/*.html` — 3D-mol.js viewers, opens in any browser.
   - `data/*.csv` / `*.json` — numerical results, opens in Excel / Numbers.
   - `receptor/*.pdb*` — receptor structures, opens in PyMOL / ChimeraX.

## Layout

| Folder | What's inside |
|---|---|
| `figures/` | All PNGs embedded in the deck — re-usable. |
| `cavity18_viewers/` | Interactive 3Dmol.js HTMLs + the complex PDBs. |
| `receptor/` | Phase-6c hardened apo + holo dimer PDBQT/PDB. |
| `data/` | Master result CSVs, per-strategy summaries, MM-GBSA + HADDOCK3 outputs. |
| `docs/` | Project README, Phase 14 educational README, technical notes. |

## The live repo

Browse, fork, re-run: **https://github.com/ArioMoniri/aminak**

Live 3D viewers on the web: **https://ariomoniri.github.io/aminak/viewers/**

## Interactive pipeline DAG

Open `viewers/pipeline/index.html` (or live: <https://ariomoniri.github.io/aminak/viewers/pipeline/>) — a topologically-sorted Kahn longest-path layout of the 8 phases. Hover any node to trace its full upstream + downstream lineage; click to pin a detail drawer. *Design handoff from Claude Design.*

## Embedded Web Viewer (optional, manual install)

To make any slide carry the live interactive plot or 3D-mol viewer *inside* the slide:

1. Open the deck in PowerPoint (Win, Mac, or Office Online).
2. **Insert → Get Add-ins → Store** → search **"Web Viewer"** by Microsoft → **Add**.
3. **Insert → My Add-ins → Web Viewer**. A frame appears on the slide.
4. Paste any of these URLs into the address bar at the bottom of the frame and click **Preview**:
   - Pipeline DAG: <https://ariomoniri.github.io/aminak/viewers/pipeline/>
   - Cavity-18 indazole: <https://ariomoniri.github.io/aminak/14_inhibitor_design/04_allosteric/cavity18_evidence/viewers/cavity18_indazole.html>
   - Cavity-18 ibuprofen: <https://ariomoniri.github.io/aminak/14_inhibitor_design/04_allosteric/cavity18_evidence/viewers/cavity18_ibuprofen.html>

(I tried to bake the Web Viewer add-in into the deck programmatically but PowerPoint Mac's strict schema validator rejected every variant of the required OOXML I produced. The deep-link buttons on the affected slides open the same URLs in your default browser instead.)
