molstar 4.3.0 → 4.4.0

package/lib/commonjs/extensions/mvs/tree/generic/tree-schema.js

@@ -5,7 +5,14 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.treeSchemaToMarkdown = exports.treeSchemaToString = exports.validateTree = exports.treeValidationIssues = exports.TreeSchemaWithAllRequired = exports.TreeSchema = exports.getChildren = exports.getParams = void 0;
+exports.getParams = getParams;
+exports.getChildren = getChildren;
+exports.TreeSchema = TreeSchema;
+exports.TreeSchemaWithAllRequired = TreeSchemaWithAllRequired;
+exports.treeValidationIssues = treeValidationIssues;
+exports.validateTree = validateTree;
+exports.treeSchemaToString = treeSchemaToString;
+exports.treeSchemaToMarkdown = treeSchemaToMarkdown;
 const json_1 = require("../../../../mol-util/json");
 const object_1 = require("../../../../mol-util/object");
 const params_schema_1 = require("./params-schema");
@@ -15,24 +22,20 @@ function getParams(node) {
     var _a;
     return (_a = node.params) !== null && _a !== void 0 ? _a : {};
 }
-exports.getParams = getParams;
 /** Get children from a tree node */
 function getChildren(tree) {
     var _a;
     return (_a = tree.children) !== null && _a !== void 0 ? _a : [];
 }
-exports.getChildren = getChildren;
 function TreeSchema(schema) {
     return schema;
 }
-exports.TreeSchema = TreeSchema;
 function TreeSchemaWithAllRequired(schema) {
     return {
         ...schema,
         nodes: (0, object_1.mapObjectMap)(schema.nodes, node => ({ ...node, params: (0, params_schema_1.AllRequired)(node.params) })),
     };
 }
-exports.TreeSchemaWithAllRequired = TreeSchemaWithAllRequired;
 /** Return `undefined` if a tree conforms to the given schema,
  * return validation issues (as a list of lines) if it does not conform.
  * If `options.requireAll`, all parameters (including optional) must have a value provided.
@@ -60,7 +63,6 @@ function treeValidationIssues(schema, tree, options = {}) {
     }
     return undefined;
 }
-exports.treeValidationIssues = treeValidationIssues;
 /** Validate a tree against the given schema.
  * Do nothing if OK; print validation issues on console and throw an error is the tree does not conform.
  * Include `label` in the printed output. */
@@ -75,17 +77,14 @@ function validateTree(schema, tree, label) {
         throw new Error('FormatError');
     }
 }
-exports.validateTree = validateTree;
 /** Return documentation for a tree schema as plain text */
 function treeSchemaToString(schema, defaults) {
     return treeSchemaToString_(schema, defaults, false);
 }
-exports.treeSchemaToString = treeSchemaToString;
 /** Return documentation for a tree schema as markdown text */
 function treeSchemaToMarkdown(schema, defaults) {
     return treeSchemaToString_(schema, defaults, true);
 }
-exports.treeSchemaToMarkdown = treeSchemaToMarkdown;
 function treeSchemaToString_(schema, defaults, markdown = false) {
     var _a;
     const out = [];

package/lib/commonjs/extensions/mvs/tree/generic/tree-utils.js

@@ -5,7 +5,16 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.resolveUris = exports.addDefaults = exports.condenseTree = exports.convertTree = exports.copyTree = exports.copyNode = exports.copyNodeWithoutChildren = exports.formatObject = exports.treeToString = exports.dfs = void 0;
+exports.dfs = dfs;
+exports.treeToString = treeToString;
+exports.formatObject = formatObject;
+exports.copyNodeWithoutChildren = copyNodeWithoutChildren;
+exports.copyNode = copyNode;
+exports.copyTree = copyTree;
+exports.convertTree = convertTree;
+exports.condenseTree = condenseTree;
+exports.addDefaults = addDefaults;
+exports.resolveUris = resolveUris;
 const json_1 = require("../../../../mol-util/json");
 const tree_schema_1 = require("./tree-schema");
 /** Run DFS (depth-first search) algorithm on a rooted tree.
@@ -14,7 +23,6 @@ const tree_schema_1 = require("./tree-schema");
 function dfs(root, visit, postVisit) {
     return _dfs(root, undefined, visit, postVisit);
 }
-exports.dfs = dfs;
 function _dfs(root, parent, visit, postVisit) {
     var _a;
     if (visit)
@@ -32,14 +40,12 @@ function treeToString(tree) {
     dfs(tree, node => { var _a; return lines.push('  '.repeat(level++) + `- ${node.kind} ${formatObject((_a = node.params) !== null && _a !== void 0 ? _a : {})}`); }, node => level--);
     return lines.join('\n');
 }
-exports.treeToString = treeToString;
 /** Convert object to a human-friendly string (similar to JSON.stringify but without quoting keys) */
 function formatObject(obj) {
     if (!obj)
         return 'undefined';
     return JSON.stringify(obj).replace(/,("\w+":)/g, ', $1').replace(/"(\w+)":/g, '$1: ');
 }
-exports.formatObject = formatObject;
 /** Create a copy of a tree node, ignoring children. */
 function copyNodeWithoutChildren(node) {
     return {
@@ -47,7 +53,6 @@ function copyNodeWithoutChildren(node) {
         params: node.params ? { ...node.params } : undefined,
     };
 }
-exports.copyNodeWithoutChildren = copyNodeWithoutChildren;
 /** Create a copy of a tree node, including a shallow copy of children. */
 function copyNode(node) {
     return {
@@ -56,12 +61,10 @@ function copyNode(node) {
         children: node.children ? [...node.children] : undefined,
     };
 }
-exports.copyNode = copyNode;
 /** Create a deep copy of a tree. */
 function copyTree(root) {
     return convertTree(root, {});
 }
-exports.copyTree = copyTree;
 /** Apply a set of conversion rules to a tree to change to a different schema. */
 function convertTree(root, conversions) {
     const mapping = new Map();
@@ -99,7 +102,6 @@ function convertTree(root, conversions) {
     });
     return convertedRoot;
 }
-exports.convertTree = convertTree;
 /** Create a copy of the tree where twins (siblings of the same kind with the same params) are merged into one node.
  * Applies only to the node kinds listed in `condenseNodes` (or all if undefined) except node kinds in `skipNodes`. */
 function condenseTree(root, condenseNodes, skipNodes) {
@@ -129,7 +131,6 @@ function condenseTree(root, condenseNodes, skipNodes) {
     });
     return result;
 }
-exports.condenseTree = condenseTree;
 /** Create a copy of the tree where missing optional params for each node are added based on `defaults`. */
 function addDefaults(tree, defaults) {
     const rules = {};
@@ -138,7 +139,6 @@ function addDefaults(tree, defaults) {
     }
     return convertTree(tree, rules);
 }
-exports.addDefaults = addDefaults;
 /** Resolve any URI params in a tree, in place. URI params are those listed in `uriParamNames`.
  * Relative URIs are treated as relative to `baseUri`, which can in turn be relative to the window URL (if available). */
 function resolveUris(tree, baseUri, uriParamNames) {
@@ -156,7 +156,6 @@ function resolveUris(tree, baseUri, uriParamNames) {
         }
     });
 }
-exports.resolveUris = resolveUris;
 /** Resolve a sequence of URI references (relative URIs), where each reference is either absolute or relative to the next one
  * (i.e. the last one is the base URI). Skip any `undefined`.
  * E.g. `resolveUri('./unexpected.png', '/spanish/inquisition/expectations.html', 'https://example.org/spam/spam/spam')`

package/lib/commonjs/extensions/mvs/tree/molstar/conversion.js

@@ -5,7 +5,10 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.mvsSanityCheck = exports.mvsSanityCheckIssues = exports.convertMvsToMolstar = exports.ParseFormatMvsToMolstar = void 0;
+exports.ParseFormatMvsToMolstar = void 0;
+exports.convertMvsToMolstar = convertMvsToMolstar;
+exports.mvsSanityCheckIssues = mvsSanityCheckIssues;
+exports.mvsSanityCheck = mvsSanityCheck;
 const tree_utils_1 = require("../generic/tree-utils");
 const mvs_defaults_1 = require("../mvs/mvs-defaults");
 const object_1 = require("../../../../mol-util/object");
@@ -57,7 +60,6 @@ function convertMvsToMolstar(mvsTree, sourceUrl) {
     const condensed = (0, tree_utils_1.condenseTree)(converted, molstarNodesToCondense);
     return condensed;
 }
-exports.convertMvsToMolstar = convertMvsToMolstar;
 function fileExtensionMatches(filename, extensions) {
     filename = filename.toLowerCase();
     return extensions.some(ext => ext === '*' || filename.endsWith(ext));
@@ -81,7 +83,6 @@ function mvsSanityCheckIssues(tree) {
     });
     return result.length > 0 ? result : undefined;
 }
-exports.mvsSanityCheckIssues = mvsSanityCheckIssues;
 /** Run some sanity check on a MVSTree and print potential issues to the console. */
 function mvsSanityCheck(tree) {
     const issues = mvsSanityCheckIssues(tree);
@@ -92,4 +93,3 @@ function mvsSanityCheck(tree) {
         }
     }
 }
-exports.mvsSanityCheck = mvsSanityCheck;

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

@@ -96,7 +96,6 @@ 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>;
@@ -152,7 +151,6 @@ 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>;
@@ -172,7 +170,6 @@ 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>;
@@ -192,7 +189,6 @@ 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>;
@@ -280,7 +276,6 @@ 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>;
@@ -336,7 +331,6 @@ 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>;
@@ -356,7 +350,6 @@ 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>;
@@ -376,7 +369,6 @@ 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/mvs/tree/mvs/mvs-builder.js

@@ -5,7 +5,9 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.builderDemo = exports.Representation = exports.Component = exports.Structure = exports.Parse = exports.Download = exports.Root = exports.createMVSBuilder = void 0;
+exports.Representation = exports.Component = exports.Structure = exports.Parse = exports.Download = exports.Root = void 0;
+exports.createMVSBuilder = createMVSBuilder;
+exports.builderDemo = builderDemo;
 const object_1 = require("../../../../mol-util/object");
 const mvs_data_1 = require("../../mvs-data");
 const mvs_defaults_1 = require("./mvs-defaults");
@@ -23,7 +25,6 @@ const mvs_tree_1 = require("./mvs-tree");
 function createMVSBuilder() {
     return new Root();
 }
-exports.createMVSBuilder = createMVSBuilder;
 /** Base class for MVS builder pointing to anything */
 class _Base {
     constructor(_root, _node) {
@@ -242,7 +243,6 @@ function builderDemo() {
     cif.modelStructure({ model_index: 0 }).transform({ translation: [60, 0, 0], rotation: [0, 1, 0, -1, 0, 0, 0, 0, 1] }).component().representation().color({ color: '#aa0077' });
     return builder.getState();
 }
-exports.builderDemo = builderDemo;
 /** Return the current universal time, in ISO format, e.g. '2023-11-24T10:45:49.873Z' */
 function utcNowISO() {
     return new Date().toISOString();

package/lib/commonjs/extensions/pdbe/structure-quality-report/color.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureQualityReportColorThemeProvider = exports.StructureQualityReportColorTheme = exports.StructureQualityReportColorThemeParams = void 0;
+exports.StructureQualityReportColorThemeProvider = exports.StructureQualityReportColorThemeParams = void 0;
+exports.StructureQualityReportColorTheme = StructureQualityReportColorTheme;
 const prop_1 = require("./prop");
 const structure_1 = require("../../../mol-model/structure");
 const color_1 = require("../../../mol-theme/color");
@@ -80,7 +81,6 @@ function StructureQualityReportColorTheme(ctx, props) {
         legend: (0, legend_1.TableLegend)(ValidationColorTable)
     };
 }
-exports.StructureQualityReportColorTheme = StructureQualityReportColorTheme;
 exports.StructureQualityReportColorThemeProvider = {
     name: 'pdbe-structure-quality-report',
     label: 'Structure Quality Report',

package/lib/commonjs/extensions/rcsb/validation-report/color/density-fit.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DensityFitColorThemeProvider = exports.DensityFitColorTheme = void 0;
+exports.DensityFitColorThemeProvider = void 0;
+exports.DensityFitColorTheme = DensityFitColorTheme;
 const color_1 = require("../../../../mol-theme/color");
 const param_definition_1 = require("../../../../mol-util/param-definition");
 const color_2 = require("../../../../mol-util/color");
@@ -63,7 +64,6 @@ function DensityFitColorTheme(ctx, props) {
         legend: scaleRsrz.legend
     };
 }
-exports.DensityFitColorTheme = DensityFitColorTheme;
 exports.DensityFitColorThemeProvider = {
     name: prop_1.ValidationReport.Tag.DensityFit,
     label: 'Density Fit',

package/lib/commonjs/extensions/rcsb/validation-report/color/geometry-quality.js

@@ -5,7 +5,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.GeometryQualityColorThemeProvider = exports.GeometryQualityColorTheme = exports.getGeometricQualityColorThemeParams = void 0;
+exports.GeometryQualityColorThemeProvider = void 0;
+exports.getGeometricQualityColorThemeParams = getGeometricQualityColorThemeParams;
+exports.GeometryQualityColorTheme = GeometryQualityColorTheme;
 const color_1 = require("../../../../mol-theme/color");
 const param_definition_1 = require("../../../../mol-util/param-definition");
 const color_2 = require("../../../../mol-util/color");
@@ -37,7 +39,6 @@ function getGeometricQualityColorThemeParams(ctx) {
         ignore: param_definition_1.ParamDefinition.MultiSelect([], options)
     };
 }
-exports.getGeometricQualityColorThemeParams = getGeometricQualityColorThemeParams;
 function GeometryQualityColorTheme(ctx, props) {
     var _a;
     let color = () => DefaultColor;
@@ -94,7 +95,6 @@ function GeometryQualityColorTheme(ctx, props) {
         legend: ColorLegend
     };
 }
-exports.GeometryQualityColorTheme = GeometryQualityColorTheme;
 exports.GeometryQualityColorThemeProvider = {
     name: prop_1.ValidationReport.Tag.GeometryQuality,
     label: 'Geometry Quality',

package/lib/commonjs/extensions/rcsb/validation-report/color/random-coil-index.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RandomCoilIndexColorThemeProvider = exports.RandomCoilIndexColorTheme = void 0;
+exports.RandomCoilIndexColorThemeProvider = void 0;
+exports.RandomCoilIndexColorTheme = RandomCoilIndexColorTheme;
 const color_1 = require("../../../../mol-theme/color");
 const param_definition_1 = require("../../../../mol-util/param-definition");
 const color_2 = require("../../../../mol-util/color");
@@ -51,7 +52,6 @@ function RandomCoilIndexColorTheme(ctx, props) {
         legend: scale.legend
     };
 }
-exports.RandomCoilIndexColorTheme = RandomCoilIndexColorTheme;
 exports.RandomCoilIndexColorThemeProvider = {
     name: prop_1.ValidationReport.Tag.RandomCoilIndex,
     label: 'Random Coil Index',

package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts

@@ -31,6 +31,7 @@ export declare const IntraUnitClashParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -80,6 +81,7 @@ export declare const InterUnitClashParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -130,6 +132,7 @@ export declare const ClashesParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -179,6 +182,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -229,6 +233,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/commonjs/extensions/rcsb/validation-report/representation.js

@@ -5,7 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ClashesRepresentationProvider = exports.ClashesRepresentation = exports.getClashesParams = exports.ClashesParams = exports.InterUnitClashVisual = exports.InterUnitClashParams = exports.IntraUnitClashVisual = exports.IntraUnitClashParams = void 0;
+exports.ClashesRepresentationProvider = exports.ClashesParams = exports.InterUnitClashParams = exports.IntraUnitClashParams = void 0;
+exports.IntraUnitClashVisual = IntraUnitClashVisual;
+exports.InterUnitClashVisual = InterUnitClashVisual;
+exports.getClashesParams = getClashesParams;
+exports.ClashesRepresentation = ClashesRepresentation;
 const param_definition_1 = require("../../../mol-util/param-definition");
 const structure_1 = require("../../../mol-model/structure");
 const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
@@ -75,7 +79,6 @@ function IntraUnitClashVisual(materialId) {
         }
     }, materialId);
 }
-exports.IntraUnitClashVisual = IntraUnitClashVisual;
 function getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere) {
     return centroid_helper_1.CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
         unit.conformation.position(unit.elements[clashes.a[elements[i]]], pA);
@@ -181,7 +184,6 @@ function InterUnitClashVisual(materialId) {
         }
     }, materialId);
 }
-exports.InterUnitClashVisual = InterUnitClashVisual;
 function getInterClashBoundingSphere(structure, clashes, elements, boundingSphere) {
     return centroid_helper_1.CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
         const c = clashes.edges[elements[i]];
@@ -248,13 +250,11 @@ exports.ClashesParams = {
 function getClashesParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.ClashesParams);
 }
-exports.getClashesParams = getClashesParams;
 function ClashesRepresentation(ctx, getParams) {
     const repr = representation_1.Representation.createMulti('Clashes', ctx, getParams, representation_2.StructureRepresentationStateBuilder, ClashesVisuals);
     repr.setState({ markerActions: marker_action_1.MarkerActions.Highlighting });
     return repr;
 }
-exports.ClashesRepresentation = ClashesRepresentation;
 exports.ClashesRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
     name: prop_1.ValidationReport.Tag.Clashes,
     label: 'Validation Clashes',

package/lib/commonjs/extensions/sb-ncbr/partial-charges/color.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SbNcbrPartialChargesColorThemeProvider = exports.PartialChargesColorTheme = exports.getPartialChargesThemeParams = exports.PartialChargesThemeParams = void 0;
+exports.SbNcbrPartialChargesColorThemeProvider = exports.PartialChargesThemeParams = void 0;
+exports.getPartialChargesThemeParams = getPartialChargesThemeParams;
+exports.PartialChargesColorTheme = PartialChargesColorTheme;
 const structure_1 = require("../../../mol-model/structure");
 const color_1 = require("../../../mol-theme/color");
 const color_2 = require("../../../mol-util/color");
@@ -38,7 +40,6 @@ exports.PartialChargesThemeParams = {
 function getPartialChargesThemeParams() {
     return param_definition_1.ParamDefinition.clone(exports.PartialChargesThemeParams);
 }
-exports.getPartialChargesThemeParams = getPartialChargesThemeParams;
 function PartialChargesColorTheme(ctx, props) {
     var _a, _b;
     const model = (_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models[0];
@@ -106,7 +107,6 @@ function PartialChargesColorTheme(ctx, props) {
         contextHash,
     };
 }
-exports.PartialChargesColorTheme = PartialChargesColorTheme;
 exports.SbNcbrPartialChargesColorThemeProvider = {
     label: 'SB NCBR Partial Charges',
     name: 'sb-ncbr-partial-charges',

package/lib/commonjs/extensions/sb-ncbr/partial-charges/labels.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SbNcbrPartialChargesLociLabelProvider = void 0;
+exports.SbNcbrPartialChargesLociLabelProvider = SbNcbrPartialChargesLociLabelProvider;
 const structure_1 = require("../../../mol-model/structure");
 const property_1 = require("./property");
 function SbNcbrPartialChargesLociLabelProvider(ctx) {
@@ -35,4 +35,3 @@ function SbNcbrPartialChargesLociLabelProvider(ctx) {
         group: (label) => label.toString().replace(/Model [0-9]+/g, 'Models'),
     };
 }
-exports.SbNcbrPartialChargesLociLabelProvider = SbNcbrPartialChargesLociLabelProvider;

package/lib/commonjs/extensions/sb-ncbr/partial-charges/property.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SbNcbrPartialChargesPropertyProvider = exports.hasPartialChargesCategories = void 0;
+exports.SbNcbrPartialChargesPropertyProvider = void 0;
+exports.hasPartialChargesCategories = hasPartialChargesCategories;
 const param_definition_1 = require("../../../mol-util/param-definition");
 const mmcif_1 = require("../../../mol-model-formats/structure/mmcif");
 const custom_property_1 = require("../../../mol-model/custom-property");
@@ -139,7 +140,6 @@ function hasPartialChargesCategories(model) {
         'sb_ncbr_partial_atomic_charges' in categories &&
         'sb_ncbr_partial_atomic_charges_meta' in categories);
 }
-exports.hasPartialChargesCategories = hasPartialChargesCategories;
 exports.SbNcbrPartialChargesPropertyProvider = custom_model_property_1.CustomModelProperty.createProvider({
     label: 'SB NCBR Partial Charges Property Provider',
     descriptor: (0, custom_property_1.CustomPropertyDescriptor)({

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

@@ -5,7 +5,8 @@
  * @author Dušan Veľký <dvelky@mail.muni.cz>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createTunnelShape = exports.createSpheresShape = void 0;
+exports.createSpheresShape = createSpheresShape;
+exports.createTunnelShape = createTunnelShape;
 const int_1 = require("../../../mol-data/int");
 const sphere_1 = require("../../../mol-geo/geometry/mesh/builder/sphere");
 const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
@@ -52,7 +53,6 @@ async function createSpheresShape(options) {
         return shape_1.Shape.create(name, tunnel.props, mesh, () => (0, color_1.Color)(options.color), () => 1, (i) => `[${processedData[i].X.toFixed(3)}, ${processedData[i].Y.toFixed(3)}, ${processedData[i].Z.toFixed(3)}] - radius: ${processedData[i].Radius.toFixed(3)}`);
     return shape_1.Shape.create(name, tunnel.props, mesh, () => (0, color_1.Color)(options.color), () => 1, () => name);
 }
-exports.createSpheresShape = createSpheresShape;
 async function createTunnelShape(options) {
     var _a;
     const tunnel = options.tunnel;
@@ -69,7 +69,6 @@ async function createTunnelShape(options) {
             'Tunnel';
     return shape_1.Shape.create(name, tunnel.props, mesh, () => (0, color_1.Color)(options.color), () => 1, () => name);
 }
-exports.createTunnelShape = createTunnelShape;
 function profileToVec3(profile) {
     return linear_algebra_1.Vec3.create(profile.X, profile.Y, profile.Z);
 }

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

@@ -5,7 +5,8 @@
  * @author Dušan Veľký <dvelky@mail.muni.cz>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.TunnelsPreset = exports.isApplicable = exports.SbNcbrTunnels = void 0;
+exports.TunnelsPreset = exports.SbNcbrTunnels = void 0;
+exports.isApplicable = isApplicable;
 const behavior_1 = require("../../../mol-plugin/behavior");
 const actions_1 = require("./actions");
 const param_definition_1 = require("../../../mol-util/param-definition");
@@ -40,7 +41,6 @@ function isApplicable(structure) {
     return (!!structure && structure.models.length === 1 &&
         structure_1.Model.hasPdbId(structure.models[0]));
 }
-exports.isApplicable = isApplicable;
 exports.TunnelsPreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
     id: 'sb-ncbr-preset-structure-tunnels',
     display: {

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

@@ -104,18 +104,18 @@ declare const TunnelStateObject_base: {
         tunnel: Tunnel;
     }, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {
             tunnel: Tunnel;
         };
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<{
         tunnel: Tunnel;
     }, PluginStateObject.TypeInfo>;
 };
@@ -126,18 +126,18 @@ declare const TunnelsStateObject_base: {
         tunnels: Tunnel[];
     }, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {
             tunnels: Tunnel[];
         };
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<{
         tunnels: Tunnel[];
     }, PluginStateObject.TypeInfo>;
 };

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

@@ -5,7 +5,9 @@
  * @author Dušan Veľký <dvelky@mail.muni.cz>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.runVisualizeTunnel = exports.runVisualizeTunnels = exports.URL = exports.CHANNEL = exports.SUB_DB = exports.DB_URL = void 0;
+exports.URL = exports.CHANNEL = exports.SUB_DB = exports.DB_URL = void 0;
+exports.runVisualizeTunnels = runVisualizeTunnels;
+exports.runVisualizeTunnel = runVisualizeTunnel;
 const transforms_1 = require("../../../mol-plugin-state/transforms");
 const representation_1 = require("./representation");
 exports.DB_URL = 'https://channelsdb2.biodata.ceitec.cz/api/channels/';
@@ -35,7 +37,6 @@ async function runVisualizeTunnels(plugin, url = exports.URL) {
         .apply(transforms_1.StateTransforms.Representation.ShapeRepresentation3D);
     await update.commit();
 }
-exports.runVisualizeTunnels = runVisualizeTunnels;
 async function runVisualizeTunnel(plugin) {
     var _a;
     const update = plugin.build();
@@ -51,4 +52,3 @@ async function runVisualizeTunnel(plugin) {
         .apply(transforms_1.StateTransforms.Representation.ShapeRepresentation3D);
     await update.commit();
 }
-exports.runVisualizeTunnel = runVisualizeTunnel;

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

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTunnelsConfig = exports.TunnelsServerConfig = exports.TunnelsDataParams = exports.TunnelsData = void 0;
+exports.TunnelsServerConfig = exports.TunnelsDataParams = exports.TunnelsData = void 0;
+exports.getTunnelsConfig = getTunnelsConfig;
 const config_1 = require("../../../mol-plugin/config");
 const param_definition_1 = require("../../../mol-util/param-definition");
 var TunnelsData;
@@ -23,4 +24,3 @@ function getTunnelsConfig(plugin) {
         DefaultServerType: (_d = (_c = plugin.config.get(exports.TunnelsServerConfig.DefaultServerType)) !== null && _c !== void 0 ? _c : exports.TunnelsServerConfig.DefaultServerType.defaultValue) !== null && _d !== void 0 ? _d : TunnelsData.DefaultServerType,
     };
 }
-exports.getTunnelsConfig = getTunnelsConfig;