molstar 2.3.9 → 3.0.0-dev.10

package/lib/commonjs/mol-plugin-state/manager/structure/selection.js

@@ -250,7 +250,9 @@ var StructureSelectionManager = /** @class */ (function (_super) {
         var cell = this.plugin.helpers.substructureParent.get(obj.data, true);
         if (!cell)
             return;
-        ref = cell.transform.ref;
+        // only need to update the root
+        if (ref !== cell.transform.ref)
+            return;
         if (!this.entries.has(ref))
             return;
         // use structure from last decorator as reference

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

@@ -86,14 +86,14 @@ declare const StructureFromModel: StateTransformer<SO.Molecule.Model, SO.Molecul
         dynamicBonds: any;
     }>, "auto"> | PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
-    }>, "model"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+    }>, "assembly"> | PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
         ijkMin: any;
         ijkMax: any;
     }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
         dynamicBonds: any;
-        id: any;
-    }>, "assembly"> | PD.NamedParams<PD.Normalize<{
+    }>, "model"> | 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: "spheres" | "polymer" | "water" | "branched" | "ligand" | "protein" | "nucleic" | "non-standard" | "coarse" | "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<"all" | "polymer" | "water" | "branched" | "ligand" | "protein" | "nucleic" | "non-standard" | "coarse" | "ion" | "lipid", "static"> | PD.NamedParams<Expression, "expression"> | PD.NamedParams<StructureElement.Bundle, "bundle">;
+    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/commonjs/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 +86,30 @@ 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;
+            bumpiness: 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;
+            bumpiness: 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<{
@@ -118,14 +144,25 @@ declare const ModelUnitcell3D: StateTransformer<SO.Molecule.Model, SO.Shape.Repr
     cellColor: Color;
     cellScale: number;
     ref: "origin" | "model";
-    attachment: "corner" | "center";
+    attachment: "center" | "corner";
     doubleSided: boolean;
     flipSided: boolean;
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;
 export { StructureBoundingBox3D };
 declare type StructureBoundingBox3D = typeof StructureBoundingBox3D;
@@ -135,8 +172,19 @@ declare const StructureBoundingBox3D: StateTransformer<SO.Molecule.Structure, SO
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     radius: number;
     color: Color;
 }>>;
@@ -161,14 +209,23 @@ 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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     lineSizeAttenuation: boolean;
     linesColor: Color;
     linesSize: number;
@@ -194,14 +251,23 @@ 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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     ignoreLight: boolean;
     sectorOpacity: number;
     color: Color;
@@ -210,6 +276,8 @@ declare const StructureSelectionsAngle3D: StateTransformer<SO.Molecule.Structure
     flipSided: boolean;
     flatShaded: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     lineSizeAttenuation: boolean;
     linesSize: number;
     dashLength: number;
@@ -234,14 +302,23 @@ 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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     ignoreLight: boolean;
     sectorOpacity: number;
     color: Color;
@@ -250,6 +327,8 @@ declare const StructureSelectionsDihedral3D: StateTransformer<SO.Molecule.Struct
     flipSided: boolean;
     flatShaded: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     lineSizeAttenuation: boolean;
     linesSize: number;
     dashLength: number;
@@ -275,19 +354,28 @@ 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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;
 export { StructureSelectionsOrientation3D };
 declare type StructureSelectionsOrientation3D = typeof StructureSelectionsOrientation3D;
 declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Structure.Selections, SO.Shape.Representation3D, PD.Normalize<{
-    visuals: ("axes" | "ellipsoid" | "box")[];
+    visuals: ("box" | "axes" | "ellipsoid")[];
     color: Color;
     scaleFactor: number;
     radiusScale: number;
@@ -296,8 +384,19 @@ declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Str
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;
 export { StructureSelectionsPlane3D };
 declare type StructureSelectionsPlane3D = typeof StructureSelectionsPlane3D;
@@ -310,6 +409,17 @@ declare const StructureSelectionsPlane3D: StateTransformer<SO.Molecule.Structure
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     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;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
 }>>;

package/lib/commonjs/mol-plugin-state/transforms/representation.js

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureSelectionsPlane3D = exports.StructureSelectionsOrientation3D = exports.StructureSelectionsLabel3D = exports.StructureSelectionsDihedral3D = exports.StructureSelectionsAngle3D = exports.StructureSelectionsDistance3D = exports.StructureBoundingBox3D = exports.ModelUnitcell3D = exports.ShapeRepresentation3D = exports.VolumeRepresentation3DHelpers = exports.VolumeRepresentation3D = exports.ClippingStructureRepresentation3DFromBundle = exports.ClippingStructureRepresentation3DFromScript = exports.TransparencyStructureRepresentation3DFromBundle = exports.TransparencyStructureRepresentation3DFromScript = exports.OverpaintStructureRepresentation3DFromBundle = exports.OverpaintStructureRepresentation3DFromScript = exports.UnwindStructureAssemblyRepresentation3D = exports.SpinStructureRepresentation3D = exports.ExplodeStructureRepresentation3D = exports.StructureRepresentation3D = void 0;
+exports.StructureSelectionsPlane3D = exports.StructureSelectionsOrientation3D = exports.StructureSelectionsLabel3D = exports.StructureSelectionsDihedral3D = exports.StructureSelectionsAngle3D = exports.StructureSelectionsDistance3D = exports.StructureBoundingBox3D = exports.ModelUnitcell3D = exports.ShapeRepresentation3D = exports.VolumeRepresentation3DHelpers = exports.VolumeRepresentation3D = exports.ClippingStructureRepresentation3DFromBundle = exports.ClippingStructureRepresentation3DFromScript = exports.SubstanceStructureRepresentation3DFromBundle = exports.SubstanceStructureRepresentation3DFromScript = exports.TransparencyStructureRepresentation3DFromBundle = exports.TransparencyStructureRepresentation3DFromScript = exports.OverpaintStructureRepresentation3DFromBundle = exports.OverpaintStructureRepresentation3DFromScript = exports.UnwindStructureAssemblyRepresentation3D = exports.SpinStructureRepresentation3D = exports.ExplodeStructureRepresentation3D = exports.StructureRepresentation3D = void 0;
 var tslib_1 = require("tslib");
 var structure_1 = require("../../mol-model/structure");
 var volume_1 = require("../../mol-model/volume");
@@ -38,6 +38,8 @@ var mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
 var shape_1 = require("./shape");
 var shape_2 = require("../../mol-model/shape");
 var plane_1 = require("../../mol-repr/shape/loci/plane");
+var substance_1 = require("../../mol-theme/substance");
+var material_1 = require("../../mol-util/material");
 var StructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
     name: 'structure-representation-3d',
     display: '3D Representation',
@@ -73,7 +75,7 @@ var StructureRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
         return ({
             type: param_definition_1.ParamDefinition.Mapped(registry.default.name, registry.getApplicableTypes(a.data), function (name) { return param_definition_1.ParamDefinition.Group(registry.get(name).getParams(themeCtx, a.data)); }),
             colorTheme: param_definition_1.ParamDefinition.Mapped(type.defaultColorTheme.name, themeCtx.colorThemeRegistry.getApplicableTypes(dataCtx), function (name) { return param_definition_1.ParamDefinition.Group(themeCtx.colorThemeRegistry.get(name).getParams(dataCtx)); }, colorThemeInfo),
-            sizeTheme: param_definition_1.ParamDefinition.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.types, function (name) { return param_definition_1.ParamDefinition.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
+            sizeTheme: param_definition_1.ParamDefinition.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.getApplicableTypes(dataCtx), function (name) { return param_definition_1.ParamDefinition.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
         });
     }
 })({
@@ -321,26 +323,32 @@ var OverpaintStructureRepresentation3DFromScript = objects_1.PluginStateTransfor
     apply: function (_a) {
         var a = _a.a, params = _a.params;
         var structure = a.data.sourceData;
+        var geometryVersion = a.data.repr.geometryVersion;
         var overpaint = overpaint_1.Overpaint.ofScript(params.layers, structure);
         return new objects_1.PluginStateObject.Molecule.Structure.Representation3DState({
             state: { overpaint: overpaint },
             initialState: { overpaint: overpaint_1.Overpaint.Empty },
-            info: structure,
+            info: { structure: structure, geometryVersion: geometryVersion },
             repr: a.data.repr
         }, { label: "Overpaint (".concat(overpaint.layers.length, " Layers)") });
     },
     update: function (_a) {
         var a = _a.a, b = _a.b, newParams = _a.newParams, oldParams = _a.oldParams;
-        var oldStructure = b.data.info;
+        var info = b.data.info;
         var newStructure = a.data.sourceData;
-        if (newStructure !== oldStructure)
+        if (newStructure !== info.structure)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
         if (a.data.repr !== b.data.repr)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        var newGeometryVersion = a.data.repr.geometryVersion;
+        // smoothing needs to be re-calculated when geometry changes
+        if (newGeometryVersion !== info.geometryVersion && (0, base_1.hasColorSmoothingProp)(a.data.repr.props))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
         var oldOverpaint = b.data.state.overpaint;
         var newOverpaint = overpaint_1.Overpaint.ofScript(newParams.layers, newStructure);
         if (overpaint_1.Overpaint.areEqual(oldOverpaint, newOverpaint))
             return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        info.geometryVersion = newGeometryVersion;
         b.data.state.overpaint = newOverpaint;
         b.data.repr = a.data.repr;
         b.label = "Overpaint (".concat(newOverpaint.layers.length, " Layers)");
@@ -374,26 +382,32 @@ var OverpaintStructureRepresentation3DFromBundle = objects_1.PluginStateTransfor
     apply: function (_a) {
         var a = _a.a, params = _a.params;
         var structure = a.data.sourceData;
+        var geometryVersion = a.data.repr.geometryVersion;
         var overpaint = overpaint_1.Overpaint.ofBundle(params.layers, structure);
         return new objects_1.PluginStateObject.Molecule.Structure.Representation3DState({
             state: { overpaint: overpaint },
             initialState: { overpaint: overpaint_1.Overpaint.Empty },
-            info: structure,
+            info: { structure: structure, geometryVersion: geometryVersion },
             repr: a.data.repr
         }, { label: "Overpaint (".concat(overpaint.layers.length, " Layers)") });
     },
     update: function (_a) {
         var a = _a.a, b = _a.b, newParams = _a.newParams, oldParams = _a.oldParams;
-        var oldStructure = b.data.info;
+        var info = b.data.info;
         var newStructure = a.data.sourceData;
-        if (newStructure !== oldStructure)
+        if (newStructure !== info.structure)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
         if (a.data.repr !== b.data.repr)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        var newGeometryVersion = a.data.repr.geometryVersion;
+        // smoothing needs to be re-calculated when geometry changes
+        if (newGeometryVersion !== info.geometryVersion && (0, base_1.hasColorSmoothingProp)(a.data.repr.props))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
         var oldOverpaint = b.data.state.overpaint;
         var newOverpaint = overpaint_1.Overpaint.ofBundle(newParams.layers, newStructure);
         if (overpaint_1.Overpaint.areEqual(oldOverpaint, newOverpaint))
             return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        info.geometryVersion = newGeometryVersion;
         b.data.state.overpaint = newOverpaint;
         b.data.repr = a.data.repr;
         b.label = "Overpaint (".concat(newOverpaint.layers.length, " Layers)");
@@ -424,25 +438,32 @@ var TransparencyStructureRepresentation3DFromScript = objects_1.PluginStateTrans
     apply: function (_a) {
         var a = _a.a, params = _a.params;
         var structure = a.data.sourceData;
+        var geometryVersion = a.data.repr.geometryVersion;
         var transparency = transparency_1.Transparency.ofScript(params.layers, structure);
         return new objects_1.PluginStateObject.Molecule.Structure.Representation3DState({
             state: { transparency: transparency },
             initialState: { transparency: transparency_1.Transparency.Empty },
-            info: structure,
+            info: { structure: structure, geometryVersion: geometryVersion },
             repr: a.data.repr
         }, { label: "Transparency (".concat(transparency.layers.length, " Layers)") });
     },
     update: function (_a) {
         var a = _a.a, b = _a.b, newParams = _a.newParams, oldParams = _a.oldParams;
-        var structure = b.data.info;
-        if (a.data.sourceData !== structure)
+        var info = b.data.info;
+        var newStructure = a.data.sourceData;
+        if (newStructure !== info.structure)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
         if (a.data.repr !== b.data.repr)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        var newGeometryVersion = a.data.repr.geometryVersion;
+        // smoothing needs to be re-calculated when geometry changes
+        if (newGeometryVersion !== info.geometryVersion && (0, base_1.hasColorSmoothingProp)(a.data.repr.props))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
         var oldTransparency = b.data.state.transparency;
-        var newTransparency = transparency_1.Transparency.ofScript(newParams.layers, structure);
+        var newTransparency = transparency_1.Transparency.ofScript(newParams.layers, newStructure);
         if (transparency_1.Transparency.areEqual(oldTransparency, newTransparency))
             return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        info.geometryVersion = newGeometryVersion;
         b.data.state.transparency = newTransparency;
         b.data.repr = a.data.repr;
         b.label = "Transparency (".concat(newTransparency.layers.length, " Layers)");
@@ -474,25 +495,32 @@ var TransparencyStructureRepresentation3DFromBundle = objects_1.PluginStateTrans
     apply: function (_a) {
         var a = _a.a, params = _a.params;
         var structure = a.data.sourceData;
+        var geometryVersion = a.data.repr.geometryVersion;
         var transparency = transparency_1.Transparency.ofBundle(params.layers, structure);
         return new objects_1.PluginStateObject.Molecule.Structure.Representation3DState({
             state: { transparency: transparency },
             initialState: { transparency: transparency_1.Transparency.Empty },
-            info: structure,
+            info: { structure: structure, geometryVersion: geometryVersion },
             repr: a.data.repr
         }, { label: "Transparency (".concat(transparency.layers.length, " Layers)") });
     },
     update: function (_a) {
         var a = _a.a, b = _a.b, newParams = _a.newParams, oldParams = _a.oldParams;
-        var structure = b.data.info;
-        if (a.data.sourceData !== structure)
+        var info = b.data.info;
+        var newStructure = a.data.sourceData;
+        if (newStructure !== info.structure)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
         if (a.data.repr !== b.data.repr)
             return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        var newGeometryVersion = a.data.repr.geometryVersion;
+        // smoothing needs to be re-calculated when geometry changes
+        if (newGeometryVersion !== info.geometryVersion && (0, base_1.hasColorSmoothingProp)(a.data.repr.props))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
         var oldTransparency = b.data.state.transparency;
-        var newTransparency = transparency_1.Transparency.ofBundle(newParams.layers, structure);
+        var newTransparency = transparency_1.Transparency.ofBundle(newParams.layers, newStructure);
         if (transparency_1.Transparency.areEqual(oldTransparency, newTransparency))
             return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        info.geometryVersion = newGeometryVersion;
         b.data.state.transparency = newTransparency;
         b.data.repr = a.data.repr;
         b.label = "Transparency (".concat(newTransparency.layers.length, " Layers)");
@@ -500,6 +528,123 @@ var TransparencyStructureRepresentation3DFromBundle = objects_1.PluginStateTrans
     }
 });
 exports.TransparencyStructureRepresentation3DFromBundle = TransparencyStructureRepresentation3DFromBundle;
+var SubstanceStructureRepresentation3DFromScript = objects_1.PluginStateTransform.BuiltIn({
+    name: 'substance-structure-representation-3d-from-script',
+    display: 'Substance 3D Representation',
+    from: objects_1.PluginStateObject.Molecule.Structure.Representation3D,
+    to: objects_1.PluginStateObject.Molecule.Structure.Representation3DState,
+    params: function () { return ({
+        layers: param_definition_1.ParamDefinition.ObjectList({
+            script: param_definition_1.ParamDefinition.Script((0, script_1.Script)('(sel.atom.all)', 'mol-script')),
+            material: material_1.Material.getParam(),
+            clear: param_definition_1.ParamDefinition.Boolean(false)
+        }, function (e) { return "".concat(e.clear ? 'Clear' : material_1.Material.toString(e.material)); }, {
+            defaultValue: [{
+                    script: (0, script_1.Script)('(sel.atom.all)', 'mol-script'),
+                    material: (0, material_1.Material)({ roughness: 1 }),
+                    clear: false
+                }]
+        }),
+    }); }
+})({
+    canAutoUpdate: function () {
+        return true;
+    },
+    apply: function (_a) {
+        var a = _a.a, params = _a.params;
+        var structure = a.data.sourceData;
+        var geometryVersion = a.data.repr.geometryVersion;
+        var substance = substance_1.Substance.ofScript(params.layers, structure);
+        return new objects_1.PluginStateObject.Molecule.Structure.Representation3DState({
+            state: { substance: substance },
+            initialState: { substance: substance_1.Substance.Empty },
+            info: { structure: structure, geometryVersion: geometryVersion },
+            repr: a.data.repr
+        }, { label: "Substance (".concat(substance.layers.length, " Layers)") });
+    },
+    update: function (_a) {
+        var a = _a.a, b = _a.b, newParams = _a.newParams, oldParams = _a.oldParams;
+        var info = b.data.info;
+        var newStructure = a.data.sourceData;
+        if (newStructure !== info.structure)
+            return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr)
+            return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        var newGeometryVersion = a.data.repr.geometryVersion;
+        // smoothing needs to be re-calculated when geometry changes
+        if (newGeometryVersion !== info.geometryVersion && (0, base_1.hasColorSmoothingProp)(a.data.repr.props))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        var oldSubstance = b.data.state.substance;
+        var newSubstance = substance_1.Substance.ofScript(newParams.layers, newStructure);
+        if (substance_1.Substance.areEqual(oldSubstance, newSubstance))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        info.geometryVersion = newGeometryVersion;
+        b.data.state.substance = newSubstance;
+        b.data.repr = a.data.repr;
+        b.label = "Substance (".concat(newSubstance.layers.length, " Layers)");
+        return mol_state_1.StateTransformer.UpdateResult.Updated;
+    }
+});
+exports.SubstanceStructureRepresentation3DFromScript = SubstanceStructureRepresentation3DFromScript;
+var SubstanceStructureRepresentation3DFromBundle = objects_1.PluginStateTransform.BuiltIn({
+    name: 'substance-structure-representation-3d-from-bundle',
+    display: 'Substance 3D Representation',
+    from: objects_1.PluginStateObject.Molecule.Structure.Representation3D,
+    to: objects_1.PluginStateObject.Molecule.Structure.Representation3DState,
+    params: function () { return ({
+        layers: param_definition_1.ParamDefinition.ObjectList({
+            bundle: param_definition_1.ParamDefinition.Value(structure_1.StructureElement.Bundle.Empty),
+            material: material_1.Material.getParam(),
+            clear: param_definition_1.ParamDefinition.Boolean(false)
+        }, function (e) { return "".concat(e.clear ? 'Clear' : material_1.Material.toString(e.material)); }, {
+            defaultValue: [{
+                    bundle: structure_1.StructureElement.Bundle.Empty,
+                    material: (0, material_1.Material)({ roughness: 1 }),
+                    clear: false
+                }],
+            isHidden: true
+        }),
+    }); }
+})({
+    canAutoUpdate: function () {
+        return true;
+    },
+    apply: function (_a) {
+        var a = _a.a, params = _a.params;
+        var structure = a.data.sourceData;
+        var geometryVersion = a.data.repr.geometryVersion;
+        var substance = substance_1.Substance.ofBundle(params.layers, structure);
+        return new objects_1.PluginStateObject.Molecule.Structure.Representation3DState({
+            state: { substance: substance },
+            initialState: { substance: substance_1.Substance.Empty },
+            info: { structure: structure, geometryVersion: geometryVersion },
+            repr: a.data.repr
+        }, { label: "Substance (".concat(substance.layers.length, " Layers)") });
+    },
+    update: function (_a) {
+        var a = _a.a, b = _a.b, newParams = _a.newParams, oldParams = _a.oldParams;
+        var info = b.data.info;
+        var newStructure = a.data.sourceData;
+        if (newStructure !== info.structure)
+            return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        if (a.data.repr !== b.data.repr)
+            return mol_state_1.StateTransformer.UpdateResult.Recreate;
+        var newGeometryVersion = a.data.repr.geometryVersion;
+        // smoothing needs to be re-calculated when geometry changes
+        if (newGeometryVersion !== info.geometryVersion && (0, base_1.hasColorSmoothingProp)(a.data.repr.props))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        var oldSubstance = b.data.state.substance;
+        var newSubstance = substance_1.Substance.ofBundle(newParams.layers, newStructure);
+        if (substance_1.Substance.areEqual(oldSubstance, newSubstance))
+            return mol_state_1.StateTransformer.UpdateResult.Unchanged;
+        info.geometryVersion = newGeometryVersion;
+        b.data.state.substance = newSubstance;
+        b.data.repr = a.data.repr;
+        b.label = "Substance (".concat(newSubstance.layers.length, " Layers)");
+        return mol_state_1.StateTransformer.UpdateResult.Updated;
+    }
+});
+exports.SubstanceStructureRepresentation3DFromBundle = SubstanceStructureRepresentation3DFromBundle;
 var ClippingStructureRepresentation3DFromScript = objects_1.PluginStateTransform.BuiltIn({
     name: 'clipping-structure-representation-3d-from-script',
     display: 'Clipping 3D Representation',
@@ -656,7 +801,7 @@ var VolumeRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
         return ({
             type: param_definition_1.ParamDefinition.Mapped(registry.default.name, registry.types, function (name) { return param_definition_1.ParamDefinition.Group(registry.get(name).getParams(themeCtx, a.data)); }),
             colorTheme: param_definition_1.ParamDefinition.Mapped(type.defaultColorTheme.name, themeCtx.colorThemeRegistry.getApplicableTypes(dataCtx), function (name) { return param_definition_1.ParamDefinition.Group(themeCtx.colorThemeRegistry.get(name).getParams(dataCtx)); }),
-            sizeTheme: param_definition_1.ParamDefinition.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.types, function (name) { return param_definition_1.ParamDefinition.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
+            sizeTheme: param_definition_1.ParamDefinition.Mapped(type.defaultSizeTheme.name, themeCtx.sizeThemeRegistry.getApplicableTypes(dataCtx), function (name) { return param_definition_1.ParamDefinition.Group(themeCtx.sizeThemeRegistry.get(name).getParams(dataCtx)); })
         });
     }
 })({