molstar 4.2.0 → 4.4.0

package/lib/commonjs/extensions/mvs/load-helpers.js

@@ -5,7 +5,23 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeNearestReprMap = exports.colorThemeForNode = exports.representationProps = exports.componentFromXProps = exports.labelFromXProps = exports.prettyNameFromSelector = exports.componentPropsFromSelector = exports.structureProps = exports.isPhantomComponent = exports.collectInlineLabels = exports.collectInlineTooltips = exports.collectAnnotationTooltips = exports.collectAnnotationReferences = exports.transformProps = exports.transformFromRotationTranslation = exports.AnnotationFromSourceKinds = exports.AnnotationFromUriKinds = exports.UpdateTarget = exports.loadTree = void 0;
+exports.AnnotationFromSourceKinds = exports.AnnotationFromUriKinds = exports.UpdateTarget = void 0;
+exports.loadTree = loadTree;
+exports.transformFromRotationTranslation = transformFromRotationTranslation;
+exports.transformProps = transformProps;
+exports.collectAnnotationReferences = collectAnnotationReferences;
+exports.collectAnnotationTooltips = collectAnnotationTooltips;
+exports.collectInlineTooltips = collectInlineTooltips;
+exports.collectInlineLabels = collectInlineLabels;
+exports.isPhantomComponent = isPhantomComponent;
+exports.structureProps = structureProps;
+exports.componentPropsFromSelector = componentPropsFromSelector;
+exports.prettyNameFromSelector = prettyNameFromSelector;
+exports.labelFromXProps = labelFromXProps;
+exports.componentFromXProps = componentFromXProps;
+exports.representationProps = representationProps;
+exports.colorThemeForNode = colorThemeForNode;
+exports.makeNearestReprMap = makeNearestReprMap;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const representation_1 = require("../../mol-plugin-state/transforms/representation");
 const array_1 = require("../../mol-util/array");
@@ -46,7 +62,6 @@ async function loadTree(plugin, tree, loadingActions, context, options) {
     });
     await exports.UpdateTarget.commit(updateRoot);
 }
-exports.loadTree = loadTree;
 exports.UpdateTarget = {
     /** Create a new update, with `selector` pointing to the root. */
     create(plugin, replaceExisting) {
@@ -134,7 +149,6 @@ function transformFromRotationTranslation(rotation, translation) {
         throw new Error(`'rotation' param for 'transform' is not a valid rotation matrix: ${rotation}`);
     return T;
 }
-exports.transformFromRotationTranslation = transformFromRotationTranslation;
 /** Adjust values in a close-to-rotation matrix `a` to ensure it is a proper rotation matrix
  * (i.e. its columns and rows are orthonormal and determinant equal to 1, within available precission). */
 function ensureRotationMatrix(out, a) {
@@ -161,7 +175,6 @@ function transformProps(node) {
     }
     return result;
 }
-exports.transformProps = transformProps;
 /** Collect distinct annotation specs from all nodes in `tree` and set `context.annotationMap[node]` to respective annotationIds */
 function collectAnnotationReferences(tree, context) {
     const distinctSpecs = {};
@@ -184,7 +197,6 @@ function collectAnnotationReferences(tree, context) {
     });
     return Object.values(distinctSpecs);
 }
-exports.collectAnnotationReferences = collectAnnotationReferences;
 function blockSpec(header, index) {
     if ((0, utils_1.isDefined)(header)) {
         return { name: 'header', params: { header: header } };
@@ -208,7 +220,6 @@ function collectAnnotationTooltips(tree, context) {
     });
     return (0, array_1.arrayDistinct)(annotationTooltips);
 }
-exports.collectAnnotationTooltips = collectAnnotationTooltips;
 /** Collect inline tooltips from all nodes in `tree`. */
 function collectInlineTooltips(tree, context) {
     const inlineTooltips = [];
@@ -236,7 +247,6 @@ function collectInlineTooltips(tree, context) {
     });
     return inlineTooltips;
 }
-exports.collectInlineTooltips = collectInlineTooltips;
 /** Collect inline labels from all nodes in `tree`. */
 function collectInlineLabels(tree, context) {
     const inlineLabels = [];
@@ -274,13 +284,11 @@ function collectInlineLabels(tree, context) {
     });
     return inlineLabels;
 }
-exports.collectInlineLabels = collectInlineLabels;
 /** Return `true` for components nodes which only serve for tooltip placement (not to be created in the MolStar object hierarchy) */
 function isPhantomComponent(node) {
     return node.children && node.children.every(child => child.kind === 'tooltip' || child.kind === 'label');
     // These nodes could theoretically be removed when converting MVS to Molstar tree, but would get very tricky if we allow nested components
 }
-exports.isPhantomComponent = isPhantomComponent;
 /** Create props for `StructureFromModel` transformer from a structure node. */
 function structureProps(node) {
     var _a;
@@ -318,7 +326,6 @@ function structureProps(node) {
             throw new Error(`NotImplementedError: Loading action for "structure" node, type "${params.type}"`);
     }
 }
-exports.structureProps = structureProps;
 /** Create value for `type` prop for `StructureComponent` transformer based on a MVS selector. */
 function componentPropsFromSelector(selector) {
     if (selector === undefined) {
@@ -334,7 +341,6 @@ function componentPropsFromSelector(selector) {
         return { name: 'expression', params: (0, selections_1.rowToExpression)(selector) };
     }
 }
-exports.componentPropsFromSelector = componentPropsFromSelector;
 /** Return a pretty name for a value of selector param, e.g.  "protein" -> 'Protein', {label_asym_id: "A"} -> 'Custom Selection: {label_asym_id: "A"}' */
 function prettyNameFromSelector(selector) {
     if (selector === undefined) {
@@ -350,7 +356,6 @@ function prettyNameFromSelector(selector) {
         return `Custom Selection: ${(0, tree_utils_1.formatObject)(selector)}`;
     }
 }
-exports.prettyNameFromSelector = prettyNameFromSelector;
 /** Create props for `StructureRepresentation3D` transformer from a label_from_* node. */
 function labelFromXProps(node, context) {
     var _a, _b;
@@ -362,7 +367,6 @@ function labelFromXProps(node, context) {
         colorTheme: colorThemeForNode(nearestReprNode, context),
     };
 }
-exports.labelFromXProps = labelFromXProps;
 /** Create props for `AnnotationStructureComponent` transformer from a component_from_* node. */
 function componentFromXProps(node, context) {
     var _a;
@@ -375,7 +379,6 @@ function componentFromXProps(node, context) {
         nullIfEmpty: false,
     };
 }
-exports.componentFromXProps = componentFromXProps;
 /** Create props for `StructureRepresentation3D` transformer from a representation node. */
 function representationProps(params) {
     switch (params.type) {
@@ -396,7 +399,6 @@ function representationProps(params) {
             throw new Error('NotImplementedError');
     }
 }
-exports.representationProps = representationProps;
 /** Create value for `colorTheme` prop for `StructureRepresentation3D` transformer from a representation node based on color* nodes in its subtree. */
 function colorThemeForNode(node, context) {
     var _a;
@@ -445,7 +447,6 @@ function colorThemeForNode(node, context) {
         };
     }
 }
-exports.colorThemeForNode = colorThemeForNode;
 function appliesColorToWholeRepr(node) {
     if (node.kind === 'color') {
         return !(0, utils_1.isDefined)(node.params.selector) || node.params.selector === 'all';
@@ -476,4 +477,3 @@ function makeNearestReprMap(root) {
     });
     return map;
 }
-exports.makeNearestReprMap = makeNearestReprMap;

package/lib/commonjs/extensions/mvs/load.js

@@ -5,7 +5,7 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.loadMVS = void 0;
+exports.loadMVS = loadMVS;
 const data_1 = require("../../mol-plugin-state/transforms/data");
 const model_1 = require("../../mol-plugin-state/transforms/model");
 const representation_1 = require("../../mol-plugin-state/transforms/representation");
@@ -43,7 +43,6 @@ async function loadMVS(plugin, data, options = {}) {
         throw err;
     }
 }
-exports.loadMVS = loadMVS;
 /** Load a `MolstarTree` into the Mol* plugin.
  * If `replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state. */
 async function loadMolstarTree(plugin, tree, options) {

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

@@ -5,7 +5,14 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.paramsValidationIssues = exports.AllRequired = exports.fieldValidationIssues = exports.OptionalField = exports.RequiredField = exports.literal = exports.nullable = exports.union = exports.list = exports.tuple = exports.bool = exports.float = exports.int = exports.str = void 0;
+exports.union = exports.list = exports.tuple = exports.bool = exports.float = exports.int = exports.str = void 0;
+exports.nullable = nullable;
+exports.literal = literal;
+exports.RequiredField = RequiredField;
+exports.OptionalField = OptionalField;
+exports.fieldValidationIssues = fieldValidationIssues;
+exports.AllRequired = AllRequired;
+exports.paramsValidationIssues = paramsValidationIssues;
 const tslib_1 = require("tslib");
 const iots = tslib_1.__importStar(require("io-ts"));
 const PathReporter_1 = require("io-ts/PathReporter");
@@ -29,7 +36,6 @@ exports.union = iots.union;
 function nullable(type) {
     return (0, exports.union)([type, iots.null]);
 }
-exports.nullable = nullable;
 /** Type definition for literal types, e.g. `literal('red', 'green', 'blue')` means 'red' or 'green' or 'blue'  */
 function literal(...values) {
     if (values.length === 0) {
@@ -38,15 +44,12 @@ function literal(...values) {
     const typeName = `(${values.map(v => (0, json_1.onelinerJsonString)(v)).join(' | ')})`;
     return new iots.Type(typeName, ((value) => values.includes(value)), (value, ctx) => values.includes(value) ? { _tag: 'Right', right: value } : { _tag: 'Left', left: [{ value: value, context: ctx, message: `"${value}" is not a valid value for literal type ${typeName}` }] }, value => value);
 }
-exports.literal = literal;
 function RequiredField(type, description) {
     return { type, required: true, description };
 }
-exports.RequiredField = RequiredField;
 function OptionalField(type, description) {
     return { type, required: false, description };
 }
-exports.OptionalField = OptionalField;
 /** Return `undefined` if `value` has correct type for `field`, regardsless of if required or optional.
  * Return description of validation issues, if `value` has wrong type. */
 function fieldValidationIssues(field, value) {
@@ -58,11 +61,9 @@ function fieldValidationIssues(field, value) {
         return PathReporter_1.PathReporter.report(validation);
     }
 }
-exports.fieldValidationIssues = fieldValidationIssues;
 function AllRequired(paramsSchema) {
     return (0, object_1.mapObjectMap)(paramsSchema, field => RequiredField(field.type, field.description));
 }
-exports.AllRequired = AllRequired;
 /** Return `undefined` if `values` contains correct value types for `schema`,
  * return description of validation issues, if `values` have wrong type.
  * If `options.requireAll`, all parameters (including optional) must have a value provided.
@@ -94,4 +95,3 @@ function paramsValidationIssues(schema, values, options = {}) {
     }
     return undefined;
 }
-exports.paramsValidationIssues = paramsValidationIssues;

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

@@ -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">;
@@ -266,7 +265,6 @@ 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">;

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/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; } });