megane-viewer 0.6.2 → 0.8.0

package/README.md

@@ -32,8 +32,8 @@
 ## Features
 
 - **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, CIF, XTC, LAMMPS, and ASE .traj parsers shared between Python (PyO3) and browser (WASM) — parse once, run anywhere.
-- **Visual Pipeline Editor** — Build visualization workflows by wiring nodes or let the AI generator build them from natural language. 11 node types with 7 typed data channels flowing through color-coded edges. Load multiple structures with layer-based rendering to compare systems side by side.
+- **Runs Everywhere** — Jupyter widget, CLI server, React component, and VSCode extension. Rust-based parsers for 15 formats (PDB, GRO, XYZ, MOL/SDF, MOL2, CIF, mmCIF, LAMMPS data, AMBER topology, XTC, DCD, ASE .traj, LAMMPS dump, AMBER NetCDF) shared between Python (PyO3) and browser (WASM) — parse once, run anywhere.
+- **Visual Pipeline Editor** — Build visualization workflows by wiring nodes or let the AI generator build them from natural language. 16 node types with 7 typed data channels flowing through color-coded edges. Load multiple structures with layer-based rendering to compare systems side by side.
 - **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
@@ -49,19 +49,22 @@ One codebase, every environment.
 | Environment | How | Install |
 |---|---|---|
 | **Jupyter** | anywidget inline viewer | `pip install megane` |
+| **JupyterLab** | Open .pdb, .gro, .xyz, .mol, .sdf, .mol2, .cif, .mmcif, .data/.lammps, .prmtop, .traj, .xtc, .dcd, .nc, .lammpstrj/.dump, .megane.json from the file browser | `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, .mol, .sdf, .cif | Extension |
+| **VSCode** | Custom editor for .pdb, .gro, .xyz, .mol, .sdf, .mol2, .cif, .mmcif, .data/.lammps, .prmtop, .traj, .xtc, .lammpstrj, .dump, .dcd, .nc, .megane.json | Extension |
 
-The secret: PDB, GRO, XYZ, MOL, CIF, XTC, LAMMPS, and ASE .traj parsers are written in **Rust** and compiled to both **PyO3** (Python) and **WASM** (browser). Parse once, run anywhere.
+For a per-platform breakdown of supported formats and UI features (including known gaps), see [Platform Support](https://hodakamori.github.io/megane/platform-support).
+
+The secret: parsers for 15 formats (PDB, GRO, XYZ, MOL/SDF, MOL2, CIF, mmCIF, LAMMPS data, AMBER topology, XTC, DCD, ASE .traj, LAMMPS dump, AMBER NetCDF) 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.
 
-**11 node types** across 5 categories: load data (structure, trajectory, streaming, vector), process (filter, modify), overlay (bonds, labels, polyhedra, vectors), and display in a 3D viewport.
+**16 node types** across 5 categories: load data (structure, trajectory, streaming, vector, volumetric), bonds, process (filter, modify, color, representation), overlay (labels, polyhedra, surface meshes, isosurfaces, vectors), and display in a 3D viewport.
 
-**7 typed data channels** — particle, bond, cell, label, mesh, trajectory, vector — flow through color-coded edges. Only matching types can connect.
+**8 typed data channels** — particle, bond, cell, label, mesh, trajectory, vector, volumetric — 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.
 
@@ -130,17 +133,21 @@ docker run --rm -p 8080:8080 -v ./mydata:/data megane \
 ### React
 
 ```tsx
-import { MeganeViewer, parseStructureFile } from "megane-viewer/lib";
+import { useCallback } from "react";
+import { MeganeViewer, usePipelineStore } from "megane-viewer/lib";
 
 function App() {
-  const [snapshot, setSnapshot] = useState(null);
-
-  const handleUpload = async (file: File) => {
-    const result = await parseStructureFile(file);
-    setSnapshot(result.snapshot);
-  };
-
-  return <MeganeViewer snapshot={snapshot} mode="local" /* ... */ />;
+  const handleUpload = useCallback((file: File) => {
+    usePipelineStore.getState().openFile(file);
+  }, []);
+
+  return (
+    <MeganeViewer
+      onUploadStructure={handleUpload}
+      width="100%"
+      height="600px"
+    />
+  );
 }
 ```
 
@@ -154,16 +161,21 @@ function App() {
 | GRO | `.gro` | GROMACS structure file |
 | XYZ | `.xyz` | Cartesian coordinate format |
 | MOL/SDF | `.mol`, `.sdf` | MDL Molfile (V2000) |
+| MOL2 | `.mol2` | Tripos MOL2 (multi-molecule, aromatic bonds) |
 | LAMMPS data | `.data`, `.lammps` | LAMMPS data file |
 | CIF | `.cif` | Crystallographic Information File |
+| mmCIF | `.mmcif` | Macromolecular CIF (PDBx/mmCIF) |
+| AMBER topology | `.prmtop` | AMBER parameter/topology file (atom names, elements, bonds) |
+| ASE .traj | `.traj` | ASE trajectory (ULM binary format) — self-contained with elements, bonds, and frames |
 
 ### Trajectory formats (`LoadTrajectory` node)
 
 | Format | Extension | Description |
 |--------|-----------|-------------|
 | XTC | `.xtc` | GROMACS compressed trajectory |
-| ASE .traj | `.traj` | ASE trajectory (ULM binary format) |
-| LAMMPS dump | `.lammpstrj` | LAMMPS dump trajectory |
+| DCD | `.dcd` | CHARMM/NAMD binary trajectory |
+| AMBER NetCDF | `.nc` | AMBER NetCDF trajectory |
+| LAMMPS dump | `.lammpstrj`, `.dump` | LAMMPS dump trajectory |
 
 ## Development
 
@@ -226,7 +238,7 @@ make test-all              # All tests
 src/                     TypeScript frontend
   renderer/              Three.js rendering (impostor, mesh, shaders)
   protocol/              Binary protocol decoder + web workers
-  parsers/               WASM-based file parsers (PDB, GRO, XYZ, MOL, CIF, XTC, LAMMPS, .traj)
+  parsers/               WASM-based file parsers (15 formats: PDB, GRO, XYZ, MOL/SDF, MOL2, CIF, mmCIF, LAMMPS data/dump, AMBER topology/NetCDF, XTC, DCD, ASE .traj)
   logic/                 Bond / label / vector source logic
   components/            React UI components
   hooks/                 Custom React hooks
@@ -236,7 +248,7 @@ crates/                  Rust workspace
   megane-python/         PyO3 Python extension
   megane-wasm/           WASM bindings (wasm-bindgen)
 python/megane/           Python backend
-  parsers/               PDB / XTC parsers
+  parsers/               Python wrappers for 13 of the 15 supported formats (mmCIF and AMBER prmtop are accessible via the raw megane_parser PyO3 extension)
   pipeline.py            Pipeline builder (NetworkX-style DAG)
   protocol.py            Binary protocol encoder
   server.py              FastAPI WebSocket server

package/dist/assets/decode.worker-BcZeHdFu.js

@@ -0,0 +1 @@
+(function(){"use strict";function d(r){const e=new DataView(r),s=e.getUint32(0,!0);if(s!==1313293645)throw new Error(`Invalid magic: 0x${s.toString(16)}, expected 0x4e47454d`);return{msgType:e.getUint8(4),flags:e.getUint8(5)}}function l(r){const e=new DataView(r),s=e.getUint8(5);let n=8;const t=e.getUint32(n,!0);n+=4;const o=e.getUint32(n,!0);n+=4;const m=new Float32Array(r,n,t*3);n+=t*3*4;const A=new Uint8Array(r,n,t);n+=t,n+=(4-n%4)%4;const g=new Uint32Array(r,n,o*2);n+=o*2*4;let a=null;s&1&&(a=new Uint8Array(r,n,o),n+=o,n+=(4-n%4)%4);let c=null;return s&2&&(c=new Float32Array(r,n,9),n+=36),{nAtoms:t,nBonds:o,nFileBonds:o,positions:m,elements:A,bonds:g,bondOrders:a,box:c,atomChainIds:null,atomBFactors:null}}function f(r){const e=new DataView(r);let s=8;const n=e.getUint32(s,!0);s+=4;const t=e.getUint32(s,!0);s+=4;const o=new Float32Array(r,s,t*3);return{frameId:n,nAtoms:t,positions:o}}const i=self;i.onmessage=r=>{const{id:e,buffer:s}=r.data;try{const{msgType:n}=d(s);if(n===0){const t=l(s),o=[t.positions.buffer,t.elements.buffer,t.bonds.buffer];t.bondOrders&&o.push(t.bondOrders.buffer),t.box&&o.push(t.box.buffer),i.postMessage({id:e,type:"snapshot",data:{nAtoms:t.nAtoms,nBonds:t.nBonds,nFileBonds:t.nFileBonds,positions:t.positions,elements:t.elements,bonds:t.bonds,bondOrders:t.bondOrders,box:t.box,atomChainIds:null,atomBFactors:null}},o)}else if(n===1){const t=f(s),o=[t.positions.buffer];i.postMessage({id:e,type:"frame",data:{frameId:t.frameId,nAtoms:t.nAtoms,positions:t.positions}},o)}}catch(n){i.postMessage({id:e,type:"error",error:n instanceof Error?n.message:String(n)})}}})();

package/dist/{gif-BkoUK__l.js → gif-CsP6AQIk.js}

@@ -1,4 +1,4 @@
-import { g as A } from "./lib-Bf1GV7sy.js";
+import { g as A } from "./lib-d68cwxNq.js";
 function j(_, E) {
   for (var m = 0; m < E.length; m++) {
     const p = E[m];