molstar 2.3.9 → 3.0.0-dev.2

package/lib/mol-plugin-state/manager/structure/component.js

@@ -23,6 +23,8 @@ import { Clipping } from '../../../mol-theme/clipping';
 import { setStructureClipping } from '../../helpers/structure-clipping';
 import { setStructureTransparency } from '../../helpers/structure-transparency';
 import { StructureFocusRepresentation } from '../../../mol-plugin/behavior/dynamic/selection/structure-focus-representation';
+import { setStructureSubstance } from '../../helpers/structure-substance';
+import { Material } from '../../../mol-util/material';
 export { StructureComponentManager };
 var StructureComponentManager = /** @class */ (function (_super) {
     __extends(StructureComponentManager, _super);
@@ -72,6 +74,7 @@ var StructureComponentManager = /** @class */ (function (_super) {
                                     _a.sent();
                                     return [4 /*yield*/, this.plugin.state.updateBehavior(StructureFocusRepresentation, function (p) {
                                             p.ignoreHydrogens = !options.showHydrogens;
+                                            p.material = options.materialStyle;
                                         })];
                                 case 2:
                                     _a.sent();
@@ -88,17 +91,18 @@ var StructureComponentManager = /** @class */ (function (_super) {
         });
     };
     StructureComponentManager.prototype.updateReprParams = function (update, component) {
-        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality;
+        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle;
         var ignoreHydrogens = !showHydrogens;
         for (var _i = 0, _b = component.representations; _i < _b.length; _i++) {
             var r = _b[_i];
             if (r.cell.transform.transformer !== StructureRepresentation3D)
                 continue;
             var params = r.cell.transform.params;
-            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality) {
+            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || params.type.params.material !== material) {
                 update.to(r.cell).update(function (old) {
                     old.type.params.ignoreHydrogens = ignoreHydrogens;
                     old.type.params.quality = quality;
+                    old.type.params.material = material;
                 });
             }
         }
@@ -370,9 +374,9 @@ var StructureComponentManager = /** @class */ (function (_super) {
         var _this = this;
         if (components.length === 0)
             return;
-        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality;
+        var _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle;
         var ignoreHydrogens = !showHydrogens;
-        var typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality };
+        var typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, material: material };
         return this.plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
             var _i, components_9, component;
             return __generator(this, function (_a) {
@@ -433,16 +437,16 @@ var StructureComponentManager = /** @class */ (function (_super) {
             var _this = this;
             return __generator(this, function (_a) {
                 return [2 /*return*/, this.plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
-                        var xs, _a, showHydrogens, quality, ignoreHydrogens, typeParams, componentKey, _i, xs_1, s, component;
+                        var xs, _a, showHydrogens, quality, material, ignoreHydrogens, typeParams, componentKey, _i, xs_1, s, component;
                         return __generator(this, function (_b) {
                             switch (_b.label) {
                                 case 0:
                                     xs = structures || this.currentStructures;
                                     if (xs.length === 0)
                                         return [2 /*return*/];
-                                    _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality;
+                                    _a = this.state.options, showHydrogens = _a.showHydrogens, quality = _a.visualQuality, material = _a.materialStyle;
                                     ignoreHydrogens = !showHydrogens;
-                                    typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality };
+                                    typeParams = { ignoreHydrogens: ignoreHydrogens, quality: quality, material: material };
                                     componentKey = UUID.create22();
                                     _i = 0, xs_1 = xs;
                                     _b.label = 1;
@@ -488,7 +492,7 @@ var StructureComponentManager = /** @class */ (function (_super) {
             var _this = this;
             return __generator(this, function (_a) {
                 return [2 /*return*/, this.plugin.dataTransaction(function (ctx) { return __awaiter(_this, void 0, void 0, function () {
-                        var xs, getLoci, _i, xs_2, s, p, p, p;
+                        var xs, getLoci, _i, xs_2, s, p, p, p, p;
                         var _this = this;
                         return __generator(this, function (_a) {
                             switch (_a.label) {
@@ -507,38 +511,51 @@ var StructureComponentManager = /** @class */ (function (_super) {
                                     _i = 0, xs_2 = xs;
                                     _a.label = 1;
                                 case 1:
-                                    if (!(_i < xs_2.length)) return [3 /*break*/, 10];
+                                    if (!(_i < xs_2.length)) return [3 /*break*/, 14];
                                     s = xs_2[_i];
-                                    if (!(params.action.name === 'reset')) return [3 /*break*/, 3];
-                                    return [4 /*yield*/, setStructureOverpaint(this.plugin, s.components, -1, getLoci, params.representations)];
+                                    if (!(params.action.name === 'color')) return [3 /*break*/, 3];
+                                    p = params.action.params;
+                                    return [4 /*yield*/, setStructureOverpaint(this.plugin, s.components, p.color, getLoci, params.representations)];
                                 case 2:
                                     _a.sent();
-                                    return [3 /*break*/, 9];
+                                    return [3 /*break*/, 13];
                                 case 3:
-                                    if (!(params.action.name === 'color')) return [3 /*break*/, 5];
-                                    p = params.action.params;
-                                    return [4 /*yield*/, setStructureOverpaint(this.plugin, s.components, p.color, getLoci, params.representations)];
+                                    if (!(params.action.name === 'resetColor')) return [3 /*break*/, 5];
+                                    return [4 /*yield*/, setStructureOverpaint(this.plugin, s.components, -1, getLoci, params.representations)];
                                 case 4:
                                     _a.sent();
-                                    return [3 /*break*/, 9];
+                                    return [3 /*break*/, 13];
                                 case 5:
                                     if (!(params.action.name === 'transparency')) return [3 /*break*/, 7];
                                     p = params.action.params;
                                     return [4 /*yield*/, setStructureTransparency(this.plugin, s.components, p.value, getLoci, params.representations)];
                                 case 6:
                                     _a.sent();
-                                    return [3 /*break*/, 9];
+                                    return [3 /*break*/, 13];
                                 case 7:
-                                    if (!(params.action.name === 'clipping')) return [3 /*break*/, 9];
+                                    if (!(params.action.name === 'material')) return [3 /*break*/, 9];
                                     p = params.action.params;
-                                    return [4 /*yield*/, setStructureClipping(this.plugin, s.components, Clipping.Groups.fromNames(p.excludeGroups), getLoci, params.representations)];
+                                    return [4 /*yield*/, setStructureSubstance(this.plugin, s.components, p.material, getLoci, params.representations)];
                                 case 8:
                                     _a.sent();
-                                    _a.label = 9;
+                                    return [3 /*break*/, 13];
                                 case 9:
+                                    if (!(params.action.name === 'resetMaterial')) return [3 /*break*/, 11];
+                                    return [4 /*yield*/, setStructureSubstance(this.plugin, s.components, void 0, getLoci, params.representations)];
+                                case 10:
+                                    _a.sent();
+                                    return [3 /*break*/, 13];
+                                case 11:
+                                    if (!(params.action.name === 'clipping')) return [3 /*break*/, 13];
+                                    p = params.action.params;
+                                    return [4 /*yield*/, setStructureClipping(this.plugin, s.components, Clipping.Groups.fromNames(p.excludeGroups), getLoci, params.representations)];
+                                case 12:
+                                    _a.sent();
+                                    _a.label = 13;
+                                case 13:
                                     _i++;
                                     return [3 /*break*/, 1];
-                                case 10: return [2 /*return*/];
+                                case 14: return [2 /*return*/];
                             }
                         });
                     }); }, { canUndo: 'Apply Theme' })];
@@ -604,6 +621,7 @@ var StructureComponentManager = /** @class */ (function (_super) {
     StructureComponentManager.OptionsParams = {
         showHydrogens: PD.Boolean(true, { description: 'Toggle display of hydrogen atoms in representations' }),
         visualQuality: PD.Select('auto', VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
+        materialStyle: Material.getParam(),
         interactions: PD.Group(InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),
     };
     function getAddParams(plugin, params) {
@@ -627,10 +645,14 @@ var StructureComponentManager = /** @class */ (function (_super) {
                 color: PD.Group({
                     color: PD.Color(ColorNames.blue, { isExpanded: true }),
                 }, { isFlat: true }),
-                reset: PD.EmptyGroup({ label: 'Reset Color' }),
+                resetColor: PD.EmptyGroup({ label: 'Reset Color' }),
                 transparency: PD.Group({
                     value: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
                 }, { isFlat: true }),
+                material: PD.Group({
+                    material: Material.getParam({ isFlat: true }),
+                }, { isFlat: true }),
+                resetMaterial: PD.EmptyGroup({ label: 'Reset Material' }),
                 clipping: PD.Group({
                     excludeGroups: PD.MultiSelect([], PD.objectToOptions(Clipping.Groups.Names)),
                 }, { isFlat: true }),

package/lib/mol-plugin-state/transforms/data.d.ts

@@ -42,7 +42,7 @@ declare const DownloadBlob: StateTransformer<SO.Root, SO.Data.Blob, PD.Normalize
 }>>;
 declare type RawData = typeof RawData;
 declare const RawData: StateTransformer<SO.Root, SO.Data.String | SO.Data.Binary, PD.Normalize<{
-    data: string | Uint8Array | number[] | ArrayBuffer;
+    data: string | ArrayBuffer | Uint8Array | number[];
     label: string | undefined;
 }>>;
 declare type ReadFile = typeof ReadFile;

package/lib/mol-plugin-state/transforms/model.d.ts

@@ -85,15 +85,15 @@ declare const StructureFromModel: StateTransformer<SO.Molecule.Model, SO.Molecul
     type: PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
     }>, "auto"> | PD.NamedParams<PD.Normalize<{
+        dynamicBonds: any;
+        id: any;
+    }>, "assembly"> | PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
         ijkMin: any;
         ijkMax: any;
     }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
     }>, "model"> | PD.NamedParams<PD.Normalize<{
-        dynamicBonds: any;
-        id: any;
-    }>, "assembly"> | PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
         radius: any;
     }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
@@ -154,11 +154,11 @@ export declare const StructureComplexElementTypes: {
 export declare type StructureComplexElementTypes = keyof typeof StructureComplexElementTypes;
 declare type StructureComplexElement = typeof StructureComplexElement;
 declare const StructureComplexElement: StateTransformer<SO.Molecule.Structure, SO.Molecule.Structure, PD.Normalize<{
-    type: "polymer" | "water" | "branched" | "ligand" | "spheres" | "coarse" | "protein" | "nucleic" | "non-standard" | "atomic-sequence" | "atomic-het";
+    type: "spheres" | "polymer" | "water" | "branched" | "ligand" | "coarse" | "protein" | "nucleic" | "non-standard" | "atomic-sequence" | "atomic-het";
 }>>;
 declare type StructureComponent = typeof StructureComponent;
 declare const StructureComponent: StateTransformer<SO.Molecule.Structure, SO.Molecule.Structure, PD.Normalize<{
-    type: PD.NamedParams<Script, "script"> | PD.NamedParams<"polymer" | "water" | "branched" | "ligand" | "ion" | "lipid" | "all" | "coarse" | "protein" | "nucleic" | "non-standard", "static"> | PD.NamedParams<StructureElement.Bundle, "bundle"> | PD.NamedParams<Expression, "expression">;
+    type: PD.NamedParams<"all" | "polymer" | "water" | "branched" | "ligand" | "ion" | "lipid" | "coarse" | "protein" | "nucleic" | "non-standard", "static"> | PD.NamedParams<Script, "script"> | PD.NamedParams<StructureElement.Bundle, "bundle"> | PD.NamedParams<Expression, "expression">;
     nullIfEmpty: boolean | undefined;
     label: string;
 }>>;

package/lib/mol-plugin-state/transforms/representation.d.ts

@@ -25,6 +25,8 @@ export { OverpaintStructureRepresentation3DFromScript };
 export { OverpaintStructureRepresentation3DFromBundle };
 export { TransparencyStructureRepresentation3DFromScript };
 export { TransparencyStructureRepresentation3DFromBundle };
+export { SubstanceStructureRepresentation3DFromScript };
+export { SubstanceStructureRepresentation3DFromBundle };
 export { ClippingStructureRepresentation3DFromScript };
 export { ClippingStructureRepresentation3DFromBundle };
 export { VolumeRepresentation3D };
@@ -45,13 +47,13 @@ declare const ExplodeStructureRepresentation3D: StateTransformer<SO.Molecule.Str
 declare type SpinStructureRepresentation3D = typeof SpinStructureRepresentation3D;
 declare const SpinStructureRepresentation3D: StateTransformer<SO.Molecule.Structure.Representation3D, SO.Molecule.Structure.Representation3DState, PD.Normalize<{
     axis: PD.NamedParams<PD.Normalize<{
-        vector: any;
-    }>, "custom"> | PD.NamedParams<PD.Normalize<{
         principalAxis: any;
-    }>, "structure">;
-    origin: PD.NamedParams<PD.Normalize<{
+    }>, "structure"> | PD.NamedParams<PD.Normalize<{
+        vector: any;
+    }>, "custom">;
+    origin: PD.NamedParams<PD.Normalize<unknown>, "structure"> | PD.NamedParams<PD.Normalize<{
         vector: any;
-    }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "structure">;
+    }>, "custom">;
     t: number;
 }>>;
 declare type OverpaintStructureRepresentation3DFromScript = typeof OverpaintStructureRepresentation3DFromScript;
@@ -84,6 +86,28 @@ declare const TransparencyStructureRepresentation3DFromBundle: StateTransformer<
         value: number;
     }>[];
 }>>;
+declare type SubstanceStructureRepresentation3DFromScript = typeof SubstanceStructureRepresentation3DFromScript;
+declare const SubstanceStructureRepresentation3DFromScript: StateTransformer<SO.Molecule.Structure.Representation3D, SO.Molecule.Structure.Representation3DState, PD.Normalize<{
+    layers: PD.Normalize<{
+        script: Script;
+        material: {
+            metalness: number;
+            roughness: number;
+        };
+        clear: boolean;
+    }>[];
+}>>;
+declare type SubstanceStructureRepresentation3DFromBundle = typeof SubstanceStructureRepresentation3DFromBundle;
+declare const SubstanceStructureRepresentation3DFromBundle: StateTransformer<SO.Molecule.Structure.Representation3D, SO.Molecule.Structure.Representation3DState, PD.Normalize<{
+    layers: PD.Normalize<{
+        bundle: StructureElement.Bundle;
+        material: {
+            metalness: number;
+            roughness: number;
+        };
+        clear: boolean;
+    }>[];
+}>>;
 declare type ClippingStructureRepresentation3DFromScript = typeof ClippingStructureRepresentation3DFromScript;
 declare const ClippingStructureRepresentation3DFromScript: StateTransformer<SO.Molecule.Structure.Representation3D, SO.Molecule.Structure.Representation3DState, PD.Normalize<{
     layers: PD.Normalize<{
@@ -125,7 +149,11 @@ declare const ModelUnitcell3D: StateTransformer<SO.Molecule.Model, SO.Shape.Repr
     ignoreLight: boolean;
     xrayShaded: boolean;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
 }>>;
 export { StructureBoundingBox3D };
 declare type StructureBoundingBox3D = typeof StructureBoundingBox3D;
@@ -136,14 +164,18 @@ declare const StructureBoundingBox3D: StateTransformer<SO.Molecule.Structure, SO
     ignoreLight: boolean;
     xrayShaded: boolean;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
     radius: number;
     color: Color;
 }>>;
 export { StructureSelectionsDistance3D };
 declare type StructureSelectionsDistance3D = typeof StructureSelectionsDistance3D;
 declare const StructureSelectionsDistance3D: StateTransformer<SO.Molecule.Structure.Selections, SO.Shape.Representation3D, PD.Normalize<{
-    visuals: ("lines" | "text")[];
+    visuals: ("text" | "lines")[];
     unitLabel: string;
     borderWidth: number;
     customText: string;
@@ -161,14 +193,18 @@ declare const StructureSelectionsDistance3D: StateTransformer<SO.Molecule.Struct
     tether: boolean;
     tetherLength: number;
     tetherBaseWidth: number;
-    attachment: "middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right";
+    attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right";
     fontFamily: import("../../mol-geo/geometry/text/font-atlas").FontFamily;
     fontQuality: number;
     fontStyle: import("../../mol-geo/geometry/text/font-atlas").FontStyle;
     fontVariant: import("../../mol-geo/geometry/text/font-atlas").FontVariant;
     fontWeight: import("../../mol-geo/geometry/text/font-atlas").FontWeight;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
     lineSizeAttenuation: boolean;
     linesColor: Color;
     linesSize: number;
@@ -194,14 +230,18 @@ declare const StructureSelectionsAngle3D: StateTransformer<SO.Molecule.Structure
     tether: boolean;
     tetherLength: number;
     tetherBaseWidth: number;
-    attachment: "middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right";
+    attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right";
     fontFamily: import("../../mol-geo/geometry/text/font-atlas").FontFamily;
     fontQuality: number;
     fontStyle: import("../../mol-geo/geometry/text/font-atlas").FontStyle;
     fontVariant: import("../../mol-geo/geometry/text/font-atlas").FontVariant;
     fontWeight: import("../../mol-geo/geometry/text/font-atlas").FontWeight;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
     ignoreLight: boolean;
     sectorOpacity: number;
     color: Color;
@@ -234,14 +274,18 @@ declare const StructureSelectionsDihedral3D: StateTransformer<SO.Molecule.Struct
     tether: boolean;
     tetherLength: number;
     tetherBaseWidth: number;
-    attachment: "middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right";
+    attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right";
     fontFamily: import("../../mol-geo/geometry/text/font-atlas").FontFamily;
     fontQuality: number;
     fontStyle: import("../../mol-geo/geometry/text/font-atlas").FontStyle;
     fontVariant: import("../../mol-geo/geometry/text/font-atlas").FontVariant;
     fontWeight: import("../../mol-geo/geometry/text/font-atlas").FontWeight;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
     ignoreLight: boolean;
     sectorOpacity: number;
     color: Color;
@@ -275,14 +319,18 @@ declare const StructureSelectionsLabel3D: StateTransformer<SO.Molecule.Structure
     tether: boolean;
     tetherLength: number;
     tetherBaseWidth: number;
-    attachment: "middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right";
+    attachment: "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right";
     fontFamily: import("../../mol-geo/geometry/text/font-atlas").FontFamily;
     fontQuality: number;
     fontStyle: import("../../mol-geo/geometry/text/font-atlas").FontStyle;
     fontVariant: import("../../mol-geo/geometry/text/font-atlas").FontVariant;
     fontWeight: import("../../mol-geo/geometry/text/font-atlas").FontWeight;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
 }>>;
 export { StructureSelectionsOrientation3D };
 declare type StructureSelectionsOrientation3D = typeof StructureSelectionsOrientation3D;
@@ -297,7 +345,11 @@ declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Str
     ignoreLight: boolean;
     xrayShaded: boolean;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
 }>>;
 export { StructureSelectionsPlane3D };
 declare type StructureSelectionsPlane3D = typeof StructureSelectionsPlane3D;
@@ -311,5 +363,9 @@ declare const StructureSelectionsPlane3D: StateTransformer<SO.Molecule.Structure
     ignoreLight: boolean;
     xrayShaded: boolean;
     alpha: number;
-    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+    }>;
 }>>;