megane-viewer 0.5.0 → 0.6.0

package/README.md

@@ -96,23 +96,21 @@ npm install megane-viewer
 ### Jupyter Notebook
 
 ```python
-from megane import Pipeline, LoadStructure, AddBonds, Viewport, MolecularViewer
-
-# Build a pipeline
-pipe = Pipeline()
-s = pipe.add_node(LoadStructure("protein.pdb"))
-bonds = pipe.add_node(AddBonds(source="distance"))
-v = pipe.add_node(Viewport())
-pipe.add_edge(s.out.particle, bonds.inp.particle)
-pipe.add_edge(s.out.particle, v.inp.particle)
-pipe.add_edge(bonds.out.bond, v.inp.bond)
-
-# Display in notebook
-viewer = MolecularViewer()
-viewer.set_pipeline(pipe)
-viewer
+import megane
+
+viewer = megane.view("protein.pdb")
+viewer  # displays in notebook
+```
+
+With a trajectory:
+
+```python
+viewer = megane.view_traj("protein.pdb", xtc="trajectory.xtc")
+viewer.frame_index = 50  # jump to frame 50
 ```
 
+For advanced usage (filtering, multi-layer rendering, custom pipelines), see the [Pipeline API](https://hodakamori.github.io/megane/guide/pipeline#python-pipeline-api).
+
 ### CLI (Docker)
 
 ```bash
@@ -132,7 +130,7 @@ docker run --rm -p 8080:8080 -v ./mydata:/data megane \
 ### React
 
 ```tsx
-import { MeganeViewer, parseStructureFile } from "megane-viewer";
+import { MeganeViewer, parseStructureFile } from "megane-viewer/lib";
 
 function App() {
   const [snapshot, setSnapshot] = useState(null);
@@ -148,15 +146,22 @@ function App() {
 
 ## Supported File Formats
 
+### Structure formats (`LoadStructure` node)
+
 | Format | Extension | Description |
 |--------|-----------|-------------|
 | PDB | `.pdb` | Protein Data Bank |
 | GRO | `.gro` | GROMACS structure file |
 | XYZ | `.xyz` | Cartesian coordinate format |
 | MOL/SDF | `.mol`, `.sdf` | MDL Molfile (V2000) |
-| XTC | `.xtc` | GROMACS compressed trajectory |
-| CIF | `.cif` | Crystallographic Information File |
 | LAMMPS data | `.data`, `.lammps` | LAMMPS data file |
+| CIF | `.cif` | Crystallographic Information File |
+
+### 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 |
 

package/dist/assets/decode.worker-COS7O5zc.js

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

package/dist/gif-BkZ9uDOZ.js

@@ -0,0 +1,284 @@
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+    }
+  }
+  return Object.freeze(Object.defineProperty(_, Symbol.toStringTag, { value: "Module" }));
+}
+function L(_) {
+  throw new Error('Could not dynamically require "' + _ + '". Please configure the dynamicRequireTargets or/and ignoreDynamicRequires option of @rollup/plugin-commonjs appropriately for this require call to work.');
+}
+var D = { exports: {} }, R;
+function M() {
+  return R || (R = 1, (function(_, E) {
+    (function(m) {
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+          g(a, n), f = { workerScript: "gif.worker.js", workers: 2, repeat: 0, background: "#fff", quality: 10, width: null, height: null, transparent: null, debug: !1, dither: !1 }, c = { delay: 500, copy: !1 };
+          function a(e) {
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+          }, a.prototype.setOptions = function(e) {
+            var r, i, h;
+            i = [];
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+            else
+              throw new Error("Invalid image");
+            return this.frames.push(i);
+          }, a.prototype.render = function() {
+            var e, r, i;
+            if (this.running)
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+            if (this.options.width == null || this.options.height == null)
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+            return this.emit("start"), this.emit("progress", 0);
+          }, a.prototype.abort = function() {
+            for (var e; e = this.activeWorkers.shift(), e != null; )
+              this.log("killing active worker"), e.terminate();
+            return this.running = !1, this.emit("abort");
+          }, a.prototype.spawnWorkers = function() {
+            var e, r, i;
+            return e = Math.min(this.options.workers, this.frames.length), (function() {
+              i = [];
+              for (var h = r = this.freeWorkers.length; r <= e ? h < e : h > e; r <= e ? h++ : h--)
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+              };
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+          }, a.prototype.frameFinished = function(e) {
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+            if (this.log("frame " + e.index + " finished - " + this.activeWorkers.length + " active"), this.finishedFrames++, this.emit("progress", this.finishedFrames / this.frames.length), this.imageParts[e.index] = e, this.options.globalPalette === !0 && (this.options.globalPalette = e.globalPalette, this.log("global palette analyzed"), this.frames.length > 2))
+              for (r = 1, i = this.freeWorkers.length; 1 <= i ? r < i : r > i; 1 <= i ? ++r : --r)
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+            return t.call(this.imageParts, null) >= 0 ? this.renderNextFrame() : this.finishRendering();
+          }, a.prototype.finishRendering = function() {
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+            return h = new Blob([e], { type: "image/gif" }), this.emit("finished", h, e);
+          }, a.prototype.renderNextFrame = function() {
+            var e, r, i;
+            if (this.freeWorkers.length === 0)
+              throw new Error("No free workers");
+            if (!(this.nextFrame >= this.frames.length))
+              return e = this.frames[this.nextFrame++], i = this.freeWorkers.shift(), r = this.getTask(e), this.log("starting frame " + (r.index + 1) + " of " + this.frames.length), this.activeWorkers.push(i), i.postMessage(r);
+          }, a.prototype.getContextData = function(e) {
+            return e.getImageData(0, 0, this.options.width, this.options.height).data;
+          }, a.prototype.getImageData = function(e) {
+            var r;
+            return this._canvas == null && (this._canvas = document.createElement("canvas"), this._canvas.width = this.options.width, this._canvas.height = this.options.height), r = this._canvas.getContext("2d"), r.setFill = this.options.background, r.fillRect(0, 0, this.options.width, this.options.height), r.drawImage(e, 0, 0), this.getContextData(r);
+          }, a.prototype.getTask = function(e) {
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+            else if (e.image != null)
+              i.data = this.getImageData(e.image);
+            else
+              throw new Error("Invalid frame");
+            return i;
+          }, a.prototype.log = function() {
+            var e;
+            if (e = 1 <= arguments.length ? s.call(arguments, 0) : [], !!this.options.debug)
+              return console.log.apply(console, e);
+          }, a;
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+}
+var q = M();
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+}, [q]);
+export {
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