molstar 4.0.1 → 4.2.0

package/lib/extensions/dnatco/ntc-tube/behavior.d.ts

@@ -24,23 +24,23 @@ export declare const NtCTubePreset: StructureRepresentationPresetProvider<{
     representations?: undefined;
 } | {
     components: {
-        tube: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        tube: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        tube: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        tube: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        tube: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        tube: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
         branched: undefined;
     };
     representations: {
-        tubeRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        tubeRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        tubeRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        tubeRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     } | {
-        tubeRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        tubeRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare function NtCTubeSegmentLabel(step: DnatcoTypes.Step): string;

package/lib/extensions/dnatco/ntc-tube/behavior.js

@@ -41,10 +41,10 @@ export const NtCTubePreset = StructureRepresentationPresetProvider({
     }
 });
 export function NtCTubeSegmentLabel(step) {
-    return `
-        <b>${step.auth_asym_id_1}</b> |
-        <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
-           ${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
-        <i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
+    return `
+        <b>${step.auth_asym_id_1}</b> |
+        <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
+           ${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
+        <i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
     `;
 }

package/lib/extensions/dnatco/ntc-tube/representation.d.ts

@@ -41,6 +41,7 @@ export declare const NtCTubeParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -79,6 +80,7 @@ export declare function getNtCTubeParams(ctx: ThemeRegistryContext, structure: S
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -118,6 +120,7 @@ export declare const NtCTubeRepresentationProvider: StructureRepresentationProvi
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/extensions/g3d/format.d.ts

@@ -23,7 +23,7 @@ declare const G3dHeaderObject_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
-        id: import("../../mol-util/uuid").UUID;
+        id: import("../../mol-util").UUID;
         type: SO.TypeInfo;
         label: string;
         description?: string | undefined;
@@ -36,7 +36,7 @@ declare const G3dHeaderObject_base: {
         };
     };
     type: SO.TypeInfo;
-    is(obj?: import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../mol-state/object").StateObject<{
+    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<{
         header: G3dHeader;
         urlOrData: Uint8Array | string;
         cache: {
@@ -47,19 +47,19 @@ declare const G3dHeaderObject_base: {
 export declare class G3dHeaderObject extends G3dHeaderObject_base {
 }
 export type G3DHeaderFromFile = typeof G3DHeaderFromFile;
-export declare const G3DHeaderFromFile: import("../../mol-state/transformer").StateTransformer<SO.Data.Binary, G3dHeaderObject, ParamDefinition.Normalize<{}>>;
+export declare const G3DHeaderFromFile: import("../../mol-state").StateTransformer<SO.Data.Binary, G3dHeaderObject, ParamDefinition.Normalize<{}>>;
 export type G3DHeaderFromUrl = typeof G3DHeaderFromUrl;
-export declare const G3DHeaderFromUrl: import("../../mol-state/transformer").StateTransformer<SO.Root, G3dHeaderObject, ParamDefinition.Normalize<{
+export declare const G3DHeaderFromUrl: import("../../mol-state").StateTransformer<SO.Root, G3dHeaderObject, ParamDefinition.Normalize<{
     url: string;
 }>>;
 export type G3DTrajectory = typeof G3DHeaderFromUrl;
-export declare const G3DTrajectory: import("../../mol-state/transformer").StateTransformer<G3dHeaderObject, SO.Molecule.Trajectory, ParamDefinition.Normalize<{
+export declare const G3DTrajectory: import("../../mol-state").StateTransformer<G3dHeaderObject, SO.Molecule.Trajectory, ParamDefinition.Normalize<{
     resolution: number;
 }>>;
 export declare const LoadG3D: StateAction<SO.Root, void, ParamDefinition.Normalize<{
     url: string;
 }>>;
-export declare const G3DFormat: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const G3DFormat: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showTooltip: boolean;
 }>;

package/lib/extensions/geo-export/glb-exporter.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/extensions/geo-export/glb-exporter.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -129,8 +129,8 @@ export class GlbExporter extends MeshExporter {
         }
         return this.addBuffer(colorBuffer, UNSIGNED_BYTE, 'VEC4', vertexCount, ARRAY_BUFFER, undefined, undefined, true);
     }
-    addMaterial(metalness, roughness, doubleSided, alpha) {
-        const hash = `${metalness}|${roughness}|${doubleSided}`;
+    addMaterial(metalness, roughness, emissive, doubleSided, alpha) {
+        const hash = `${metalness}|${roughness}|${emissive}|${doubleSided}`;
         if (!this.materialMap.has(hash)) {
             this.materialMap.set(hash, this.materials.length);
             this.materials.push({
@@ -139,6 +139,7 @@ export class GlbExporter extends MeshExporter {
                     metallicFactor: metalness,
                     roughnessFactor: roughness
                 },
+                emissiveFactor: [emissive, emissive, emissive],
                 doubleSided,
                 alphaMode: alpha ? 'BLEND' : 'OPAQUE',
             });
@@ -157,9 +158,10 @@ export class GlbExporter extends MeshExporter {
         const instanceCount = values.uInstanceCount.ref.value;
         const metalness = values.uMetalness.ref.value;
         const roughness = values.uRoughness.ref.value;
+        const emissive = values.uEmissive.ref.value;
         const doubleSided = ((_a = values.uDoubleSided) === null || _a === void 0 ? void 0 : _a.ref.value) || values.hasReflection.ref.value;
         const alpha = values.uAlpha.ref.value < 1;
-        const material = this.addMaterial(metalness, roughness, doubleSided, alpha);
+        const material = this.addMaterial(metalness, roughness, emissive, doubleSided, alpha);
         let interpolatedColors;
         if (webgl && mesh && (colorType === 'volume' || colorType === 'volumeInstance')) {
             const stride = isGeoTexture ? 4 : 3;

package/lib/extensions/geo-export/index.d.ts

@@ -4,4 +4,4 @@
  * @author Sukolsak Sakshuwong <sukolsak@stanford.edu>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const GeometryExport: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
+export declare const GeometryExport: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/extensions/geo-export/usdz-exporter.js

@@ -24,20 +24,20 @@ export class UsdzExporter extends MeshExporter {
         const materialKey = this.materialMap.size;
         this.materialMap.set(hash, materialKey);
         const [r, g, b] = Color.toRgbNormalized(color).map(v => Math.round(v * 1000) / 1000);
-        this.materials.push(`
-def Material "material${materialKey}"
-{
-    token outputs:surface.connect = </material${materialKey}/shader.outputs:surface>
-    def Shader "shader"
-    {
-        uniform token info:id = "UsdPreviewSurface"
-        color3f inputs:diffuseColor = (${r},${g},${b})
-        float inputs:opacity = ${alpha}
-        float inputs:metallic = ${metalness}
-        float inputs:roughness = ${roughness}
-        token outputs:surface
-    }
-}
+        this.materials.push(`
+def Material "material${materialKey}"
+{
+    token outputs:surface.connect = </material${materialKey}/shader.outputs:surface>
+    def Shader "shader"
+    {
+        uniform token info:id = "UsdPreviewSurface"
+        color3f inputs:diffuseColor = (${r},${g},${b})
+        float inputs:opacity = ${alpha}
+        float inputs:metallic = ${metalness}
+        float inputs:roughness = ${roughness}
+        token outputs:surface
+    }
+}
 `);
         return materialKey;
     }
@@ -144,41 +144,41 @@ def Material "material${materialKey}"
             else {
                 const geomSubsets = [];
                 faceIndicesByMaterial.forEach((faceIndices, materialKey) => {
-                    geomSubsets.push(`
-    def GeomSubset "g${materialKey}"
-    {
-        uniform token elementType = "face"
-        uniform token familyName = "materialBind"
-        int[] indices = [${faceIndices.join(',')}]
-        rel material:binding = </material${materialKey}>
-    }
+                    geomSubsets.push(`
+    def GeomSubset "g${materialKey}"
+    {
+        uniform token elementType = "face"
+        uniform token familyName = "materialBind"
+        int[] indices = [${faceIndices.join(',')}]
+        rel material:binding = </material${materialKey}>
+    }
 `);
                 });
                 materialBinding = geomSubsets.join('');
             }
-            this.meshes.push(`
-def Mesh "mesh${this.meshes.length}"
-{
-    int[] faceVertexCounts = [${new Array(drawCount / 3).fill(3).join(',')}]
-    int[] faceVertexIndices = [${StringBuilder.getString(indexBuilder)}]
-    point3f[] points = [${StringBuilder.getString(vertexBuilder)}]
-    normal3f[] primvars:normals = [${StringBuilder.getString(normalBuilder)}] (
-        interpolation = "vertex"
-    )
-    uniform token subdivisionScheme = "none"
-    ${materialBinding}
-}
+            this.meshes.push(`
+def Mesh "mesh${this.meshes.length}"
+{
+    int[] faceVertexCounts = [${new Array(drawCount / 3).fill(3).join(',')}]
+    int[] faceVertexIndices = [${StringBuilder.getString(indexBuilder)}]
+    point3f[] points = [${StringBuilder.getString(vertexBuilder)}]
+    normal3f[] primvars:normals = [${StringBuilder.getString(normalBuilder)}] (
+        interpolation = "vertex"
+    )
+    uniform token subdivisionScheme = "none"
+    ${materialBinding}
+}
 `);
         }
     }
     async getData(ctx) {
-        const header = `#usda 1.0
-(
-    customLayerData = {
-        string creator = "Mol* ${PLUGIN_VERSION}"
-    }
-    metersPerUnit = 1
-)
+        const header = `#usda 1.0
+(
+    customLayerData = {
+        string creator = "Mol* ${PLUGIN_VERSION}"
+    }
+    metersPerUnit = 1
+)
 `;
         const usda = [header, ...this.materials, ...this.meshes].join('');
         const usdaData = new Uint8Array(usda.length);

package/lib/extensions/meshes/mesh-extension.d.ts

@@ -39,17 +39,16 @@ declare const MeshlistStateObject_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
-        id: import("../../mol-util/uuid").UUID;
+        id: import("../../mol-util").UUID;
         /** Data type for `MeshlistStateObject` - list of meshes */
         type: PluginStateObject.TypeInfo;
         /** Data type for `MeshlistStateObject` - list of meshes */
         label: string;
-        /** Data type for `MeshlistStateObject` - list of meshes */
         description?: string | undefined;
         data: MeshlistData;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../mol-state/object").StateObject<MeshlistData, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<MeshlistData, PluginStateObject.TypeInfo>;
 };
 export declare class MeshlistStateObject extends MeshlistStateObject_base {
 }

package/lib/extensions/meshes/mesh-streaming/behavior.d.ts

@@ -27,7 +27,7 @@ declare const MeshStreaming_base: {
         data: MeshStreaming.Behavior;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../../mol-state/object").StateObject<MeshStreaming.Behavior, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<MeshStreaming.Behavior, PluginStateObject.TypeInfo>;
 };
 export declare class MeshStreaming extends MeshStreaming_base {
 }

package/lib/extensions/meshes/mesh-streaming/server-info.d.ts

@@ -16,7 +16,7 @@ declare const MeshServerInfo_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
-        id: import("../../../mol-util/uuid").UUID;
+        id: import("../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
         description?: string | undefined;
@@ -27,7 +27,7 @@ declare const MeshServerInfo_base: {
         }>;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../../mol-state/object").StateObject<PD.Values<{
+    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<PD.Values<{
         serverUrl: PD.Text<string>;
         source: PD.Select<"emdb" | "empiar">;
         entryId: PD.Text<string>;

package/lib/extensions/model-archive/quality-assessment/behavior.d.ts

@@ -6,7 +6,7 @@
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
 import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
-export declare const MAQualityAssessment: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const MAQualityAssessment: import("../../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showTooltip: boolean;
 }>;
@@ -28,18 +28,18 @@ export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPreset
     representations?: undefined;
 } | {
     components: {
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     };
     representations: {
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     };
 } | {
     components: {
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
         branched: undefined;
     };
     representations: {
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare const QualityAssessmentQmeanPreset: StructureRepresentationPresetProvider<{
@@ -60,17 +60,17 @@ export declare const QualityAssessmentQmeanPreset: StructureRepresentationPreset
     representations?: undefined;
 } | {
     components: {
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     };
     representations: {
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     };
 } | {
     components: {
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
         branched: undefined;
     };
     representations: {
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;

package/lib/extensions/model-export/index.d.ts

@@ -4,4 +4,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const ModelExport: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
+export declare const ModelExport: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/extensions/mp4-export/index.d.ts

@@ -4,4 +4,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const Mp4Export: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
+export declare const Mp4Export: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/extensions/mvs/behavior.d.ts

@@ -5,6 +5,6 @@
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
 /** Registers everything needed for loading MolViewSpec files */
-export declare const MolViewSpec: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const MolViewSpec: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
 }>;

package/lib/extensions/mvs/camera.d.ts

@@ -7,6 +7,8 @@ import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
 import { ParamsOfKind } from './tree/generic/tree-schema';
 import { MolstarTree } from './tree/molstar/molstar-tree';
+/** Set the camera position to the current position (thus suppress automatic adjustment). */
+export declare function suppressCameraAutoreset(plugin: PluginContext): Promise<void>;
 /** Set the camera based on a camera node params. */
 export declare function setCamera(plugin: PluginContext, params: ParamsOfKind<MolstarTree, 'camera'>): Promise<void>;
 /** Focus the camera on the bounding sphere of a (sub)structure (or on the whole scene if `structureNodeSelector` is null).

package/lib/extensions/mvs/camera.js

@@ -3,6 +3,7 @@
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
+import { Canvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { Loci } from '../../mol-model/loci';
@@ -19,6 +20,13 @@ const DefaultFocusOptions = {
 };
 const DefaultCanvasBackgroundColor = ColorNames.white;
 const _tmpVec = Vec3();
+/** Set the camera position to the current position (thus suppress automatic adjustment). */
+export async function suppressCameraAutoreset(plugin) {
+    var _a;
+    const snapshot = { ...(_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.camera.state, radius: Infinity }; // `radius: Infinity` avoids clipping when the scene expands
+    adjustSceneRadiusFactor(plugin, snapshot.target);
+    await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
+}
 /** Set the camera based on a camera node params. */
 export async function setCamera(plugin, params) {
     const target = Vec3.create(...params.target);
@@ -27,7 +35,8 @@ export async function setCamera(plugin, params) {
         position = fovAdjustedPosition(target, position, plugin.canvas3d.camera.state.mode, plugin.canvas3d.camera.state.fov);
     const up = Vec3.create(...params.up);
     Vec3.orthogonalize(up, Vec3.sub(_tmpVec, target, position), up);
-    const snapshot = { target, position, up, radius: 10000, 'radiusMax': 10000 };
+    const snapshot = { target, position, up, radius: Infinity }; // `radius: Infinity` avoids clipping (ensures covering the whole scene)
+    adjustSceneRadiusFactor(plugin, snapshot.target);
     await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
 }
 /** Focus the camera on the bounding sphere of a (sub)structure (or on the whole scene if `structureNodeSelector` is null).
@@ -57,9 +66,26 @@ export async function setFocus(plugin, structureNodeSelector, params = MVSDefaul
             up,
             direction,
         });
+        resetSceneRadiusFactor(plugin);
         await PluginCommands.Camera.SetSnapshot(plugin, { snapshot });
     }
 }
+/** Adjust `sceneRadiusFactor` property so that the current scene is not cropped */
+function adjustSceneRadiusFactor(plugin, cameraTarget) {
+    var _a;
+    if (!cameraTarget)
+        return;
+    const boundingSphere = getPluginBoundingSphere(plugin);
+    const offset = Vec3.distance(cameraTarget, boundingSphere.center);
+    const sceneRadiusFactor = boundingSphere.radius > 0 ? ((boundingSphere.radius + offset) / boundingSphere.radius) : 1;
+    (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.setProps({ sceneRadiusFactor });
+}
+/** Reset `sceneRadiusFactor` property to the default value */
+function resetSceneRadiusFactor(plugin) {
+    var _a;
+    const sceneRadiusFactor = Canvas3DParams.sceneRadiusFactor.defaultValue;
+    (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.setProps({ sceneRadiusFactor });
+}
 /** Return camera snapshot for focusing a sphere with given `center` and `radius`,
  * while ensuring given view `direction` (aligns with vector position->target)
  * and `up` (aligns with screen Y axis). */

package/lib/extensions/mvs/components/annotation-label/representation.d.ts

@@ -51,6 +51,7 @@ export declare const MVSAnnotationLabelParams: {
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;
@@ -76,6 +77,7 @@ export declare const MVSAnnotationLabelParams: {
     ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
+    /** Parameter values for representation type "MVS Annotation Label" */
     annotationId: PD.Text<string>;
     fieldName: PD.Text<string>;
 };
@@ -127,6 +129,7 @@ export declare const MVSAnnotationLabelRepresentationProvider: StructureRepresen
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;
@@ -152,6 +155,7 @@ export declare const MVSAnnotationLabelRepresentationProvider: StructureRepresen
     ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
+    /** Parameter values for representation type "MVS Annotation Label" */
     annotationId: PD.Text<string>;
     fieldName: PD.Text<string>;
 }, "mvs-annotation-label">;

package/lib/extensions/mvs/components/annotation-label/visual.d.ts

@@ -48,6 +48,7 @@ export declare const MVSAnnotationLabelTextParams: {
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;

package/lib/extensions/mvs/components/custom-label/representation.d.ts

@@ -15,7 +15,7 @@ export declare const CustomLabelParams: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
         isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined; /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
+        isOptional?: boolean | undefined;
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../../../mol-util/legend").Legend | undefined;
@@ -51,6 +51,7 @@ export declare const CustomLabelParams: {
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;
@@ -100,7 +101,7 @@ export declare const CustomLabelRepresentationProvider: StructureRepresentationP
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
         isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined; /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
+        isOptional?: boolean | undefined;
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../../../mol-util/legend").Legend | undefined;
@@ -136,6 +137,7 @@ export declare const CustomLabelRepresentationProvider: StructureRepresentationP
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;

package/lib/extensions/mvs/components/custom-label/visual.d.ts

@@ -48,6 +48,7 @@ export declare const CustomLabelTextParams: {
     fontWeight: PD.Select<import("../../../../mol-geo/geometry/text/font-atlas").FontWeight>;
     background: PD.BooleanParam;
     borderWidth: PD.Numeric;
+    emissive: PD.Numeric;
     batchSize: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;