molstar 3.3.0 → 3.5.0

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

@@ -16,6 +16,7 @@ var lines_1 = require("../../../../mol-geo/geometry/lines/lines");
 var lines_builder_1 = require("../../../../mol-geo/geometry/lines/lines-builder");
 var cylinders_1 = require("../../../../mol-geo/geometry/cylinders/cylinders");
 var cylinders_builder_1 = require("../../../../mol-geo/geometry/cylinders/cylinders-builder");
+var sphere3d_1 = require("../../../../mol-math/geometry/primitives/sphere3d");
 exports.LinkCylinderParams = {
     linkScale: param_definition_1.ParamDefinition.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
     linkSpacing: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 2, step: 0.01 }),
@@ -79,13 +80,15 @@ var v3dot = linear_algebra_1.Vec3.dot;
 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_1.Mesh.createEmpty(mesh);
+        return { mesh: mesh_1.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 = mesh_builder_1.MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
     var va = (0, linear_algebra_1.Vec3)();
     var vb = (0, linear_algebra_1.Vec3)();
     var vShift = (0, linear_algebra_1.Vec3)();
+    var center = (0, linear_algebra_1.Vec3)();
+    var count = 0;
     var cylinderProps = {
         radiusTop: 1,
         radiusBottom: 1,
@@ -98,6 +101,9 @@ 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);
@@ -185,7 +191,18 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
         }
     }
-    return mesh_builder_1.MeshBuilder.getMesh(builderState);
+    var oldBoundingSphere = mesh ? sphere3d_1.Sphere3D.clone(mesh.boundingSphere) : undefined;
+    var m = mesh_builder_1.MeshBuilder.getMesh(builderState);
+    if (count === 0)
+        return { mesh: m };
+    // re-use boundingSphere if it has not changed much
+    linear_algebra_1.Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        return { mesh: m, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { mesh: m };
+    }
 }
 exports.createLinkCylinderMesh = createLinkCylinderMesh;
 /**
@@ -195,7 +212,7 @@ exports.createLinkCylinderMesh = createLinkCylinderMesh;
 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_1.Cylinders.createEmpty(cylinders);
+        return { cylinders: cylinders_1.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 = cylinders_builder_1.CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
@@ -203,6 +220,8 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
     var vb = (0, linear_algebra_1.Vec3)();
     var vm = (0, linear_algebra_1.Vec3)();
     var vShift = (0, linear_algebra_1.Vec3)();
+    var center = (0, linear_algebra_1.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);
@@ -212,6 +231,9 @@ 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);
@@ -274,7 +296,18 @@ 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_1.Sphere3D.clone(cylinders.boundingSphere) : undefined;
+    var c = builder.getCylinders();
+    if (count === 0)
+        return { cylinders: c };
+    // re-use boundingSphere if it has not changed much
+    linear_algebra_1.Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        return { cylinders: c, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { cylinders: c };
+    }
 }
 exports.createLinkCylinderImpostors = createLinkCylinderImpostors;
 /**
@@ -284,7 +317,7 @@ exports.createLinkCylinderImpostors = createLinkCylinderImpostors;
 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_1.Lines.createEmpty(lines);
+        return { lines: lines_1.Lines.createEmpty(lines) };
     var linkScale = props.linkScale, linkSpacing = props.linkSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount;
     var linesCountEstimate = linkCount * 2;
     var builder = lines_builder_1.LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
@@ -292,6 +325,8 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
     var vb = (0, linear_algebra_1.Vec3)();
     var vm = (0, linear_algebra_1.Vec3)();
     var vShift = (0, linear_algebra_1.Vec3)();
+    var center = (0, linear_algebra_1.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);
@@ -303,6 +338,9 @@ 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);
@@ -360,6 +398,17 @@ 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_1.Sphere3D.clone(lines.boundingSphere) : undefined;
+    var l = builder.getLines();
+    if (count === 0)
+        return { lines: l };
+    // re-use boundingSphere if it has not changed much
+    linear_algebra_1.Vec3.scale(center, center, 1 / count);
+    if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) {
+        return { lines: l, boundingSphere: oldBoundingSphere };
+    }
+    else {
+        return { lines: l };
+    }
 }
 exports.createLinkLines = createLinkLines;

package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js

@@ -25,15 +25,15 @@ function getPositionDataAndMaxRadius(structure, unit, sizeTheme, props) {
             maxRadius = r;
         radii[j] = r + probeRadius;
     }
-    return { position: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, position), { radius: radii }), boundary: boundary, maxRadius: maxRadius };
+    return { position: tslib_1.__assign(tslib_1.__assign({}, position), { radius: radii }), boundary: boundary, maxRadius: maxRadius };
 }
 function computeUnitMolecularSurface(structure, unit, sizeTheme, props) {
     var _this = this;
     var box = unit.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props);
     var _a = getPositionDataAndMaxRadius(structure, unit, sizeTheme, p), position = _a.position, boundary = _a.boundary, maxRadius = _a.maxRadius;
-    return mol_task_1.Task.create('Molecular Surface', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Molecular Surface', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, MolecularSurface(ctx, position, boundary, maxRadius, box, p)];
                 case 1: return [2 /*return*/, _a.sent()];
@@ -44,8 +44,8 @@ function computeUnitMolecularSurface(structure, unit, sizeTheme, props) {
 exports.computeUnitMolecularSurface = computeUnitMolecularSurface;
 //
 function MolecularSurface(ctx, position, boundary, maxRadius, box, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, (0, molecular_surface_1.calcMolecularSurface)(ctx, position, boundary, maxRadius, box, props)];
         });
     });

package/lib/commonjs/mol-repr/structure/visual/util/polymer.js

@@ -13,10 +13,10 @@ var int_1 = require("../../../../mol-data/int");
 var loci_1 = require("../../../../mol-model/loci");
 var location_iterator_1 = require("../../../../mol-geo/util/location-iterator");
 var common_1 = require("./common");
-(0, tslib_1.__exportStar)(require("./polymer/backbone"), exports);
-(0, tslib_1.__exportStar)(require("./polymer/gap-iterator"), exports);
-(0, tslib_1.__exportStar)(require("./polymer/trace-iterator"), exports);
-(0, tslib_1.__exportStar)(require("./polymer/curve-segment"), exports);
+tslib_1.__exportStar(require("./polymer/backbone"), exports);
+tslib_1.__exportStar(require("./polymer/gap-iterator"), exports);
+tslib_1.__exportStar(require("./polymer/trace-iterator"), exports);
+tslib_1.__exportStar(require("./polymer/curve-segment"), exports);
 exports.StandardTension = 0.5;
 exports.HelixTension = 0.9;
 exports.StandardShift = 0.5;

package/lib/commonjs/mol-repr/util.js

@@ -47,7 +47,7 @@ exports.DefaultQualityThresholds = {
 };
 function getStructureQuality(structure, tresholds) {
     if (tresholds === void 0) { tresholds = {}; }
-    var t = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.DefaultQualityThresholds), tresholds);
+    var t = tslib_1.__assign(tslib_1.__assign({}, exports.DefaultQualityThresholds), tresholds);
     var score = structure.elementCount * t.elementCountFactor;
     if (structure.isCoarseGrained)
         score *= t.coarseGrainedFactor;

package/lib/commonjs/mol-repr/volume/direct-volume.js

@@ -74,9 +74,9 @@ function createDirectVolume3d(ctx, webgl, volume, directVolume) {
 exports.createDirectVolume3d = createDirectVolume3d;
 //
 function createDirectVolume(ctx, volume, theme, props, directVolume) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var runtime, webgl;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             runtime = ctx.runtime, webgl = ctx.webgl;
             if (webgl === undefined)
                 throw new Error('DirectVolumeVisual requires `webgl` in props');
@@ -103,7 +103,7 @@ function eachDirectVolume(loci, volume, props, apply) {
 }
 exports.eachDirectVolume = eachDirectVolume;
 //
-exports.DirectVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, direct_volume_1.DirectVolume.Params), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, direct_volume_1.DirectVolume.Params.quality), { isEssential: false }) });
+exports.DirectVolumeParams = tslib_1.__assign(tslib_1.__assign({}, direct_volume_1.DirectVolume.Params), { quality: tslib_1.__assign(tslib_1.__assign({}, direct_volume_1.DirectVolume.Params.quality), { isEssential: false }) });
 function getDirectVolumeParams(ctx, volume) {
     return param_definition_1.ParamDefinition.clone(exports.DirectVolumeParams);
 }

package/lib/commonjs/mol-repr/volume/isosurface.js

@@ -66,9 +66,9 @@ function eachIsosurface(loci, volume, props, apply) {
 exports.eachIsosurface = eachIsosurface;
 //
 function createVolumeIsosurfaceMesh(ctx, volume, theme, props, mesh) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ids, surface, transform;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     ctx.runtime.update({ message: 'Marching cubes...' });
@@ -94,7 +94,7 @@ function createVolumeIsosurfaceMesh(ctx, volume, theme, props, mesh) {
     });
 }
 exports.createVolumeIsosurfaceMesh = createVolumeIsosurfaceMesh;
-exports.IsosurfaceMeshParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), texture_mesh_1.TextureMesh.Params), exports.VolumeIsosurfaceParams), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params.quality), { isEssential: false }), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true) });
+exports.IsosurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), texture_mesh_1.TextureMesh.Params), exports.VolumeIsosurfaceParams), { quality: tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params.quality), { isEssential: false }), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true) });
 function IsosurfaceMeshVisual(materialId) {
     return (0, representation_1.VolumeVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceMeshParams),
@@ -151,9 +151,9 @@ var VolumeIsosurfaceTexture;
     VolumeIsosurfaceTexture.get = get;
 })(VolumeIsosurfaceTexture || (VolumeIsosurfaceTexture = {}));
 function createVolumeIsosurfaceTextureMesh(ctx, volume, theme, props, textureMesh) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var _a, max, min, diff, value, isoLevel, _b, texture, gridDimension, gridTexDim, gridTexScale, transform, axisOrder, buffer, gv, surface;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             if (!ctx.webgl)
                 throw new Error('webgl context required to create volume isosurface texture-mesh');
             if (volume.grid.cells.data.length <= 1) {
@@ -198,9 +198,9 @@ function IsosurfaceTextureMeshVisual(materialId) {
 exports.IsosurfaceTextureMeshVisual = IsosurfaceTextureMeshVisual;
 //
 function createVolumeIsosurfaceWireframe(ctx, volume, theme, props, lines) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ids, wireframe, transform;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     ctx.runtime.update({ message: 'Marching cubes...' });
@@ -221,7 +221,7 @@ function createVolumeIsosurfaceWireframe(ctx, volume, theme, props, lines) {
     });
 }
 exports.createVolumeIsosurfaceWireframe = createVolumeIsosurfaceWireframe;
-exports.IsosurfaceWireframeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params), exports.VolumeIsosurfaceParams), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, lines_1.Lines.Params.quality), { isEssential: false }), sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }) });
+exports.IsosurfaceWireframeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params), exports.VolumeIsosurfaceParams), { quality: tslib_1.__assign(tslib_1.__assign({}, lines_1.Lines.Params.quality), { isEssential: false }), sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }) });
 function IsosurfaceWireframeVisual(materialId) {
     return (0, representation_1.VolumeVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceWireframeParams),
@@ -242,7 +242,7 @@ var IsosurfaceVisuals = {
     'solid': function (ctx, getParams) { return (0, representation_1.VolumeRepresentation)('Isosurface mesh', ctx, getParams, IsosurfaceVisual, getLoci); },
     'wireframe': function (ctx, getParams) { return (0, representation_1.VolumeRepresentation)('Isosurface wireframe', ctx, getParams, IsosurfaceWireframeVisual, getLoci); },
 };
-exports.IsosurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, exports.IsosurfaceMeshParams), exports.IsosurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['solid'], param_definition_1.ParamDefinition.objectToOptions(IsosurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
+exports.IsosurfaceParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, exports.IsosurfaceMeshParams), exports.IsosurfaceWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['solid'], param_definition_1.ParamDefinition.objectToOptions(IsosurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getIsosurfaceParams(ctx, volume) {
     var p = param_definition_1.ParamDefinition.clone(exports.IsosurfaceParams);
     p.isoValue = volume_1.Volume.createIsoValueParam(volume_1.Volume.IsoValue.relative(2), volume.grid.stats);

package/lib/commonjs/mol-repr/volume/registry.js

@@ -13,7 +13,7 @@ var object_1 = require("../../mol-util/object");
 var slice_1 = require("./slice");
 var direct_volume_1 = require("./direct-volume");
 var VolumeRepresentationRegistry = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(VolumeRepresentationRegistry, _super);
+    tslib_1.__extends(VolumeRepresentationRegistry, _super);
     function VolumeRepresentationRegistry() {
         var _this = _super.call(this) || this;
         (0, object_1.objectForEach)(VolumeRepresentationRegistry.BuiltIn, function (p, k) {

package/lib/commonjs/mol-repr/volume/representation.js

@@ -136,9 +136,9 @@ function VolumeVisual(builder, materialId) {
         get geometryVersion() { return geometryVersion; },
         createOrUpdate: function (ctx, theme, props, volume) {
             if (props === void 0) { props = {}; }
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var newGeometry;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     prepareUpdate(theme, props, volume || currentVolume);
                     if (updateState.createGeometry) {
                         newGeometry = createGeometry(ctx, newVolume, newTheme, newProps, geometry);
@@ -198,7 +198,7 @@ exports.VolumeVisual = VolumeVisual;
 function VolumeRepresentationProvider(p) { return p; }
 exports.VolumeRepresentationProvider = VolumeRepresentationProvider;
 //
-exports.VolumeParams = (0, tslib_1.__assign)({}, base_1.BaseGeometry.Params);
+exports.VolumeParams = tslib_1.__assign({}, base_1.BaseGeometry.Params);
 function VolumeRepresentation(label, ctx, getParams, visualCtor, getLoci) {
     var version = 0;
     var webgl = ctx.webgl;
@@ -223,10 +223,10 @@ function VolumeRepresentation(label, ctx, getParams, visualCtor, getLoci) {
         }
         var qualityProps = (0, util_1.getQualityProps)(Object.assign({}, _props, props), _volume);
         Object.assign(_props, props, qualityProps);
-        return mol_task_1.Task.create('Creating or updating VolumeRepresentation', function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+        return mol_task_1.Task.create('Creating or updating VolumeRepresentation', function (runtime) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
             var promise;
             var _a;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         if (!visual) {

package/lib/commonjs/mol-repr/volume/slice.js

@@ -21,9 +21,9 @@ var color_2 = require("../../mol-theme/color");
 var number_packing_1 = require("../../mol-util/number-packing");
 var util_2 = require("./util");
 function createImage(ctx, volume, theme, props, image) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var dim, isoValue, _a, space, data, _b, min, max, isoVal, color, _c, r, g, b, _d, width, height, x, y, z, x0, y0, z0, nx, ny, nz, corners, imageArray, groupArray, i, iy, ix, iz, val, normVal, imageTexture, groupTexture, transform;
-        return (0, tslib_1.__generator)(this, function (_e) {
+        return tslib_1.__generator(this, function (_e) {
             dim = props.dimension.name, isoValue = props.isoValue;
             _a = volume.grid.cells, space = _a.space, data = _a.data;
             _b = volume.grid.stats, min = _b.min, max = _b.max;
@@ -141,7 +141,7 @@ function eachSlice(loci, volume, props, apply) {
     return (0, util_2.eachVolumeLoci)(loci, volume, undefined, apply);
 }
 //
-exports.SliceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, image_1.Image.Params), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, image_1.Image.Params.quality), { isEssential: false }), dimension: param_definition_1.ParamDefinition.MappedStatic('x', {
+exports.SliceParams = tslib_1.__assign(tslib_1.__assign({}, image_1.Image.Params), { quality: tslib_1.__assign(tslib_1.__assign({}, image_1.Image.Params.quality), { isEssential: false }), dimension: param_definition_1.ParamDefinition.MappedStatic('x', {
         x: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 0, step: 1 }),
         y: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 0, step: 1 }),
         z: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 0, step: 1 }),
@@ -171,7 +171,7 @@ function SliceVisual(materialId) {
                 !volume_1.Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats) ||
                 !color_2.ColorTheme.areEqual(newTheme.color, currentTheme.color));
         },
-        geometryUtils: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, image_1.Image.Utils), { createRenderableState: function (props) {
+        geometryUtils: tslib_1.__assign(tslib_1.__assign({}, image_1.Image.Utils), { createRenderableState: function (props) {
                 var state = image_1.Image.Utils.createRenderableState(props);
                 updateRenderableState(state, props);
                 return state;

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

@@ -9,6 +9,7 @@ exports.parseMolScript = void 0;
 var monadic_parser_1 = require("../../mol-util/monadic-parser");
 var expression_1 = require("./expression");
 var builder_1 = require("./builder");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 function parseMolScript(input) {
     return Language.parse(input);
 }
@@ -63,15 +64,15 @@ var Language;
                     case '[': return builder_1.MolScriptBuilder.core.type.list(withoutComments(expr.nodes).map(visitExpr));
                     case '{': return builder_1.MolScriptBuilder.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_1.Expression.Apply(head, getArgs(expr.nodes));
                     }
+                    default: (0, type_helpers_1.assertUnreachable)(expr.bracket);
                 }
-                return 0;
-            }
-            default: {
-                throw new Error('should not happen');
             }
+            default: (0, type_helpers_1.assertUnreachable)(expr);
         }
     }
     function getArgs(nodes) {
@@ -102,6 +103,8 @@ 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/commonjs/mol-script/language/symbol-table/internal.js

@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.internal = void 0;
 var tslib_1 = require("tslib");
 var type_1 = require("../type");
-var Struct = (0, tslib_1.__importStar)(require("./structure-query"));
+var Struct = tslib_1.__importStar(require("./structure-query"));
 var symbol_1 = require("../symbol");
 var helpers_1 = require("../helpers");
 var generator = {

package/lib/commonjs/mol-script/language/symbol-table/structure-query.js

@@ -9,7 +9,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.structureQuery = exports.Types = void 0;
 var tslib_1 = require("tslib");
 var type_1 = require("../type");
-var Core = (0, tslib_1.__importStar)(require("./core"));
+var Core = tslib_1.__importStar(require("./core"));
 var symbol_1 = require("../symbol");
 var helpers_1 = require("../helpers");
 var Types;

package/lib/commonjs/mol-script/runtime/query/compiler.js

@@ -6,5 +6,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./base"), exports);
+tslib_1.__exportStar(require("./base"), exports);
 require("./table");

package/lib/commonjs/mol-script/script/mol-script/symbols.js

@@ -29,7 +29,7 @@ function Macro(symbol, translate) {
     }
     symbol.info.namespace = 'molscript-macro';
     symbol.id = "molscript-macro.".concat(symbol.info.name);
-    return { kind: 'macro', symbol: symbol, translate: translate, aliases: (0, tslib_1.__spreadArray)([symbol.info.name], aliases, true) };
+    return { kind: 'macro', symbol: symbol, translate: translate, aliases: tslib_1.__spreadArray([symbol.info.name], aliases, true) };
 }
 function isMolScriptSymbol(x) {
     return x.kind === 'alias' || x.kind === 'macro';

package/lib/commonjs/mol-state/action.js

@@ -41,7 +41,7 @@ var StateAction;
     var Builder;
     (function (Builder) {
         function root(info) {
-            return function (def) { return create((0, tslib_1.__assign)({ from: info.from instanceof Array
+            return function (def) { return create(tslib_1.__assign({ from: info.from instanceof Array
                     ? info.from
                     : !!info.from ? [info.from] : [], display: typeof info.display === 'string'
                     ? { name: info.display }

package/lib/commonjs/mol-state/index.js

@@ -6,11 +6,11 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./object"), exports);
-(0, tslib_1.__exportStar)(require("./tree"), exports);
-(0, tslib_1.__exportStar)(require("./state"), exports);
-(0, tslib_1.__exportStar)(require("./state/builder"), exports);
-(0, tslib_1.__exportStar)(require("./state/selection"), exports);
-(0, tslib_1.__exportStar)(require("./transformer"), exports);
-(0, tslib_1.__exportStar)(require("./transform"), exports);
-(0, tslib_1.__exportStar)(require("./action"), exports);
+tslib_1.__exportStar(require("./object"), exports);
+tslib_1.__exportStar(require("./tree"), exports);
+tslib_1.__exportStar(require("./state"), exports);
+tslib_1.__exportStar(require("./state/builder"), exports);
+tslib_1.__exportStar(require("./state/selection"), exports);
+tslib_1.__exportStar(require("./transformer"), exports);
+tslib_1.__exportStar(require("./transform"), exports);
+tslib_1.__exportStar(require("./action"), exports);

package/lib/commonjs/mol-state/state/builder.js

@@ -145,7 +145,7 @@ var StateBuilder;
                 return to;
             }
             else {
-                return this.apply(tr, params, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, options), { ref: ref }));
+                return this.apply(tr, params, tslib_1.__assign(tslib_1.__assign({}, options), { ref: ref }));
             }
         };
         /**
@@ -170,7 +170,7 @@ var StateBuilder;
                     return to;
                 }
             }
-            var t = tr.apply(applyRoot, params, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, options), { tags: tagsUnion(tags, options && options.tags) }));
+            var t = tr.apply(applyRoot, params, tslib_1.__assign(tslib_1.__assign({}, options), { tags: tagsUnion(tags, options && options.tags) }));
             this.state.tree.add(t);
             this.editInfo.count++;
             this.editInfo.lastUpdate = t.ref;

package/lib/commonjs/mol-state/state/selection.js

@@ -49,7 +49,7 @@ var StateSelection;
             for (var _i = 0; _i < arguments.length; _i++) {
                 args[_i] = arguments[_i];
             }
-            return f.call.apply(f, (0, tslib_1.__spreadArray)([void 0, this], args, false));
+            return f.call.apply(f, tslib_1.__spreadArray([void 0, this], args, false));
         };
     }
     function build(compile) {