megane-viewer 0.5.0 → 0.6.1

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-BOhv0bDx.js

@@ -0,0 +1,284 @@
+import { g as A } from "./lib-D3sqoP7c.js";
+function j(_, E) {
+  for (var m = 0; m < E.length; m++) {
+    const p = E[m];
+    if (typeof p != "string" && !Array.isArray(p)) {
+      for (const v in p)
+        if (v !== "default" && !(v in _)) {
+          const o = Object.getOwnPropertyDescriptor(p, v);
+          o && Object.defineProperty(_, v, o.get ? o : {
+            enumerable: !0,
+            get: () => p[v]
+          });
+        }
+    }
+  }
+  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) {
+      _.exports = m();
+    })(function() {
+      return (function m(p, v, o) {
+        function l(u, t) {
+          if (!v[u]) {
+            if (!p[u]) {
+              var s = typeof L == "function" && L;
+              if (!t && s) return s(u, !0);
+              if (x) return x(u, !0);
+              var n = new Error("Cannot find module '" + u + "'");
+              throw n.code = "MODULE_NOT_FOUND", n;
+            }
+            var f = v[u] = { exports: {} };
+            p[u][0].call(f.exports, function(c) {
+              var a = p[u][1][c];
+              return l(a || c);
+            }, f, f.exports, m, p, v, o);
+          }
+          return v[u].exports;
+        }
+        for (var x = typeof L == "function" && L, g = 0; g < o.length; g++) l(o[g]);
+        return l;
+      })({ 1: [function(m, p, v) {
+        function o() {
+          this._events = this._events || {}, this._maxListeners = this._maxListeners || void 0;
+        }
+        p.exports = o, o.EventEmitter = o, o.prototype._events = void 0, o.prototype._maxListeners = void 0, o.defaultMaxListeners = 10, o.prototype.setMaxListeners = function(t) {
+          if (!x(t) || t < 0 || isNaN(t)) throw TypeError("n must be a positive number");
+          return this._maxListeners = t, this;
+        }, o.prototype.emit = function(t) {
+          var s, n, f, c, a, e;
+          if (this._events || (this._events = {}), t === "error" && (!this._events.error || g(this._events.error) && !this._events.error.length)) {
+            if (s = arguments[1], s instanceof Error)
+              throw s;
+            var r = new Error('Uncaught, unspecified "error" event. (' + s + ")");
+            throw r.context = s, r;
+          }
+          if (n = this._events[t], u(n)) return !1;
+          if (l(n))
+            switch (arguments.length) {
+              case 1:
+                n.call(this);
+                break;
+              case 2:
+                n.call(this, arguments[1]);
+                break;
+              case 3:
+                n.call(this, arguments[1], arguments[2]);
+                break;
+              default:
+                c = Array.prototype.slice.call(arguments, 1), n.apply(this, c);
+            }
+          else if (g(n))
+            for (c = Array.prototype.slice.call(arguments, 1), e = n.slice(), f = e.length, a = 0; a < f; a++) e[a].apply(this, c);
+          return !0;
+        }, o.prototype.addListener = function(t, s) {
+          var n;
+          if (!l(s)) throw TypeError("listener must be a function");
+          return this._events || (this._events = {}), this._events.newListener && this.emit("newListener", t, l(s.listener) ? s.listener : s), this._events[t] ? g(this._events[t]) ? this._events[t].push(s) : this._events[t] = [this._events[t], s] : this._events[t] = s, g(this._events[t]) && !this._events[t].warned && (u(this._maxListeners) ? n = o.defaultMaxListeners : n = this._maxListeners, n && n > 0 && this._events[t].length > n && (this._events[t].warned = !0, console.error("(node) warning: possible EventEmitter memory leak detected. %d listeners added. Use emitter.setMaxListeners() to increase limit.", this._events[t].length), typeof console.trace == "function" && console.trace())), this;
+        }, o.prototype.on = o.prototype.addListener, o.prototype.once = function(t, s) {
+          if (!l(s)) throw TypeError("listener must be a function");
+          var n = !1;
+          function f() {
+            this.removeListener(t, f), n || (n = !0, s.apply(this, arguments));
+          }
+          return f.listener = s, this.on(t, f), this;
+        }, o.prototype.removeListener = function(t, s) {
+          var n, f, c, a;
+          if (!l(s)) throw TypeError("listener must be a function");
+          if (!this._events || !this._events[t]) return this;
+          if (n = this._events[t], c = n.length, f = -1, n === s || l(n.listener) && n.listener === s)
+            delete this._events[t], this._events.removeListener && this.emit("removeListener", t, s);
+          else if (g(n)) {
+            for (a = c; a-- > 0; )
+              if (n[a] === s || n[a].listener && n[a].listener === s) {
+                f = a;
+                break;
+              }
+            if (f < 0) return this;
+            n.length === 1 ? (n.length = 0, delete this._events[t]) : n.splice(f, 1), this._events.removeListener && this.emit("removeListener", t, s);
+          }
+          return this;
+        }, o.prototype.removeAllListeners = function(t) {
+          var s, n;
+          if (!this._events) return this;
+          if (!this._events.removeListener)
+            return arguments.length === 0 ? this._events = {} : this._events[t] && delete this._events[t], this;
+          if (arguments.length === 0) {
+            for (s in this._events)
+              s !== "removeListener" && this.removeAllListeners(s);
+            return this.removeAllListeners("removeListener"), this._events = {}, this;
+          }
+          if (n = this._events[t], l(n))
+            this.removeListener(t, n);
+          else if (n)
+            for (; n.length; ) this.removeListener(t, n[n.length - 1]);
+          return delete this._events[t], this;
+        }, o.prototype.listeners = function(t) {
+          var s;
+          return !this._events || !this._events[t] ? s = [] : l(this._events[t]) ? s = [this._events[t]] : s = this._events[t].slice(), s;
+        }, o.prototype.listenerCount = function(t) {
+          if (this._events) {
+            var s = this._events[t];
+            if (l(s)) return 1;
+            if (s) return s.length;
+          }
+          return 0;
+        }, o.listenerCount = function(t, s) {
+          return t.listenerCount(s);
+        };
+        function l(t) {
+          return typeof t == "function";
+        }
+        function x(t) {
+          return typeof t == "number";
+        }
+        function g(t) {
+          return typeof t == "object" && t !== null;
+        }
+        function u(t) {
+          return t === void 0;
+        }
+      }, {}], 2: [function(m, p, v) {
+        var o, l, x, g, u;
+        u = navigator.userAgent.toLowerCase(), g = navigator.platform.toLowerCase(), o = u.match(/(opera|ie|firefox|chrome|version)[\s\/:]([\w\d\.]+)?.*?(safari|version[\s\/:]([\w\d\.]+)|$)/) || [null, "unknown", 0], x = o[1] === "ie" && document.documentMode, l = { name: o[1] === "version" ? o[3] : o[1], version: x || parseFloat(o[1] === "opera" && o[4] ? o[4] : o[2]), platform: { name: u.match(/ip(?:ad|od|hone)/) ? "ios" : (u.match(/(?:webos|android)/) || g.match(/mac|win|linux/) || ["other"])[0] } }, l[l.name] = !0, l[l.name + parseInt(l.version, 10)] = !0, l.platform[l.platform.name] = !0, p.exports = l;
+      }, {}], 3: [function(m, p, v) {
+        var o, l, x, g = function(n, f) {
+          for (var c in f)
+            u.call(f, c) && (n[c] = f[c]);
+          function a() {
+            this.constructor = n;
+          }
+          return a.prototype = f.prototype, n.prototype = new a(), n.__super__ = f.prototype, n;
+        }, u = {}.hasOwnProperty, t = [].indexOf || function(n) {
+          for (var f = 0, c = this.length; f < c; f++)
+            if (f in this && this[f] === n) return f;
+          return -1;
+        }, s = [].slice;
+        o = m("events").EventEmitter, x = m("./browser.coffee"), l = (function(n) {
+          var f, c;
+          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) {
+            var r, i, h;
+            this.running = !1, this.options = {}, this.frames = [], this.freeWorkers = [], this.activeWorkers = [], this.setOptions(e);
+            for (i in f)
+              h = f[i], (r = this.options)[i] == null && (r[i] = h);
+          }
+          return a.prototype.setOption = function(e, r) {
+            if (this.options[e] = r, this._canvas != null && (e === "width" || e === "height"))
+              return this._canvas[e] = r;
+          }, a.prototype.setOptions = function(e) {
+            var r, i, h;
+            i = [];
+            for (r in e)
+              u.call(e, r) && (h = e[r], i.push(this.setOption(r, h)));
+            return i;
+          }, a.prototype.addFrame = function(e, r) {
+            var i, h;
+            r == null && (r = {}), i = {}, i.transparent = this.options.transparent;
+            for (h in c)
+              i[h] = r[h] || c[h];
+            if (this.options.width == null && this.setOption("width", e.width), this.options.height == null && this.setOption("height", e.height), typeof ImageData < "u" && ImageData !== null && e instanceof ImageData)
+              i.data = e.data;
+            else if (typeof CanvasRenderingContext2D < "u" && CanvasRenderingContext2D !== null && e instanceof CanvasRenderingContext2D || typeof WebGLRenderingContext < "u" && WebGLRenderingContext !== null && e instanceof WebGLRenderingContext)
+              r.copy ? i.data = this.getContextData(e) : i.context = e;
+            else if (e.childNodes != null)
+              r.copy ? i.data = this.getImageData(e) : i.image = e;
+            else
+              throw new Error("Invalid image");
+            return this.frames.push(i);
+          }, a.prototype.render = function() {
+            var e, r, i;
+            if (this.running)
+              throw new Error("Already running");
+            if (this.options.width == null || this.options.height == null)
+              throw new Error("Width and height must be set prior to rendering");
+            if (this.running = !0, this.nextFrame = 0, this.finishedFrames = 0, this.imageParts = (function() {
+              var h, w, d;
+              for (d = [], h = 0, w = this.frames.length; 0 <= w ? h < w : h > w; 0 <= w ? ++h : --h)
+                d.push(null);
+              return d;
+            }).call(this), r = this.spawnWorkers(), this.options.globalPalette === !0)
+              this.renderNextFrame();
+            else
+              for (e = 0, i = r; 0 <= i ? e < i : e > i; 0 <= i ? ++e : --e)
+                this.renderNextFrame();
+            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--)
+                i.push(h);
+              return i;
+            }).apply(this).forEach(/* @__PURE__ */ (function(h) {
+              return function(w) {
+                var d;
+                return h.log("spawning worker " + w), d = new Worker(h.options.workerScript), d.onmessage = function(y) {
+                  return h.activeWorkers.splice(h.activeWorkers.indexOf(d), 1), h.freeWorkers.push(d), h.frameFinished(y.data);
+                }, h.freeWorkers.push(d);
+              };
+            })(this)), e;
+          }, a.prototype.frameFinished = function(e) {
+            var r, i;
+            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)
+                this.renderNextFrame();
+            return t.call(this.imageParts, null) >= 0 ? this.renderNextFrame() : this.finishRendering();
+          }, a.prototype.finishRendering = function() {
+            var e, r, i, h, w, d, y, b, O, P, I, k, N, C, W, F;
+            for (b = 0, C = this.imageParts, w = 0, O = C.length; w < O; w++)
+              r = C[w], b += (r.data.length - 1) * r.pageSize + r.cursor;
+            for (b += r.pageSize - r.cursor, this.log("rendering finished - filesize " + Math.round(b / 1e3) + "kb"), e = new Uint8Array(b), k = 0, W = this.imageParts, d = 0, P = W.length; d < P; d++)
+              for (r = W[d], F = r.data, i = y = 0, I = F.length; y < I; i = ++y)
+                N = F[i], e.set(N, k), i === r.data.length - 1 ? k += r.cursor : k += r.pageSize;
+            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) {
+            var r, i;
+            if (r = this.frames.indexOf(e), i = { index: r, last: r === this.frames.length - 1, delay: e.delay, transparent: e.transparent, width: this.options.width, height: this.options.height, quality: this.options.quality, dither: this.options.dither, globalPalette: this.options.globalPalette, repeat: this.options.repeat, canTransfer: x.name === "chrome" }, e.data != null)
+              i.data = e.data;
+            else if (e.context != null)
+              i.data = this.getContextData(e.context);
+            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;
+        })(o), p.exports = l;
+      }, { "./browser.coffee": 2, events: 1 }] }, {}, [3])(3);
+    });
+  })(D)), D.exports;
+}
+var q = M();
+const T = /* @__PURE__ */ A(q), S = /* @__PURE__ */ j({
+  __proto__: null,
+  default: T
+}, [q]);
+export {
+  S as g
+};