molstar 4.2.0 → 4.4.0

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

@@ -11,24 +11,24 @@ export declare const MVSAnnotationLabelTextParams: {
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;

package/lib/commonjs/extensions/mvs/components/annotation-label/visual.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MVSAnnotationLabelTextVisual = exports.MVSAnnotationLabelTextParams = void 0;
+exports.MVSAnnotationLabelTextParams = void 0;
+exports.MVSAnnotationLabelTextVisual = MVSAnnotationLabelTextVisual;
 const tslib_1 = require("tslib");
 const text_builder_1 = require("../../../../mol-geo/geometry/text/text-builder");
 const complex_visual_1 = require("../../../../mol-repr/structure/complex-visual");
@@ -36,7 +37,6 @@ function MVSAnnotationLabelTextVisual(materialId) {
         }
     }, materialId);
 }
-exports.MVSAnnotationLabelTextVisual = MVSAnnotationLabelTextVisual;
 function createLabelText(ctx, structure, theme, props, text) {
     var _a;
     const { annotation, model } = (0, annotation_prop_1.getMVSAnnotationForStructure)(structure, props.annotationId);

package/lib/commonjs/extensions/mvs/components/annotation-prop.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MVSAnnotation = exports.getMVSAnnotationForStructure = exports.MVSAnnotations = exports.MVSAnnotationsProvider = exports.MVSAnnotationsParams = void 0;
+exports.MVSAnnotation = exports.MVSAnnotations = exports.MVSAnnotationsProvider = exports.MVSAnnotationsParams = void 0;
+exports.getMVSAnnotationForStructure = getMVSAnnotationForStructure;
 const db_1 = require("../../../mol-data/db");
 const cif_1 = require("../../../mol-io/reader/cif");
 const schema_1 = require("../../../mol-io/reader/cif/schema");
@@ -109,7 +110,6 @@ function getMVSAnnotationForStructure(structure, annotationId) {
     }
     return { annotation: undefined, model: undefined };
 }
-exports.getMVSAnnotationForStructure = getMVSAnnotationForStructure;
 /** Main class for processing MVS annotation */
 class MVSAnnotation {
     constructor(data, schema) {

package/lib/commonjs/extensions/mvs/components/annotation-structure-component.js

@@ -5,7 +5,10 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.updateMVSAnnotationStructureComponent = exports.createMVSAnnotationStructureComponent = exports.createMVSAnnotationSubstructure = exports.MVSAnnotationStructureComponent = exports.MVSTransform = exports.MVSAnnotationStructureComponentParams = void 0;
+exports.MVSAnnotationStructureComponent = exports.MVSTransform = exports.MVSAnnotationStructureComponentParams = void 0;
+exports.createMVSAnnotationSubstructure = createMVSAnnotationSubstructure;
+exports.createMVSAnnotationStructureComponent = createMVSAnnotationStructureComponent;
+exports.updateMVSAnnotationStructureComponent = updateMVSAnnotationStructureComponent;
 const structure_1 = require("../../../mol-model/structure");
 const structure_query_1 = require("../../../mol-plugin-state/helpers/structure-query");
 const objects_1 = require("../../../mol-plugin-state/objects");
@@ -64,7 +67,6 @@ function createMVSAnnotationSubstructure(structure, params) {
         return structure_1.Structure.Empty;
     }
 }
-exports.createMVSAnnotationSubstructure = createMVSAnnotationSubstructure;
 /** Create a substructure PSO based on `MVSAnnotationStructureComponentProps` */
 function createMVSAnnotationStructureComponent(structure, params) {
     const component = createMVSAnnotationSubstructure(structure, params);
@@ -90,7 +92,6 @@ function createMVSAnnotationStructureComponent(structure, params) {
     const props = { label, description: structure_1.Structure.elementDescription(component) };
     return new objects_1.PluginStateObject.Molecule.Structure(component, props);
 }
-exports.createMVSAnnotationStructureComponent = createMVSAnnotationStructureComponent;
 /** Update a substructure PSO based on `MVSAnnotationStructureComponentProps` */
 function updateMVSAnnotationStructureComponent(a, b, oldParams, newParams) {
     const change = !(0, mol_util_1.deepEqual)(newParams, oldParams);
@@ -104,4 +105,3 @@ function updateMVSAnnotationStructureComponent(a, b, oldParams, newParams) {
     }
     return mol_state_1.StateTransformer.UpdateResult.Recreate;
 }
-exports.updateMVSAnnotationStructureComponent = updateMVSAnnotationStructureComponent;

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

@@ -14,24 +14,24 @@ export declare const CustomLabelParams: {
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;
@@ -100,24 +100,24 @@ export declare const CustomLabelRepresentationProvider: StructureRepresentationP
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;

package/lib/commonjs/extensions/mvs/components/custom-label/representation.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CustomLabelRepresentationProvider = exports.CustomLabelRepresentation = exports.CustomLabelParams = void 0;
+exports.CustomLabelRepresentationProvider = exports.CustomLabelParams = void 0;
+exports.CustomLabelRepresentation = CustomLabelRepresentation;
 const representation_1 = require("../../../../mol-repr/representation");
 const representation_2 = require("../../../../mol-repr/structure/representation");
 const marker_action_1 = require("../../../../mol-util/marker-action");
@@ -25,7 +26,6 @@ function CustomLabelRepresentation(ctx, getParams) {
     repr.setState({ pickable: false, markerActions: marker_action_1.MarkerAction.None });
     return repr;
 }
-exports.CustomLabelRepresentation = CustomLabelRepresentation;
 /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
 exports.CustomLabelRepresentationProvider = (0, representation_2.StructureRepresentationProvider)({
     name: 'mvs-custom-label',

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

@@ -11,24 +11,24 @@ export declare const CustomLabelTextParams: {
     borderColor: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
-        isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
-        label?: string | undefined;
-        description?: string | undefined;
-        legend?: import("../../../../mol-util/legend").Legend | undefined;
+        isExpanded?: boolean;
+        isOptional?: boolean;
+        label?: string;
+        description?: string;
+        legend?: import("../../../../mol-util/legend").Legend;
         fieldLabels?: {
             [name: string]: string;
-        } | undefined;
-        isHidden?: boolean | undefined;
-        shortLabel?: boolean | undefined;
-        twoColumns?: boolean | undefined;
-        isEssential?: boolean | undefined;
-        category?: string | undefined;
-        hideIf?: ((currentGroup: any) => boolean) | undefined;
-        help?: ((value: any) => {
-            description?: string | undefined;
-            legend?: import("../../../../mol-util/legend").Legend | undefined;
-        }) | undefined;
+        };
+        isHidden?: boolean;
+        shortLabel?: boolean;
+        twoColumns?: boolean;
+        isEssential?: boolean;
+        category?: string;
+        hideIf?: (currentGroup: any) => boolean;
+        help?: (value: any) => {
+            description?: string;
+            legend?: import("../../../../mol-util/legend").Legend;
+        };
     };
     clip: PD.Group<PD.Normalize<{
         variant: import("../../../../mol-util/clip").Clip.Variant;

package/lib/commonjs/extensions/mvs/components/custom-label/visual.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CustomLabelTextVisual = exports.CustomLabelTextParams = void 0;
+exports.CustomLabelTextParams = void 0;
+exports.CustomLabelTextVisual = CustomLabelTextVisual;
 const tslib_1 = require("tslib");
 const int_1 = require("../../../../mol-data/int");
 const text_builder_1 = require("../../../../mol-geo/geometry/text/text-builder");
@@ -49,7 +50,6 @@ function CustomLabelTextVisual(materialId) {
         }
     }, materialId);
 }
-exports.CustomLabelTextVisual = CustomLabelTextVisual;
 function createLabelText(ctx, structure, theme, props, text) {
     var _a;
     const count = props.items.length;

package/lib/commonjs/extensions/mvs/components/formats.d.ts

@@ -13,24 +13,24 @@ import { MVSData } from '../mvs-data';
 declare const Mvs_base: {
     new (data: {
         mvsData: MVSData;
-        sourceUrl?: string | undefined;
+        sourceUrl?: string;
     }, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: SO.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {
             mvsData: MVSData;
-            sourceUrl?: string | undefined;
+            sourceUrl?: string;
         };
     };
     type: SO.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<{
         mvsData: MVSData;
-        sourceUrl?: string | undefined;
+        sourceUrl?: string;
     }, SO.TypeInfo>;
 };
 /** Plugin state object storing `MVSData` */

package/lib/commonjs/extensions/mvs/components/formats.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.loadMVSX = exports.MVSXFormatProvider = exports.MVSJFormatProvider = exports.LoadMvsData = exports.LoadMvsDataParams = exports.ParseMVSX = exports.ParseMVSJ = exports.Mvs = void 0;
+exports.MVSXFormatProvider = exports.MVSJFormatProvider = exports.LoadMvsData = exports.LoadMvsDataParams = exports.ParseMVSX = exports.ParseMVSJ = exports.Mvs = void 0;
+exports.loadMVSX = loadMVSX;
 const util_1 = require("../../../mol-data/util");
 const provider_1 = require("../../../mol-plugin-state/formats/provider");
 const objects_1 = require("../../../mol-plugin-state/objects");
@@ -121,7 +122,6 @@ async function loadMVSX(plugin, runtimeCtx, data, mainFilePath = 'index.mvsj') {
     const sourceUrl = arcpUri(archiveId, mainFilePath);
     return { mvsData, sourceUrl };
 }
-exports.loadMVSX = loadMVSX;
 /** If the PluginStateObject `pso` comes from a Download transform, try to get its `url` parameter. */
 function tryGetDownloadUrl(pso, plugin) {
     var _a;

package/lib/commonjs/extensions/mvs/components/is-mvs-model-prop.js

@@ -5,7 +5,9 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isMVSStructure = exports.isMVSModel = exports.IsMVSModelProvider = exports.IsMVSModelParams = void 0;
+exports.IsMVSModelProvider = exports.IsMVSModelParams = void 0;
+exports.isMVSModel = isMVSModel;
+exports.isMVSStructure = isMVSStructure;
 const custom_model_property_1 = require("../../../mol-model-props/common/custom-model-property");
 const custom_property_1 = require("../../../mol-model/custom-property");
 const param_definition_1 = require("../../../mol-util/param-definition");
@@ -29,9 +31,7 @@ function isMVSModel(model) {
     var _a;
     return !!((_a = exports.IsMVSModelProvider.props(model)) === null || _a === void 0 ? void 0 : _a.isMvs);
 }
-exports.isMVSModel = isMVSModel;
 /** Decide if the structure is flagged as managed by MolViewSpec */
 function isMVSStructure(structure) {
     return structure.models.some(isMVSModel);
 }
-exports.isMVSStructure = isMVSStructure;

package/lib/commonjs/extensions/mvs/components/multilayer-color-theme.js

@@ -5,7 +5,9 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeMultilayerColorThemeProvider = exports.MultilayerColorThemeName = exports.DefaultMultilayerColorThemeProps = exports.makeMultilayerColorThemeParams = exports.NoColor = void 0;
+exports.MultilayerColorThemeName = exports.DefaultMultilayerColorThemeProps = exports.NoColor = void 0;
+exports.makeMultilayerColorThemeParams = makeMultilayerColorThemeParams;
+exports.makeMultilayerColorThemeProvider = makeMultilayerColorThemeProvider;
 const structure_1 = require("../../../mol-model/structure");
 const color_1 = require("../../../mol-theme/color");
 const color_2 = require("../../../mol-util/color");
@@ -41,7 +43,6 @@ function makeMultilayerColorThemeParams(colorThemeRegistry, ctx) {
         background: param_definition_1.ParamDefinition.Color(DefaultBackgroundColor, { description: 'Color for elements where no layer applies' }),
     };
 }
-exports.makeMultilayerColorThemeParams = makeMultilayerColorThemeParams;
 /** Default values for `MultilayerColorThemeProps` */
 exports.DefaultMultilayerColorThemeProps = { layers: [], background: DefaultBackgroundColor };
 /** Return color theme that assigns colors based on a list of nested color themes (layers).
@@ -126,4 +127,3 @@ function makeMultilayerColorThemeProvider(colorThemeRegistry) {
         isApplicable: (ctx) => !!ctx.structure && (0, is_mvs_model_prop_1.isMVSStructure)(ctx.structure),
     };
 }
-exports.makeMultilayerColorThemeProvider = makeMultilayerColorThemeProvider;

package/lib/commonjs/extensions/mvs/components/selector.js

@@ -5,7 +5,9 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.substructureFromSelector = exports.ElementSet = exports.isSelectorAll = exports.SelectorAll = exports.SelectorParams = exports.StaticSelectorChoice = void 0;
+exports.ElementSet = exports.SelectorAll = exports.SelectorParams = exports.StaticSelectorChoice = void 0;
+exports.isSelectorAll = isSelectorAll;
+exports.substructureFromSelector = substructureFromSelector;
 const int_1 = require("../../../mol-data/int");
 const structure_1 = require("../../../mol-model/structure");
 const structure_component_1 = require("../../../mol-plugin-state/helpers/structure-component");
@@ -33,7 +35,6 @@ exports.SelectorAll = { name: 'static', params: 'all' };
 function isSelectorAll(props) {
     return props.name === 'static' && props.params === 'all';
 }
-exports.isSelectorAll = isSelectorAll;
 exports.ElementSet = {
     /** Create an `ElementSet` from the substructure of `structure` defined by `selector` */
     fromSelector(structure, selector) {
@@ -67,4 +68,3 @@ function substructureFromSelector(structure, selector) {
         : (0, structure_component_1.createStructureComponent)(structure, { type: selector, label: '', nullIfEmpty: false }, { source: structure });
     return objects_1.PluginStateObject.Molecule.Structure.is(pso) ? pso.data : structure_1.Structure.Empty;
 }
-exports.substructureFromSelector = substructureFromSelector;

package/lib/commonjs/extensions/mvs/helpers/indexing.d.ts

@@ -37,9 +37,9 @@ export declare const Sorting: {
     create<K extends number, V extends number>(keys: K[], valueFunction: (k: K) => V): Sorting<K, V>;
     /** Return a newly allocated array of keys which have value equal to `target`.
      * The returned keys are sorted by their value. */
-    getKeysWithValue<K_1, V_1 extends number>(sorting: Sorting<K_1, V_1>, target: V_1): K_1[];
+    getKeysWithValue<K, V extends number>(sorting: Sorting<K, V>, target: V): K[];
     /** Return a newly allocated array of keys which have value within interval `[min, max]` (inclusive).
      * The returned keys are sorted by their value.
      * Undefined `min` is interpreted as negative infitity, undefined `max` is interpreted as positive infinity. */
-    getKeysWithValueInRange<K_2, V_2 extends number>(sorting: Sorting<K_2, V_2>, min: V_2 | undefined, max: V_2 | undefined): K_2[];
+    getKeysWithValueInRange<K, V extends number>(sorting: Sorting<K, V>, min: V | undefined, max: V | undefined): K[];
 };

package/lib/commonjs/extensions/mvs/helpers/label-text.js

@@ -5,7 +5,7 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.textPropsForSelection = void 0;
+exports.textPropsForSelection = textPropsForSelection;
 const boundary_helper_1 = require("../../../mol-math/geometry/boundary-helper");
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const structure_1 = require("../../../mol-model/structure");
@@ -56,7 +56,6 @@ function textPropsForSelection(structure, sizeFunction, rows, onlyInModel) {
         return { center, depth: radius, scale, group: group };
     }
 }
-exports.textPropsForSelection = textPropsForSelection;
 /** Calculate the boundary sphere for a set of points given by their flattened coordinates (`flatCoords.slice(0,3)` is the first point etc.) */
 function boundarySphere(flatCoords) {
     const length = flatCoords.length;

package/lib/commonjs/extensions/mvs/helpers/param-definition.js

@@ -5,13 +5,13 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MaybeStringParamDefinition = exports.MaybeIntegerParamDefinition = void 0;
+exports.MaybeIntegerParamDefinition = MaybeIntegerParamDefinition;
+exports.MaybeStringParamDefinition = MaybeStringParamDefinition;
 const param_definition_1 = require("../../../mol-util/param-definition");
 /** Similar to `PD.Numeric` but allows leaving empty field in UI (treated as `undefined`) */
 function MaybeIntegerParamDefinition(defaultValue, info) {
     return param_definition_1.ParamDefinition.Converted(stringifyMaybeInt, parseMaybeInt, param_definition_1.ParamDefinition.Text(stringifyMaybeInt(defaultValue), info));
 }
-exports.MaybeIntegerParamDefinition = MaybeIntegerParamDefinition;
 /** The magic with negative zero looks crazy, but it's needed if we want to be able to write negative numbers, LOL. Please help if you know a better solution. */
 function parseMaybeInt(input) {
     if (input.trim() === '-')
@@ -30,7 +30,6 @@ function stringifyMaybeInt(num) {
 function MaybeStringParamDefinition(defaultValue, info) {
     return param_definition_1.ParamDefinition.Converted(stringifyMaybeString, parseMaybeString, param_definition_1.ParamDefinition.Text(stringifyMaybeString(defaultValue), info));
 }
-exports.MaybeStringParamDefinition = MaybeStringParamDefinition;
 function parseMaybeString(input) {
     return input === '' ? undefined : input;
 }

package/lib/commonjs/extensions/mvs/helpers/schemas.d.ts

@@ -56,6 +56,6 @@ declare const FieldsForSchemas: {
     auth_residue_range: ("auth_asym_id" | "beg_auth_seq_id" | "end_auth_seq_id" | "group_id")[];
     atom: ("label_asym_id" | "label_atom_id" | "label_entity_id" | "label_seq_id" | "type_symbol" | "group_id" | "atom_id" | "atom_index")[];
     auth_atom: ("auth_asym_id" | "auth_atom_id" | "auth_seq_id" | "type_symbol" | "pdbx_PDB_ins_code" | "group_id" | "atom_id" | "atom_index")[];
-    all_atomic: ("auth_asym_id" | "auth_atom_id" | "auth_seq_id" | "label_asym_id" | "label_atom_id" | "label_entity_id" | "label_seq_id" | "type_symbol" | "pdbx_PDB_ins_code" | "beg_label_seq_id" | "beg_auth_seq_id" | "end_label_seq_id" | "end_auth_seq_id" | "group_id" | "atom_id" | "atom_index")[];
+    all_atomic: (keyof typeof AllAtomicCifAnnotationSchema)[];
 };
 export {};

package/lib/commonjs/extensions/mvs/helpers/schemas.js

@@ -5,7 +5,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getCifAnnotationSchema = exports.MVSAnnotationSchema = void 0;
+exports.MVSAnnotationSchema = void 0;
+exports.getCifAnnotationSchema = getCifAnnotationSchema;
 const db_1 = require("../../../mol-data/db");
 const object_1 = require("../../../mol-util/object");
 const param_choice_1 = require("../../../mol-util/param-choice");
@@ -27,7 +28,6 @@ exports.MVSAnnotationSchema = new param_choice_1.Choice({
 function getCifAnnotationSchema(schemaName) {
     return (0, object_1.pickObjectKeys)(AllAtomicCifAnnotationSchema, FieldsForSchemas[schemaName]);
 }
-exports.getCifAnnotationSchema = getCifAnnotationSchema;
 /** Definition of `all_atomic` schema for CIF (other atomic schemas are subschemas of this one) */
 const AllAtomicCifAnnotationSchema = {
     /** Tag for grouping multiple annotation rows with the same `group_id` (e.g. to show one label for two chains);

package/lib/commonjs/extensions/mvs/helpers/selections.js

@@ -5,7 +5,12 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.groupRows = exports.rowsToExpression = exports.rowToExpression = exports.atomQualifies = exports.getAtomRangesForRows = exports.getAtomRangesForRow = void 0;
+exports.getAtomRangesForRow = getAtomRangesForRow;
+exports.getAtomRangesForRows = getAtomRangesForRows;
+exports.atomQualifies = atomQualifies;
+exports.rowToExpression = rowToExpression;
+exports.rowsToExpression = rowsToExpression;
+exports.groupRows = groupRows;
 const db_1 = require("../../../mol-data/db");
 const builder_1 = require("../../../mol-script/language/builder");
 const array_1 = require("../../../mol-util/array");
@@ -53,7 +58,6 @@ function getAtomRangesForRow(model, row, indices) {
     }
     return ranges;
 }
-exports.getAtomRangesForRow = getAtomRangesForRow;
 /** Return atom ranges in `model` which satisfy criteria given by any of `rows` (atoms that satisfy more rows are still included only once) */
 function getAtomRangesForRows(model, rows, indices) {
     if (Array.isArray(rows)) {
@@ -63,7 +67,6 @@ function getAtomRangesForRows(model, rows, indices) {
         return getAtomRangesForRow(model, rows, indices);
     }
 }
-exports.getAtomRangesForRows = getAtomRangesForRows;
 /** Return an array of chain indexes which satisfy criteria given by `row` */
 function getQualifyingChains(model, row, indices) {
     var _a, _b, _c;
@@ -248,7 +251,6 @@ function atomQualifies(model, iAtom, row) {
         return false;
     return true;
 }
-exports.atomQualifies = atomQualifies;
 /** Return true if `value` equals `requiredValue` or if `requiredValue` if not defined.  */
 function matches(requiredValue, value) {
     return !(0, utils_1.isDefined)(requiredValue) || value === requiredValue;
@@ -323,13 +325,11 @@ function rowToExpression(row) {
     }
     return builder_1.MolScriptBuilder.struct.generator.atomGroups(propTests);
 }
-exports.rowToExpression = rowToExpression;
 /** Convert multiple annotation rows into a MolScript expression.
  * (with union semantics, i.e. an atom qualifies if it qualifies for at least one of the rows) */
 function rowsToExpression(rows) {
     return unionExpression(rows.map(rowToExpression));
 }
-exports.rowsToExpression = rowsToExpression;
 /** Create MolScript expression covering the set union of the given expressions */
 function unionExpression(expressions) {
     return builder_1.MolScriptBuilder.struct.combinator.merge(expressions.map(e => builder_1.MolScriptBuilder.struct.modifier.union([e])));
@@ -365,4 +365,3 @@ function groupRows(rows) {
     offsets.push(rowIndices.length);
     return { count: offsets.length - 1, offsets, grouped: rowIndices };
 }
-exports.groupRows = groupRows;

package/lib/commonjs/extensions/mvs/helpers/utils.d.ts

@@ -55,5 +55,5 @@ export declare function decodeColor(colorString: string | undefined): Color | un
 export type HexColor = `#${string}`;
 export declare const HexColor: {
     /** Decide if a string is a valid hexadecimal color string (6-digit or 3-digit, e.g. '#FF1100' or '#f10') */
-    is(str: any): str is `#${string}`;
+    is(str: any): str is HexColor;
 };

package/lib/commonjs/extensions/mvs/helpers/utils.js

@@ -5,7 +5,13 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.HexColor = exports.decodeColor = exports.stringHash = exports.filterDefined = exports.isAnyDefined = exports.isDefined = exports.NumberMap = exports.MultiMap = exports.safePromise = void 0;
+exports.HexColor = exports.NumberMap = exports.MultiMap = void 0;
+exports.safePromise = safePromise;
+exports.isDefined = isDefined;
+exports.isAnyDefined = isAnyDefined;
+exports.filterDefined = filterDefined;
+exports.stringHash = stringHash;
+exports.decodeColor = decodeColor;
 const util_1 = require("../../../mol-data/util");
 const color_1 = require("../../../mol-util/color");
 const names_1 = require("../../../mol-util/color/names");
@@ -19,7 +25,6 @@ async function safePromise(promise) {
         return { ok: false, error };
     }
 }
-exports.safePromise = safePromise;
 /** A map where values are arrays. Handles missing keys when adding values. */
 class MultiMap {
     constructor() {
@@ -68,17 +73,14 @@ exports.NumberMap = NumberMap;
 function isDefined(value) {
     return value !== undefined && value !== null;
 }
-exports.isDefined = isDefined;
 /** Return `true` if at least one of `values` is not `undefined` or `null`. */
 function isAnyDefined(...values) {
     return values.some(v => isDefined(v));
 }
-exports.isAnyDefined = isAnyDefined;
 /** Return filtered array containing all original elements except `undefined` or `null`. */
 function filterDefined(elements) {
     return elements.filter(x => x !== undefined && x !== null);
 }
-exports.filterDefined = filterDefined;
 /** Create an 8-hex-character hash for a given input string, e.g. 'spanish inquisition' -> '7f9ac4be' */
 function stringHash32(input) {
     const uint32hash = (0, util_1.hashString)(input) >>> 0; // >>>0 converts to uint32, LOL
@@ -89,7 +91,6 @@ function stringHash(input) {
     const reversed = input.split('').reverse().join('');
     return stringHash32(input) + stringHash32(reversed);
 }
-exports.stringHash = stringHash;
 /** Convert `colorString` (either X11 color name like 'magenta' or hex code like '#ff00ff') to Color.
  * Return `undefined` if `colorString` cannot be converted. */
 function decodeColor(colorString) {
@@ -110,7 +111,6 @@ function decodeColor(colorString) {
         return result;
     return undefined;
 }
-exports.decodeColor = decodeColor;
 /** Regular expression matching a hexadecimal color string, e.g. '#FF1100' or '#f10' */
 const hexColorRegex = /^#([0-9A-F]{3}){1,2}$/i;
 exports.HexColor = {

package/lib/commonjs/extensions/mvs/load-helpers.d.ts

@@ -48,7 +48,7 @@ export declare const UpdateTarget: {
     /** Create a new update, with `selector` pointing to the root. */
     create(plugin: PluginContext, replaceExisting: boolean): UpdateTarget;
     /** Add a child node to `target.selector`, return a new `UpdateTarget` pointing to the new child. */
-    apply<A extends StateObject<any, StateObject.Type<any>>, B extends StateObject<any, StateObject.Type<any>>, P extends {}>(target: UpdateTarget, transformer: StateTransformer<A, B, P>, params?: Partial<P>, options?: Partial<StateTransform.Options>): UpdateTarget;
+    apply<A extends StateObject, B extends StateObject, P extends {}>(target: UpdateTarget, transformer: StateTransformer<A, B, P>, params?: Partial<P>, options?: Partial<StateTransform.Options>): UpdateTarget;
     /** Delete all children of `target.selector`. */
     deleteChildren(target: UpdateTarget): UpdateTarget;
     /** Commit all changes done in the current update. */