molstar 4.0.1 → 4.2.0

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -36,8 +36,9 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
         variant: any;
         objects: any;
     }>;
+    emissive: number;
     instanceGranularity: boolean;
-    lod: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
+    lod: import("../../mol-math/linear-algebra").Vec3;
     cellSize: number;
     batchSize: number;
     sectorOpacity: number;
@@ -68,19 +69,19 @@ export declare const MembraneOrientationPreset: StructureRepresentationPresetPro
     representations?: undefined;
 } | {
     components: {
-        polymer: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, 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<PluginStateObject.Molecule.Structure, 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<PluginStateObject.Molecule.Structure, 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<PluginStateObject.Molecule.Structure, 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;
     } | undefined;
     representations: {
-        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, 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>>;
+        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     } | {
-        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, 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<PluginStateObject.Molecule.Structure.Representation3D, 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>>;
+        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        polymer: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     } | {
-        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, 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<PluginStateObject.Molecule.Structure.Representation3D, 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>>;
+        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        all: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, 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 tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>): Promise<import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, 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>>>;
+export declare function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>): Promise<import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, 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/commonjs/extensions/anvil/representation.d.ts

@@ -38,6 +38,7 @@ declare const BilayerPlanesParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -69,6 +70,7 @@ declare const BilayerRimsParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -101,6 +103,7 @@ export declare const MembraneOrientationParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -142,6 +145,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -183,6 +187,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/extensions/assembly-symmetry/behavior.d.ts

@@ -42,8 +42,9 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
         variant: any;
         objects: any;
     }>;
+    emissive: number;
     instanceGranularity: boolean;
-    lod: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
+    lod: import("../../mol-math/linear-algebra").Vec3;
     cellSize: number;
     batchSize: number;
     axesColor: PD.NamedParams<PD.Normalize<{

package/lib/commonjs/extensions/assembly-symmetry/prop.js

@@ -17,30 +17,30 @@ const builder_1 = require("../../mol-script/language/builder");
 const compiler_1 = require("../../mol-script/runtime/query/compiler");
 const custom_property_1 = require("../../mol-model/custom-property");
 const assets_1 = require("../../mol-util/assets");
-const rcsb_symmetry_gql = /* GraphQL */ `
-query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
-    assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
-        rcsb_struct_symmetry {
-            clusters {
-                avg_rmsd
-                members {
-                    asym_id
-                    pdbx_struct_oper_list_ids
-                }
-            }
-            kind
-            oligomeric_state
-            rotation_axes {
-                order
-                start
-                end
-            }
-            stoichiometry
-            symbol
-            type
-        }
-    }
-}
+const rcsb_symmetry_gql = /* GraphQL */ `
+query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
+    assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
+        rcsb_struct_symmetry {
+            clusters {
+                avg_rmsd
+                members {
+                    asym_id
+                    pdbx_struct_oper_list_ids
+                }
+            }
+            kind
+            oligomeric_state
+            rotation_axes {
+                order
+                start
+                end
+            }
+            stoichiometry
+            symbol
+            type
+        }
+    }
+}
 `;
 const BiologicalAssemblyNames = new Set([
     'author_and_software_defined_assembly',

package/lib/commonjs/extensions/assembly-symmetry/representation.d.ts

@@ -36,6 +36,7 @@ export declare const AssemblySymmetryParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/commonjs/extensions/backgrounds/index.d.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const Backgrounds: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
+export declare const Backgrounds: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/commonjs/extensions/backgrounds/index.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -80,6 +80,7 @@ exports.Backgrounds = behavior_1.PluginBehavior.create({
                                 saturation: 0,
                                 opacity: 1,
                                 blur: 0.3,
+                                rotation: { x: 0, y: 0, z: 0 },
                             }
                         }
                     }, 'Purple Nebula Skybox'],

package/lib/commonjs/extensions/dnatco/behavior.d.ts

@@ -5,7 +5,7 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const DnatcoNtCs: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const DnatcoNtCs: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showToolTip: boolean;
 }>;

package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts

@@ -24,23 +24,23 @@ export declare const ConfalPyramidsPreset: StructureRepresentationPresetProvider
     representations?: undefined;
 } | {
     components: {
-        pyramids: 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;
+        pyramids: 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;
     } | {
-        pyramids: 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;
+        pyramids: 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;
     } | {
-        pyramids: 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;
+        pyramids: 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: {
-        pyramidsRepr: 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;
+        pyramidsRepr: 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;
     } | {
-        pyramidsRepr: 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>>;
+        pyramidsRepr: 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>>;
     } | {
-        pyramidsRepr: 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>>;
+        pyramidsRepr: 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 confalPyramidLabel(step: DnatcoTypes.Step): string;

package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.js

@@ -44,11 +44,11 @@ exports.ConfalPyramidsPreset = (0, representation_preset_1.StructureRepresentati
     }
 });
 function confalPyramidLabel(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)}
     `;
 }
 exports.confalPyramidLabel = confalPyramidLabel;

package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -37,6 +37,7 @@ export declare const ConfalPyramidsParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -106,6 +108,7 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

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

@@ -44,11 +44,11 @@ exports.NtCTubePreset = (0, representation_preset_1.StructureRepresentationPrese
     }
 });
 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)}
     `;
 }
 exports.NtCTubeSegmentLabel = NtCTubeSegmentLabel;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -132,8 +132,8 @@ class GlbExporter extends mesh_exporter_1.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({
@@ -142,6 +142,7 @@ class GlbExporter extends mesh_exporter_1.MeshExporter {
                     metallicFactor: metalness,
                     roughnessFactor: roughness
                 },
+                emissiveFactor: [emissive, emissive, emissive],
                 doubleSided,
                 alphaMode: alpha ? 'BLEND' : 'OPAQUE',
             });
@@ -160,9 +161,10 @@ class GlbExporter extends mesh_exporter_1.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/commonjs/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/commonjs/extensions/geo-export/usdz-exporter.js

@@ -27,20 +27,20 @@ class UsdzExporter extends mesh_exporter_1.MeshExporter {
         const materialKey = this.materialMap.size;
         this.materialMap.set(hash, materialKey);
         const [r, g, b] = color_1.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 = ${roughness}
+        token outputs:surface
+    }
+}
 `);
         return materialKey;
     }
@@ -147,41 +147,41 @@ def Material "material${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 = [${mol_util_1.StringBuilder.getString(indexBuilder)}]
-    point3f[] points = [${mol_util_1.StringBuilder.getString(vertexBuilder)}]
-    normal3f[] primvars:normals = [${mol_util_1.StringBuilder.getString(normalBuilder)}] (
-        interpolation = "vertex"
-    )
-    uniform token subdivisionScheme = "none"
-    ${materialBinding}
-}
+            this.meshes.push(`
+def Mesh "mesh${this.meshes.length}"
+{
+    int[] faceVertexCounts = [${new Array(drawCount / 3).fill(3).join(',')}]
+    int[] faceVertexIndices = [${mol_util_1.StringBuilder.getString(indexBuilder)}]
+    point3f[] points = [${mol_util_1.StringBuilder.getString(vertexBuilder)}]
+    normal3f[] primvars:normals = [${mol_util_1.StringBuilder.getString(normalBuilder)}] (
+        interpolation = "vertex"
+    )
+    uniform token subdivisionScheme = "none"
+    ${materialBinding}
+}
 `);
         }
     }
     async getData(ctx) {
-        const header = `#usda 1.0
-(
-    customLayerData = {
-        string creator = "Mol* ${version_1.PLUGIN_VERSION}"
-    }
-    metersPerUnit = 1
-)
+        const header = `#usda 1.0
+(
+    customLayerData = {
+        string creator = "Mol* ${version_1.PLUGIN_VERSION}"
+    }
+    metersPerUnit = 1
+)
 `;
         const usda = [header, ...this.materials, ...this.meshes].join('');
         const usdaData = new Uint8Array(usda.length);