molstar 4.2.0 → 4.3.0

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/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/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);

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

@@ -44,6 +44,7 @@ declare const MeshlistStateObject_base: {
         type: PluginStateObject.TypeInfo;
         /** Data type for `MeshlistStateObject` - list of meshes */
         label: string;
+        /** Data type for `MeshlistStateObject` - list of meshes */
         description?: string | undefined;
         data: MeshlistData;
     };

package/lib/commonjs/extensions/mp4-export/encoder.js

@@ -51,7 +51,7 @@ async function encodeMp4Animation(plugin, ctx, params) {
         await plugin.managers.animation.play(params.animation.definition, params.animation.params);
         stoppedAnimation = false;
         for (let i = 0; i <= N; i++) {
-            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true });
+            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true, updateControls: true });
             const image = params.pass.getImageData(width, height, normalizedViewport);
             encoder.addFrameRgba(image.data);
             if (ctx.shouldUpdate) {

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

@@ -77,7 +77,6 @@ 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>;
 };
@@ -155,7 +154,6 @@ 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/commonjs/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;
+        isOptional?: boolean | undefined; /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../../../mol-util/legend").Legend | undefined;
@@ -101,7 +101,7 @@ export declare const CustomLabelRepresentationProvider: StructureRepresentationP
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
         isExpanded?: boolean | undefined;
-        isOptional?: 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 */
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../../../mol-util/legend").Legend | undefined;

package/lib/commonjs/extensions/mvs/tree/mvs/mvs-builder.d.ts

@@ -85,7 +85,6 @@ declare class _Base<TKind extends MVSKind> {
                 }[]>;
             };
             component_from_uri: {
-                /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
                 uri: import("../generic/params-schema").RequiredField<string>;
                 format: import("../generic/params-schema").RequiredField<"json" | "cif" | "bcif">;
@@ -97,6 +96,7 @@ declare class _Base<TKind extends MVSKind> {
             };
             component_from_source: {
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -152,6 +152,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             color_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -171,6 +172,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             label_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -190,6 +192,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             tooltip_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -266,7 +269,6 @@ declare class _Base<TKind extends MVSKind> {
                 }[]>;
             };
             component_from_uri: {
-                /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
                 uri: import("../generic/params-schema").RequiredField<string>;
                 format: import("../generic/params-schema").RequiredField<"json" | "cif" | "bcif">;
@@ -278,6 +280,7 @@ declare class _Base<TKind extends MVSKind> {
             };
             component_from_source: {
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -333,6 +336,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             color_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -352,6 +356,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             label_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -371,6 +376,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             tooltip_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;

package/lib/commonjs/extensions/sb-ncbr/index.d.ts

@@ -1,3 +1,11 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
 export { SbNcbrPartialCharges } from './partial-charges/behavior';
 export { SbNcbrPartialChargesPreset } from './partial-charges/preset';
 export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrTunnels } from './tunnels/behavior';
+export { TunnelsFromRawData, SelectTunnel, TunnelFromRawData, TunnelShapeProvider } from './tunnels/representation';

package/lib/commonjs/extensions/sb-ncbr/index.js

@@ -1,9 +1,22 @@
 "use strict";
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SbNcbrPartialChargesPropertyProvider = exports.SbNcbrPartialChargesPreset = exports.SbNcbrPartialCharges = void 0;
+exports.TunnelShapeProvider = exports.TunnelFromRawData = exports.SelectTunnel = exports.TunnelsFromRawData = exports.SbNcbrTunnels = exports.SbNcbrPartialChargesPropertyProvider = exports.SbNcbrPartialChargesPreset = exports.SbNcbrPartialCharges = void 0;
 var behavior_1 = require("./partial-charges/behavior");
 Object.defineProperty(exports, "SbNcbrPartialCharges", { enumerable: true, get: function () { return behavior_1.SbNcbrPartialCharges; } });
 var preset_1 = require("./partial-charges/preset");
 Object.defineProperty(exports, "SbNcbrPartialChargesPreset", { enumerable: true, get: function () { return preset_1.SbNcbrPartialChargesPreset; } });
 var property_1 = require("./partial-charges/property");
 Object.defineProperty(exports, "SbNcbrPartialChargesPropertyProvider", { enumerable: true, get: function () { return property_1.SbNcbrPartialChargesPropertyProvider; } });
+var behavior_2 = require("./tunnels/behavior");
+Object.defineProperty(exports, "SbNcbrTunnels", { enumerable: true, get: function () { return behavior_2.SbNcbrTunnels; } });
+var representation_1 = require("./tunnels/representation");
+Object.defineProperty(exports, "TunnelsFromRawData", { enumerable: true, get: function () { return representation_1.TunnelsFromRawData; } });
+Object.defineProperty(exports, "SelectTunnel", { enumerable: true, get: function () { return representation_1.SelectTunnel; } });
+Object.defineProperty(exports, "TunnelFromRawData", { enumerable: true, get: function () { return representation_1.TunnelFromRawData; } });
+Object.defineProperty(exports, "TunnelShapeProvider", { enumerable: true, get: function () { return representation_1.TunnelShapeProvider; } });

package/lib/commonjs/extensions/sb-ncbr/tunnels/actions.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateAction } from '../../../mol-state';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+export declare const TunnelDownloadServer: {
+    channelsdb: PD.Group<PD.Normalize<unknown>>;
+};
+export declare const DownloadTunnels: StateAction<PluginStateObject.Root, void, PD.Normalize<{
+    source: PD.NamedParams<PD.Normalize<{
+        url: any;
+    }>, "url"> | PD.NamedParams<PD.Normalize<{
+        provider: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        provider: any;
+    }>, "pdb">;
+}>>;

package/lib/commonjs/extensions/sb-ncbr/tunnels/actions.js

@@ -0,0 +1,89 @@
+"use strict";
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DownloadTunnels = exports.TunnelDownloadServer = void 0;
+const objects_1 = require("../../../mol-plugin-state/objects");
+const transforms_1 = require("../../../mol-plugin-state/transforms");
+const mol_state_1 = require("../../../mol-state");
+const mol_task_1 = require("../../../mol-task");
+const param_definition_1 = require("../../../mol-util/param-definition");
+const type_helpers_1 = require("../../../mol-util/type-helpers");
+const props_1 = require("./props");
+const representation_1 = require("./representation");
+exports.TunnelDownloadServer = {
+    'channelsdb': param_definition_1.ParamDefinition.EmptyGroup({ label: 'ChannelsDB' })
+};
+exports.DownloadTunnels = mol_state_1.StateAction.build({
+    display: { name: 'Download Tunnels', description: 'Load a tunnels from the provided source and create theirs representations' },
+    from: objects_1.PluginStateObject.Root,
+    params: (_, plugin) => {
+        return {
+            source: param_definition_1.ParamDefinition.MappedStatic('pdb', {
+                'pdb': param_definition_1.ParamDefinition.Group({
+                    provider: param_definition_1.ParamDefinition.Group({
+                        id: param_definition_1.ParamDefinition.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
+                        server: param_definition_1.ParamDefinition.MappedStatic('channelsdb', exports.TunnelDownloadServer),
+                    }, { pivot: 'id' }),
+                }, { isFlat: true, label: 'PDB' }),
+                'alphafolddb': param_definition_1.ParamDefinition.Group({
+                    provider: param_definition_1.ParamDefinition.Group({
+                        id: param_definition_1.ParamDefinition.Text('Q8W3K0', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
+                        server: param_definition_1.ParamDefinition.MappedStatic('channelsdb', exports.TunnelDownloadServer),
+                    }, { pivot: 'id' })
+                }, { isFlat: true, label: 'AlphaFold DB', description: 'Loads the predicted model if available' }),
+                'url': param_definition_1.ParamDefinition.Group({
+                    url: param_definition_1.ParamDefinition.Url(''),
+                }, { isFlat: true, label: 'URL' })
+            })
+        };
+    }
+})(({ params, state }, plugin) => mol_task_1.Task.create('Download Tunnels', async (ctx) => {
+    plugin.behaviors.layout.leftPanelTabName.next('data');
+    const src = params.source;
+    let downloadParams;
+    switch (src.name) {
+        case 'url':
+            downloadParams = [{ url: src.params.url }];
+            break;
+        case 'pdb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin === null || plugin === void 0 ? void 0 : plugin.config.get(props_1.TunnelsServerConfig.DefaultServerUrl)}/channels/pdb/${src.params.provider.id}` }]
+                : (0, type_helpers_1.assertUnreachable)(src);
+            break;
+        case 'alphafolddb':
+            downloadParams = src.params.provider.server.name === 'channelsdb'
+                ? [{ url: `${plugin === null || plugin === void 0 ? void 0 : plugin.config.get(props_1.TunnelsServerConfig.DefaultServerUrl)}/channels/alphafill/${src.params.provider.id.toLowerCase()}` }]
+                : (0, type_helpers_1.assertUnreachable)(src);
+            break;
+        default: (0, type_helpers_1.assertUnreachable)(src);
+    }
+    await state.transaction(async () => {
+        var _a;
+        const update = plugin.build();
+        const webgl = (_a = plugin.canvas3dContext) === null || _a === void 0 ? void 0 : _a.webgl;
+        for (const download of downloadParams) {
+            const response = await (await fetch(download.url.toString())).json();
+            const tunnels = [];
+            Object.entries(response.Channels).forEach(([key, values]) => {
+                if (values.length > 0) {
+                    values.forEach((item) => {
+                        tunnels.push({ data: item.Profile, props: { id: item.Id, type: item.Type } });
+                    });
+                }
+            });
+            update
+                .toRoot()
+                .apply(representation_1.TunnelsFromRawData, { data: tunnels })
+                .apply(representation_1.SelectTunnel)
+                .apply(representation_1.TunnelShapeProvider, {
+                webgl,
+            })
+                .apply(transforms_1.StateTransforms.Representation.ShapeRepresentation3D);
+            await update.commit();
+        }
+    }).runInContext(ctx);
+}));

package/lib/commonjs/extensions/sb-ncbr/tunnels/algorithm.d.ts

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { Shape } from '../../../mol-model/shape';
+import { Color } from '../../../mol-util/color';
+import { Tunnel } from './data-model';
+export declare function createSpheresShape(options: {
+    tunnel: Tunnel;
+    color: Color;
+    resolution: number;
+    sampleRate: number;
+    showRadii: boolean;
+    prev?: Shape<Mesh>;
+}): Promise<Shape<Mesh>>;
+export declare function createTunnelShape(options: {
+    tunnel: Tunnel;
+    color: Color;
+    resolution: number;
+    sampleRate: number;
+    webgl: WebGLContext | undefined;
+    prev?: Shape<Mesh>;
+}): Promise<Shape<Mesh>>;