molstar 3.3.0 → 3.5.0

package/lib/mol-repr/structure/visual/util/link.d.ts

@@ -9,6 +9,7 @@ import { Mesh } from '../../../../mol-geo/geometry/mesh/mesh';
 import { VisualContext } from '../../../visual';
 import { Lines } from '../../../../mol-geo/geometry/lines/lines';
 import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
+import { Sphere3D } from '../../../../mol-math/geometry/primitives/sphere3d';
 export declare const LinkCylinderParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
@@ -75,14 +76,23 @@ export declare const enum LinkStyle {
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, mesh?: Mesh): Mesh;
+export declare function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, mesh?: Mesh): {
+    mesh: Mesh;
+    boundingSphere?: Sphere3D;
+};
 /**
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, cylinders?: Cylinders): Cylinders;
+export declare function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkCylinderProps, cylinders?: Cylinders): {
+    cylinders: Cylinders;
+    boundingSphere?: Sphere3D;
+};
 /**
  * Each edge is included twice to allow for coloring/picking
  * the half closer to the first vertex, i.e. vertex a.
  */
-export declare function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkLineProps, lines?: Lines): Lines;
+export declare function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProps, props: LinkLineProps, lines?: Lines): {
+    lines: Lines;
+    boundingSphere?: Sphere3D;
+};

package/lib/mol-repr/structure/visual/util/link.js

@@ -13,6 +13,7 @@ import { Lines } from '../../../../mol-geo/geometry/lines/lines';
 import { LinesBuilder } from '../../../../mol-geo/geometry/lines/lines-builder';
 import { Cylinders } from '../../../../mol-geo/geometry/cylinders/cylinders';
 import { CylindersBuilder } from '../../../../mol-geo/geometry/cylinders/cylinders-builder';
+import { Sphere3D } from '../../../../mol-math/geometry/primitives/sphere3d';
 export var LinkCylinderParams = {
     linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
     linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
@@ -75,13 +76,15 @@ var v3dot = Vec3.dot;
 export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
-        return Mesh.createEmpty(mesh);
+        return { mesh: Mesh.createEmpty(mesh) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, radialSegments = props.radialSegments, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
     var vertexCountEstimate = radialSegments * 2 * linkCount * 2;
     var builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
     var va = Vec3();
     var vb = Vec3();
     var vShift = Vec3();
+    var center = Vec3();
+    var count = 0;
     var cylinderProps = {
         radiusTop: 1,
         radiusBottom: 1,
@@ -94,6 +97,9 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
         if (ignore && ignore(edgeIndex))
             continue;
         position(va, vb, edgeIndex);
+        v3add(center, center, va);
+        v3add(center, center, vb);
+        count += 2;
         v3sub(tmpV12, vb, va);
         var dirFlag = v3dot(tmpV12, up) > 0;
         var linkRadius = radius(edgeIndex);
@@ -181,7 +187,18 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             addCylinder(builderState, va, vb, 0.5, cylinderProps);
         }
     }
-    return MeshBuilder.getMesh(builderState);
+    var oldBoundingSphere = mesh ? Sphere3D.clone(mesh.boundingSphere) : undefined;
+    var m = MeshBuilder.getMesh(builderState);
+    if (count === 0)
+        return { mesh: m };
+    // re-use boundingSphere if it has not changed much
+    Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        return { mesh: m, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { mesh: m };
+    }
 }
 /**
  * Each edge is included twice to allow for coloring/picking
@@ -190,7 +207,7 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
 export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
-        return Cylinders.createEmpty(cylinders);
+        return { cylinders: Cylinders.createEmpty(cylinders) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
     var cylindersCountEstimate = linkCount * 2;
     var builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
@@ -198,6 +215,8 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
     var vb = Vec3();
     var vm = Vec3();
     var vShift = Vec3();
+    var center = Vec3();
+    var count = 0;
     // automatically adjust length for evenly spaced dashed cylinders
     var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
@@ -207,6 +226,9 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
         if (ignore && ignore(edgeIndex))
             continue;
         position(va, vb, edgeIndex);
+        v3add(center, center, va);
+        v3add(center, center, vb);
+        count += 2;
         var linkRadius = radius(edgeIndex);
         var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
@@ -269,7 +291,18 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
             builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], 1, linkCap, linkStub, edgeIndex);
         }
     }
-    return builder.getCylinders();
+    var oldBoundingSphere = cylinders ? Sphere3D.clone(cylinders.boundingSphere) : undefined;
+    var c = builder.getCylinders();
+    if (count === 0)
+        return { cylinders: c };
+    // re-use boundingSphere if it has not changed much
+    Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        return { cylinders: c, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { cylinders: c };
+    }
 }
 /**
  * Each edge is included twice to allow for coloring/picking
@@ -278,7 +311,7 @@ export function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders)
 export function createLinkLines(ctx, linkBuilder, props, lines) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, ignore = linkBuilder.ignore;
     if (!linkCount)
-        return Lines.createEmpty(lines);
+        return { lines: Lines.createEmpty(lines) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount;
     var linesCountEstimate = linkCount * 2;
     var builder = LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
@@ -286,6 +319,8 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
     var vb = Vec3();
     var vm = Vec3();
     var vShift = Vec3();
+    var center = Vec3();
+    var count = 0;
     // automatically adjust length for evenly spaced dashed lines
     var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
@@ -297,6 +332,9 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
         if (ignore && ignore(edgeIndex))
             continue;
         position(va, vb, edgeIndex);
+        v3add(center, center, va);
+        v3add(center, center, vb);
+        count += 2;
         var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
         if (linkStyle === 0 /* Solid */) {
             v3scale(vm, v3add(vm, va, vb), 0.5);
@@ -354,5 +392,16 @@ export function createLinkLines(ctx, linkBuilder, props, lines) {
             builder.add(va[0], va[1], va[2], vb[0], vb[1], vb[2], edgeIndex);
         }
     }
-    return builder.getLines();
+    var oldBoundingSphere = lines ? Sphere3D.clone(lines.boundingSphere) : undefined;
+    var l = builder.getLines();
+    if (count === 0)
+        return { lines: l };
+    // re-use boundingSphere if it has not changed much
+    Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        return { lines: l, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { lines: l };
+    }
 }

package/lib/mol-script/language/builder.d.ts

@@ -10,6 +10,7 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
+            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;

package/lib/mol-script/language/parser.js

@@ -6,6 +6,7 @@
 import { MonadicParser as P } from '../../mol-util/monadic-parser';
 import { Expression } from './expression';
 import { MolScriptBuilder as B } from './builder';
+import { assertUnreachable } from '../../mol-util/type-helpers';
 export function parseMolScript(input) {
     return Language.parse(input);
 }
@@ -59,15 +60,15 @@ var Language;
                     case '[': return B.core.type.list(withoutComments(expr.nodes).map(visitExpr));
                     case '{': return B.core.type.set(withoutComments(expr.nodes).map(visitExpr));
                     case '(': {
+                        if (expr.nodes[0].kind === 'comment')
+                            throw new Error('Invalid expression');
                         var head = visitExpr(expr.nodes[0]);
                         return Expression.Apply(head, getArgs(expr.nodes));
                     }
+                    default: assertUnreachable(expr.bracket);
                 }
-                return 0;
-            }
-            default: {
-                throw new Error('should not happen');
             }
+            default: assertUnreachable(expr);
         }
     }
     function getArgs(nodes) {
@@ -98,6 +99,8 @@ var Language;
                 }
                 if (i >= _i)
                     throw new Error("There must be a value foolowed a named arg ':".concat(name_1, "'."));
+                if (nodes[i].kind === 'comment')
+                    throw new Error('Invalid expression');
                 args[name_1] = visitExpr(nodes[i]);
                 if (isNaN(+name_1))
                     allNumeric = false;

package/lib/mol-task/util/scheduler.d.ts

@@ -5,8 +5,8 @@
  */
 /// <reference types="node" />
 declare const Scheduler: {
-    setImmediate: ((callback: (...args: any[]) => void, ...args: any[]) => number) | typeof setImmediate;
-    clearImmediate: ((handle: number) => void) | typeof clearImmediate;
+    setImmediate: typeof setImmediate | ((callback: (...args: any[]) => void, ...args: any[]) => number);
+    clearImmediate: typeof clearImmediate | ((handle: number) => void);
     immediatePromise(): Promise<void>;
     delay<T>(timeout: number, value?: T | undefined): Promise<T>;
 };

package/lib/mol-task/util/scheduler.js

@@ -5,7 +5,7 @@
  */
 import { __spreadArray } from "tslib";
 function createImmediateActions() {
-    var global = (function () {
+    var thisGlobal = (function () {
         var _window = typeof window !== 'undefined' && window;
         var _self = typeof self !== 'undefined' && typeof WorkerGlobalScope !== 'undefined' && self instanceof WorkerGlobalScope && self;
         var _global = typeof global !== 'undefined' && global;
@@ -65,14 +65,14 @@ function createImmediateActions() {
         };
     }
     function canUsePostMessage() {
-        if (global && global.postMessage && !global.importScripts) {
+        if (thisGlobal && thisGlobal.postMessage && !thisGlobal.importScripts) {
             var postMessageIsAsynchronous_1 = true;
-            var oldOnMessage = global.onmessage;
-            global.onmessage = function () {
+            var oldOnMessage = thisGlobal.onmessage;
+            thisGlobal.onmessage = function () {
                 postMessageIsAsynchronous_1 = false;
             };
-            global.postMessage('', '*');
-            global.onmessage = oldOnMessage;
+            thisGlobal.postMessage('', '*');
+            thisGlobal.onmessage = oldOnMessage;
             return postMessageIsAsynchronous_1;
         }
     }
@@ -82,7 +82,7 @@ function createImmediateActions() {
         // * http://www.whatwg.org/specs/web-apps/current-work/multipage/comms.html#crossDocumentMessages
         var messagePrefix = 'setImmediate$' + Math.random() + '$';
         var onGlobalMessage = function (event) {
-            if (event.source === global &&
+            if (event.source === thisGlobal &&
                 typeof event.data === 'string' &&
                 event.data.indexOf(messagePrefix) === 0) {
                 runIfPresent(+event.data.slice(messagePrefix.length));

package/lib/mol-theme/color/hydrophobicity.js

@@ -45,8 +45,8 @@ export function HydrophobicityColorTheme(ctx, props) {
     var scale = ColorScale.create({
         listOrName: props.list.colors,
         domain: [max, min],
-        minLabel: 'Hydrophobic',
-        maxLabel: 'Hydrophilic'
+        minLabel: 'Hydrophilic',
+        maxLabel: 'Hydrophobic'
     });
     function color(location) {
         var compId;

package/lib/mol-util/data-source.js

@@ -93,6 +93,7 @@ function getCompression(name) {
         /\.zip$/i.test(name) ? DataCompressionMethod.Zip :
             DataCompressionMethod.None;
 }
+var reFilterPath = /^(__MACOSX|.DS_Store)/;
 function decompress(ctx, data, compression) {
     return __awaiter(this, void 0, void 0, function () {
         var _a, parsed, names;
@@ -111,7 +112,7 @@ function decompress(ctx, data, compression) {
                 case 3: return [4 /*yield*/, unzip(ctx, data.buffer)];
                 case 4:
                     parsed = _b.sent();
-                    names = Object.keys(parsed);
+                    names = Object.keys(parsed).filter(function (n) { return !reFilterPath.test(n); });
                     if (names.length !== 1)
                         throw new Error('can only decompress zip files with a single entry');
                     return [2 /*return*/, parsed[names[0]]];

package/lib/mol-util/file-info.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,8 +11,6 @@ export interface FileInfo {
     ext: string;
     base: string;
     dir: string;
-    compressed: string | boolean;
-    binary: boolean;
     protocol: string;
     query: string;
     src: FileInput;

package/lib/mol-util/file-info.js

@@ -1,16 +1,13 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 // TODO only support compressed files for which uncompression support is available???
 // TODO store globally with decompression plugins?
 var compressedExtList = ['gz', 'zip'];
-// TODO store globally with parser plugins?
-var binaryExtList = ['bcif', 'ccp4', 'dcd'];
 export function getFileInfo(file) {
     var path;
-    var compressed;
     var protocol = '';
     if (file instanceof File) {
         path = file.name;
@@ -35,15 +32,10 @@ export function getFileInfo(file) {
     }
     var dir = path.substring(0, path.lastIndexOf('/') + 1);
     if (compressedExtList.includes(ext)) {
-        compressed = ext;
         var n = path.length - ext.length - 1;
         ext = (path.substr(0, n).split('.').pop() || '').toLowerCase();
         var m = base.length - ext.length - 1;
         base = base.substr(0, m);
     }
-    else {
-        compressed = false;
-    }
-    var binary = binaryExtList.includes(ext);
-    return { path: path, name: name, ext: ext, base: base, dir: dir, compressed: compressed, binary: binary, protocol: protocol, query: query, src: file };
+    return { path: path, name: name, ext: ext, base: base, dir: dir, protocol: protocol, query: query, src: file };
 }

package/lib/mol-util/index.d.ts

@@ -27,3 +27,4 @@ export declare const assign: (<T>(o: T, ...from: any[]) => T);
 export declare const merge: (<T>(source: T, ...rest: Partial<T>[]) => T);
 export declare function formatTime(d: Date): string;
 export declare function formatProgress(p: Progress): string;
+export declare function formatBytes(count: number): string;

package/lib/mol-util/index.js

@@ -200,3 +200,8 @@ export function formatProgress(p) {
     var x = (100 * tp.current / tp.max).toFixed(2);
     return "".concat(tp.message, " ").concat(x, "%");
 }
+export function formatBytes(count) {
+    var units = ['B', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB'];
+    var i = Math.floor(Math.log(count) / Math.log(1024));
+    return "".concat((count / Math.pow(1024, i)).toFixed(2), " ").concat(units[i]);
+}

package/lib/mol-util/zip/deflate.js

@@ -7,6 +7,7 @@
  * MIT License, Copyright (c) 2018 Photopea
  */
 import { __awaiter, __generator } from "tslib";
+import { assertUnreachable } from '../type-helpers';
 import { _hufTree } from './huffman';
 import { U, revCodes, makeCodes } from './util';
 function DeflateContext(data, out, opos, lvl) {
@@ -262,7 +263,7 @@ function _writeBlock(BFINAL, lits, li, ebits, data, o0, l0, out, pos) {
             pos = _codeTiny(dset, U.itree, out, pos);
         }
         else {
-            throw new Error("unknown BTYPE ".concat(BTYPE));
+            assertUnreachable(BTYPE);
         }
         var off = o0;
         for (var si = 0; si < li; si += 2) {

package/lib/mol-util/zip/zip.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -9,6 +9,12 @@
  * - added `ungzip`
  */
 import { RuntimeContext, Task } from '../../mol-task';
+export declare function Unzip(buf: ArrayBuffer, onlyNames?: boolean): Task<{
+    [k: string]: Uint8Array | {
+        size: number;
+        csize: number;
+    };
+}>;
 export declare function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames?: boolean): Promise<{
     [k: string]: Uint8Array | {
         size: number;

package/lib/mol-util/zip/zip.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -14,6 +14,10 @@ import { crc, adler } from './checksum';
 import { _inflate } from './inflate';
 import { _deflateRaw } from './deflate';
 import { Task } from '../../mol-task';
+export function Unzip(buf, onlyNames) {
+    if (onlyNames === void 0) { onlyNames = false; }
+    return Task.create('Unzip', function (ctx) { return unzip(ctx, buf, onlyNames); });
+}
 export function unzip(runtime, buf, onlyNames) {
     if (onlyNames === void 0) { onlyNames = false; }
     return __awaiter(this, void 0, void 0, function () {

package/lib/servers/model/config.d.ts

@@ -53,7 +53,7 @@ declare const DefaultModelServerConfig: {
      *
      * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
      */
-    sourceMap: ([string, string] | [string, string, "bcif" | "cif" | "cif.gz" | "bcif.gz"])[];
+    sourceMap: ([string, string] | [string, string, "cif" | "bcif" | "cif.gz" | "bcif.gz"])[];
 };
 export declare const ModelServerFetchFormats: readonly ["cif", "bcif", "cif.gz", "bcif.gz"];
 export declare type ModelServerFetchFormats = (typeof ModelServerFetchFormats)[number];
@@ -108,7 +108,7 @@ export declare const ModelServerConfig: {
      *
      * /static query uses 'pdb-cif' and 'pdb-bcif' source names.
      */
-    sourceMap: ([string, string] | [string, string, "bcif" | "cif" | "cif.gz" | "bcif.gz"])[];
+    sourceMap: ([string, string] | [string, string, "cif" | "bcif" | "cif.gz" | "bcif.gz"])[];
 };
 export declare const ModelServerConfigTemplate: ModelServerConfig;
 export declare function configureServer(): void;