megane-viewer 0.1.1 → 0.3.0

package/README.md

@@ -3,7 +3,8 @@
   megane
 </h1>
 
-<p align="center">Desktop-grade molecular visualization. Right in your browser.</p>
+<p align="center">Spectacles for atomistic data.</p>
+<p align="center"><em>1M+ atoms at 60fps. Visual pipelines. Jupyter, browser, React, VSCode.</em></p>
 
 <p align="center">
   <a href="https://github.com/hodakamori/megane/actions/workflows/ci.yml"><img src="https://github.com/hodakamori/megane/actions/workflows/ci.yml/badge.svg" alt="CI" /></a>
@@ -20,19 +21,58 @@
 </p>
 
 <p align="center">
-  <img src="docs/public/screenshots/hero.png" alt="megane screenshot" width="640" />
+  <img src="docs/public/screenshots/pipeline-complex.png" alt="megane screenshot" width="640" />
 </p>
 
 ---
 
 ## Features
 
-- **1M+ atoms at 60fps** — Billboard impostor rendering with WebGL handles massive protein complexes in real time
-- **Jupyter, CLI, React** — Use as a Jupyter widget, serve from the command line, or embed the React component in your own app
-- **Rust + WASM** — PDB, GRO, XYZ, MOL, and XTC parsers in Rust, shared between Python (PyO3) and browser (WASM)
-- **Trajectory streaming** — Stream XTC trajectories over WebSocket in real time, scrub through thousands of frames
-- **Atom selection & measurement** — Select 2–4 atoms to measure distances, angles, or dihedral angles
-- **Adaptive rendering** — High-quality InstancedMesh for small systems, auto-switches to Billboard Impostor for large systems
+- **1M+ Atoms at 60fps** — Billboard impostor rendering scales from small molecules to massive complexes in real time. InstancedMesh for small systems auto-switches to GPU-accelerated billboard impostors for large systems. Stream XTC trajectories over WebSocket.
+- **Runs Everywhere** — Jupyter widget, CLI server, React component, and VSCode extension. Rust-based PDB, GRO, XYZ, MOL, and XTC parsers shared between Python (PyO3) and browser (WASM) — parse once, run anywhere.
+- **Visual Pipeline Editor** — Build visualization workflows by wiring nodes. 8 node types (load, bond, filter, modify, labels, polyhedra, viewport) with 6 typed data channels (particle, bond, cell, label, mesh, trajectory) flowing through color-coded edges.
+- **Embed & Integrate** — Control the viewer from Plotly via ipywidgets events. Embed in MDX / Next.js docs. React to `frame_change`, `selection_change`, and `measurement` events. Use the framework-agnostic renderer from Vue, Svelte, or vanilla JS.
+
+### Scale
+
+megane renders over **1 million atoms at 60fps** in the browser. Small systems get high-quality InstancedMesh spheres and cylinders; large systems automatically switch to GPU-accelerated billboard impostors. No desktop app, no plugin — just a browser tab.
+
+Trajectory streaming works over WebSocket via a binary protocol. Load an XTC file and scrub through thousands of frames in real time, without reading everything into memory.
+
+### Anywhere
+
+One codebase, every environment.
+
+| Environment | How | Install |
+|---|---|---|
+| **Jupyter** | anywidget inline viewer | `pip install megane` |
+| **Browser** | `megane serve` local server | `pip install megane` |
+| **React** | `<MeganeViewer />` component | `npm install megane-viewer` |
+| **VSCode** | Custom editor for .pdb, .gro, .xyz | Extension |
+
+The secret: PDB, GRO, XYZ, MOL, and XTC parsers are written in **Rust** and compiled to both **PyO3** (Python) and **WASM** (browser). Parse once, run anywhere.
+
+### Visual Pipelines
+
+Wire nodes to build visualization workflows — no code required.
+
+**8 node types** across 5 categories: load data, add bonds, filter atoms by query, modify scale and opacity per-group, generate labels, render coordination polyhedra, and display in a 3D viewport.
+
+**6 typed data channels** — particle, bond, cell, label, mesh, trajectory — flow through color-coded edges. Only matching types can connect.
+
+Pipelines serialize to JSON, so you can save, share, and version-control your visualization recipes.
+
+### Integrate
+
+megane is not a walled garden. It fits into your existing workflow.
+
+**Plotly** — Click a point on a Plotly `FigureWidget` to jump to a trajectory frame. Use megane's `on_event("frame_change")` callback to update Plotly markers in sync.
+
+**MDX / Next.js** — Drop `<MeganeViewer />` or `<Viewport />` into your `.mdx` documentation. WASM parsing works out of the box with a one-line webpack config.
+
+**ipywidgets** — React to `frame_change`, `selection_change`, and `measurement` events. Compose megane with any widget in the Jupyter ecosystem.
+
+**Framework-agnostic** — `MoleculeRenderer` is a plain Three.js class. Mount it in Vue, Svelte, or a vanilla `<div>`.
 
 ## Installation
 

package/dist/megane-viewer.css

@@ -0,0 +1 @@
+.react-flow{direction:ltr;--xy-edge-stroke-default: #b1b1b7;--xy-edge-stroke-width-default: 1;--xy-edge-stroke-selected-default: #555;--xy-connectionline-stroke-default: #b1b1b7;--xy-connectionline-stroke-width-default: 1;--xy-attribution-background-color-default: rgba(255, 255, 255, .5);--xy-minimap-background-color-default: #fff;--xy-minimap-mask-background-color-default: rgba(240, 240, 240, .6);--xy-minimap-mask-stroke-color-default: transparent;--xy-minimap-mask-stroke-width-default: 1;--xy-minimap-node-background-color-default: #e2e2e2;--xy-minimap-node-stroke-color-default: transparent;--xy-minimap-node-stroke-width-default: 2;--xy-background-color-default: transparent;--xy-background-pattern-dots-color-default: #91919a;--xy-background-pattern-lines-color-default: #eee;--xy-background-pattern-cross-color-default: #e2e2e2;background-color:var(--xy-background-color, var(--xy-background-color-default));--xy-node-color-default: inherit;--xy-node-border-default: 1px solid #1a192b;--xy-node-background-color-default: #fff;--xy-node-group-background-color-default: rgba(240, 240, 240, .25);--xy-node-boxshadow-hover-default: 0 1px 4px 1px rgba(0, 0, 0, .08);--xy-node-boxshadow-selected-default: 0 0 0 .5px #1a192b;--xy-node-border-radius-default: 3px;--xy-handle-background-color-default: #1a192b;--xy-handle-border-color-default: #fff;--xy-selection-background-color-default: rgba(0, 89, 220, .08);--xy-selection-border-default: 1px dotted rgba(0, 89, 220, .8);--xy-controls-button-background-color-default: #fefefe;--xy-controls-button-background-color-hover-default: #f4f4f4;--xy-controls-button-color-default: inherit;--xy-controls-button-color-hover-default: inherit;--xy-controls-button-border-color-default: #eee;--xy-controls-box-shadow-default: 0 0 2px 1px rgba(0, 0, 0, .08);--xy-edge-label-background-color-default: #ffffff;--xy-edge-label-color-default: inherit;--xy-resize-background-color-default: #3367d9}.react-flow.dark{--xy-edge-stroke-default: #3e3e3e;--xy-edge-stroke-width-default: 1;--xy-edge-stroke-selected-default: #727272;--xy-connectionline-stroke-default: #b1b1b7;--xy-connectionline-stroke-width-default: 1;--xy-attribution-background-color-default: rgba(150, 150, 150, .25);--xy-minimap-background-color-default: #141414;--xy-minimap-mask-background-color-default: rgba(60, 60, 60, .6);--xy-minimap-mask-stroke-color-default: transparent;--xy-minimap-mask-stroke-width-default: 1;--xy-minimap-node-background-color-default: #2b2b2b;--xy-minimap-node-stroke-color-default: transparent;--xy-minimap-node-stroke-width-default: 2;--xy-background-color-default: #141414;--xy-background-pattern-dots-color-default: #777;--xy-background-pattern-lines-color-default: #777;--xy-background-pattern-cross-color-default: #777;--xy-node-color-default: #f8f8f8;--xy-node-border-default: 1px solid #3c3c3c;--xy-node-background-color-default: #1e1e1e;--xy-node-group-background-color-default: rgba(240, 240, 240, .25);--xy-node-boxshadow-hover-default: 0 1px 4px 1px rgba(255, 255, 255, .08);--xy-node-boxshadow-selected-default: 0 0 0 .5px #999;--xy-handle-background-color-default: #bebebe;--xy-handle-border-color-default: #1e1e1e;--xy-selection-background-color-default: rgba(200, 200, 220, .08);--xy-selection-border-default: 1px dotted rgba(200, 200, 220, .8);--xy-controls-button-background-color-default: #2b2b2b;--xy-controls-button-background-color-hover-default: #3e3e3e;--xy-controls-button-color-default: #f8f8f8;--xy-controls-button-color-hover-default: #fff;--xy-controls-button-border-color-default: #5b5b5b;--xy-controls-box-shadow-default: 0 0 2px 1px rgba(0, 0, 0, .08);--xy-edge-label-background-color-default: #141414;--xy-edge-label-color-default: #f8f8f8}.react-flow__background{background-color:var(--xy-background-color-props, var(--xy-background-color, var(--xy-background-color-default)));pointer-events:none;z-index:-1}.react-flow__container{position:absolute;width:100%;height:100%;top:0;left:0}.react-flow__pane{z-index:1}.react-flow__pane.draggable{cursor:grab}.react-flow__pane.dragging{cursor:grabbing}.react-flow__pane.selection{cursor:pointer}.react-flow__viewport{transform-origin:0 0;z-index:2;pointer-events:none}.react-flow__renderer{z-index:4}.react-flow__selection{z-index:6}.react-flow__nodesselection-rect:focus,.react-flow__nodesselection-rect:focus-visible{outline:none}.react-flow__edge-path{stroke:var(--xy-edge-stroke, var(--xy-edge-stroke-default));stroke-width:var(--xy-edge-stroke-width, var(--xy-edge-stroke-width-default));fill:none}.react-flow__connection-path{stroke:var(--xy-connectionline-stroke, var(--xy-connectionline-stroke-default));stroke-width:var(--xy-connectionline-stroke-width, var(--xy-connectionline-stroke-width-default));fill:none}.react-flow .react-flow__edges{position:absolute}.react-flow .react-flow__edges svg{overflow:visible;position:absolute;pointer-events:none}.react-flow__edge{pointer-events:visibleStroke}.react-flow__edge.selectable{cursor:pointer}.react-flow__edge.animated path{stroke-dasharray:5;animation:dashdraw .5s linear infinite}.react-flow__edge.animated path.react-flow__edge-interaction{stroke-dasharray:none;animation:none}.react-flow__edge.inactive{pointer-events:none}.react-flow__edge.selected,.react-flow__edge:focus,.react-flow__edge:focus-visible{outline:none}.react-flow__edge.selected .react-flow__edge-path,.react-flow__edge.selectable:focus .react-flow__edge-path,.react-flow__edge.selectable:focus-visible .react-flow__edge-path{stroke:var(--xy-edge-stroke-selected, var(--xy-edge-stroke-selected-default))}.react-flow__edge-textwrapper{pointer-events:all}.react-flow__edge .react-flow__edge-text{pointer-events:none;-webkit-user-select:none;-moz-user-select:none;user-select:none}.react-flow__arrowhead polyline{stroke:var(--xy-edge-stroke, var(--xy-edge-stroke-default))}.react-flow__arrowhead polyline.arrowclosed{fill:var(--xy-edge-stroke, var(--xy-edge-stroke-default))}.react-flow__connection{pointer-events:none}.react-flow__connection .animated{stroke-dasharray:5;animation:dashdraw .5s linear infinite}svg.react-flow__connectionline{z-index:1001;overflow:visible;position:absolute}.react-flow__nodes{pointer-events:none;transform-origin:0 0}.react-flow__node{position:absolute;-webkit-user-select:none;-moz-user-select:none;user-select:none;pointer-events:all;transform-origin:0 0;box-sizing:border-box;cursor:default}.react-flow__node.selectable{cursor:pointer}.react-flow__node.draggable{cursor:grab;pointer-events:all}.react-flow__node.draggable.dragging{cursor:grabbing}.react-flow__nodesselection{z-index:3;transform-origin:left top;pointer-events:none}.react-flow__nodesselection-rect{position:absolute;pointer-events:all;cursor:grab}.react-flow__handle{position:absolute;pointer-events:none;min-width:5px;min-height:5px;width:6px;height:6px;background-color:var(--xy-handle-background-color, var(--xy-handle-background-color-default));border:1px solid var(--xy-handle-border-color, var(--xy-handle-border-color-default));border-radius:100%}.react-flow__handle.connectingfrom{pointer-events:all}.react-flow__handle.connectionindicator{pointer-events:all;cursor:crosshair}.react-flow__handle-bottom{top:auto;left:50%;bottom:0;transform:translate(-50%,50%)}.react-flow__handle-top{top:0;left:50%;transform:translate(-50%,-50%)}.react-flow__handle-left{top:50%;left:0;transform:translate(-50%,-50%)}.react-flow__handle-right{top:50%;right:0;transform:translate(50%,-50%)}.react-flow__edgeupdater{cursor:move;pointer-events:all}.react-flow__pane.selection .react-flow__panel{pointer-events:none}.react-flow__panel{position:absolute;z-index:5;margin:15px}.react-flow__panel.top{top:0}.react-flow__panel.bottom{bottom:0}.react-flow__panel.top.center,.react-flow__panel.bottom.center{left:50%;transform:translate(-15px) translate(-50%)}.react-flow__panel.left{left:0}.react-flow__panel.right{right:0}.react-flow__panel.left.center,.react-flow__panel.right.center{top:50%;transform:translateY(-15px) translateY(-50%)}.react-flow__attribution{font-size:10px;background:var(--xy-attribution-background-color, var(--xy-attribution-background-color-default));padding:2px 3px;margin:0}.react-flow__attribution a{text-decoration:none;color:#999}@keyframes dashdraw{0%{stroke-dashoffset:10}}.react-flow__edgelabel-renderer{position:absolute;width:100%;height:100%;pointer-events:none;-webkit-user-select:none;-moz-user-select:none;user-select:none;left:0;top:0}.react-flow__viewport-portal{position:absolute;width:100%;height:100%;left:0;top:0;-webkit-user-select:none;-moz-user-select:none;user-select:none}.react-flow__minimap{background:var( --xy-minimap-background-color-props, var(--xy-minimap-background-color, var(--xy-minimap-background-color-default)) )}.react-flow__minimap-svg{display:block}.react-flow__minimap-mask{fill:var( --xy-minimap-mask-background-color-props, var(--xy-minimap-mask-background-color, var(--xy-minimap-mask-background-color-default)) );stroke:var( --xy-minimap-mask-stroke-color-props, var(--xy-minimap-mask-stroke-color, var(--xy-minimap-mask-stroke-color-default)) );stroke-width:var( --xy-minimap-mask-stroke-width-props, var(--xy-minimap-mask-stroke-width, var(--xy-minimap-mask-stroke-width-default)) )}.react-flow__minimap-node{fill:var( --xy-minimap-node-background-color-props, var(--xy-minimap-node-background-color, var(--xy-minimap-node-background-color-default)) );stroke:var( --xy-minimap-node-stroke-color-props, var(--xy-minimap-node-stroke-color, var(--xy-minimap-node-stroke-color-default)) );stroke-width:var( --xy-minimap-node-stroke-width-props, var(--xy-minimap-node-stroke-width, var(--xy-minimap-node-stroke-width-default)) )}.react-flow__background-pattern.dots{fill:var( --xy-background-pattern-color-props, var(--xy-background-pattern-color, var(--xy-background-pattern-dots-color-default)) )}.react-flow__background-pattern.lines{stroke:var( --xy-background-pattern-color-props, var(--xy-background-pattern-color, var(--xy-background-pattern-lines-color-default)) )}.react-flow__background-pattern.cross{stroke:var( --xy-background-pattern-color-props, var(--xy-background-pattern-color, var(--xy-background-pattern-cross-color-default)) )}.react-flow__controls{display:flex;flex-direction:column;box-shadow:var(--xy-controls-box-shadow, var(--xy-controls-box-shadow-default))}.react-flow__controls.horizontal{flex-direction:row}.react-flow__controls-button{display:flex;justify-content:center;align-items:center;height:26px;width:26px;padding:4px;border:none;background:var(--xy-controls-button-background-color, var(--xy-controls-button-background-color-default));border-bottom:1px solid var( --xy-controls-button-border-color-props, var(--xy-controls-button-border-color, var(--xy-controls-button-border-color-default)) );color:var( --xy-controls-button-color-props, var(--xy-controls-button-color, var(--xy-controls-button-color-default)) );cursor:pointer;-webkit-user-select:none;-moz-user-select:none;user-select:none}.react-flow__controls-button svg{width:100%;max-width:12px;max-height:12px;fill:currentColor}.react-flow__edge.updating .react-flow__edge-path{stroke:#777}.react-flow__edge-text{font-size:10px}.react-flow__node.selectable:focus,.react-flow__node.selectable:focus-visible{outline:none}.react-flow__node-input,.react-flow__node-default,.react-flow__node-output,.react-flow__node-group{padding:10px;border-radius:var(--xy-node-border-radius, var(--xy-node-border-radius-default));width:150px;font-size:12px;color:var(--xy-node-color, var(--xy-node-color-default));text-align:center;border:var(--xy-node-border, var(--xy-node-border-default));background-color:var(--xy-node-background-color, var(--xy-node-background-color-default))}.react-flow__node-input.selectable:hover,.react-flow__node-default.selectable:hover,.react-flow__node-output.selectable:hover,.react-flow__node-group.selectable:hover{box-shadow:var(--xy-node-boxshadow-hover, var(--xy-node-boxshadow-hover-default))}.react-flow__node-input.selectable.selected,.react-flow__node-input.selectable:focus,.react-flow__node-input.selectable:focus-visible,.react-flow__node-default.selectable.selected,.react-flow__node-default.selectable:focus,.react-flow__node-default.selectable:focus-visible,.react-flow__node-output.selectable.selected,.react-flow__node-output.selectable:focus,.react-flow__node-output.selectable:focus-visible,.react-flow__node-group.selectable.selected,.react-flow__node-group.selectable:focus,.react-flow__node-group.selectable:focus-visible{box-shadow:var(--xy-node-boxshadow-selected, var(--xy-node-boxshadow-selected-default))}.react-flow__node-group{background-color:var(--xy-node-group-background-color, var(--xy-node-group-background-color-default))}.react-flow__nodesselection-rect,.react-flow__selection{background:var(--xy-selection-background-color, var(--xy-selection-background-color-default));border:var(--xy-selection-border, var(--xy-selection-border-default))}.react-flow__nodesselection-rect:focus,.react-flow__nodesselection-rect:focus-visible,.react-flow__selection:focus,.react-flow__selection:focus-visible{outline:none}.react-flow__controls-button:hover{background:var( --xy-controls-button-background-color-hover-props, var(--xy-controls-button-background-color-hover, var(--xy-controls-button-background-color-hover-default)) );color:var( --xy-controls-button-color-hover-props, var(--xy-controls-button-color-hover, var(--xy-controls-button-color-hover-default)) )}.react-flow__controls-button:disabled{pointer-events:none}.react-flow__controls-button:disabled svg{fill-opacity:.4}.react-flow__controls-button:last-child{border-bottom:none}.react-flow__controls.horizontal .react-flow__controls-button{border-bottom:none;border-right:1px solid var( --xy-controls-button-border-color-props, var(--xy-controls-button-border-color, var(--xy-controls-button-border-color-default)) )}.react-flow__controls.horizontal .react-flow__controls-button:last-child{border-right:none}.react-flow__resize-control{position:absolute}.react-flow__resize-control.left,.react-flow__resize-control.right{cursor:ew-resize}.react-flow__resize-control.top,.react-flow__resize-control.bottom{cursor:ns-resize}.react-flow__resize-control.top.left,.react-flow__resize-control.bottom.right{cursor:nwse-resize}.react-flow__resize-control.bottom.left,.react-flow__resize-control.top.right{cursor:nesw-resize}.react-flow__resize-control.handle{width:5px;height:5px;border:1px solid #fff;border-radius:1px;background-color:var(--xy-resize-background-color, var(--xy-resize-background-color-default));translate:-50% -50%}.react-flow__resize-control.handle.left{left:0;top:50%}.react-flow__resize-control.handle.right{left:100%;top:50%}.react-flow__resize-control.handle.top{left:50%;top:0}.react-flow__resize-control.handle.bottom{left:50%;top:100%}.react-flow__resize-control.handle.top.left,.react-flow__resize-control.handle.bottom.left{left:0}.react-flow__resize-control.handle.top.right,.react-flow__resize-control.handle.bottom.right{left:100%}.react-flow__resize-control.line{border-color:var(--xy-resize-background-color, var(--xy-resize-background-color-default));border-width:0;border-style:solid}.react-flow__resize-control.line.left,.react-flow__resize-control.line.right{width:1px;transform:translate(-50%);top:0;height:100%}.react-flow__resize-control.line.left{left:0;border-left-width:1px}.react-flow__resize-control.line.right{left:100%;border-right-width:1px}.react-flow__resize-control.line.top,.react-flow__resize-control.line.bottom{height:1px;transform:translateY(-50%);left:0;width:100%}.react-flow__resize-control.line.top{top:0;border-top-width:1px}.react-flow__resize-control.line.bottom{border-bottom-width:1px;top:100%}.react-flow__edge-textbg{fill:var(--xy-edge-label-background-color, var(--xy-edge-label-background-color-default))}.react-flow__edge-text{fill:var(--xy-edge-label-color, var(--xy-edge-label-color-default))}