pdbe-molstar 3.4.0 → 3.6.0

package/lib/extensions/state-gallery/behavior.d.ts

@@ -19,7 +19,7 @@ export interface StateGalleryParams {
     showTitleBox: boolean;
 }
 /** `StateGallery` extension allows browsing pre-computed 3D states for a PDB entry */
-export declare const StateGallery: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, StateGalleryParams>;
+export declare const StateGallery: import("molstar/lib/mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, StateGalleryParams>;
 /** Public functions provided by the `StateGallery` extension  */
 export declare const StateGalleryExtensionFunctions: {
     StateGalleryManager: typeof StateGalleryManager;

package/lib/extensions/state-gallery/config.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getStateGalleryConfig = exports.StateGalleryConfig = exports.StateGalleryConfigDefaults = void 0;
+exports.StateGalleryConfig = exports.StateGalleryConfigDefaults = void 0;
+exports.getStateGalleryConfig = getStateGalleryConfig;
 const config_1 = require("molstar/lib/mol-plugin/config");
 const helpers_1 = require("../../helpers");
 /** Default values of plugin config items for the `StateGallery` extension */
@@ -28,4 +29,3 @@ exports.StateGalleryConfig = {
 function getStateGalleryConfig(plugin) {
     return helpers_1.PluginConfigUtils.getConfigValues(plugin, exports.StateGalleryConfig, exports.StateGalleryConfigDefaults);
 }
-exports.getStateGalleryConfig = getStateGalleryConfig;

package/lib/extensions/state-gallery/manager.js

@@ -12,6 +12,7 @@ const helpers_1 = require("../../helpers");
 const behavior_1 = require("./behavior");
 const config_1 = require("./config");
 const titles_1 = require("./titles");
+const string_like_1 = require("molstar/lib/mol-io/common/string-like");
 /** Categories of images/states */
 exports.ImageCategory = ['Entry', 'Assemblies', 'Entities', 'Ligands', 'Modified residues', 'Domains', 'Miscellaneous'];
 /** Provides functionality to get list of images (3D states) for an entry, load individual images, keeps track of the currently loaded image.
@@ -99,8 +100,8 @@ class StateGalleryManager {
     }
     /** Request to load an image (3D state). When there are multiple concurrent requests, some requests may be skipped (will resolve to `{ status: 'cancelled' }` or `{ status: 'skipped' }`) as only the last request is really important. */
     load(img) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
             if (typeof img === 'string') {
                 img = (_a = this.getImageByFilename(img)) !== null && _a !== void 0 ? _a : { filename: img };
             }
@@ -151,14 +152,14 @@ class StateGalleryManager {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             const url = (0, helpers_1.combineUrl)(this.options.ServerUrl, `${filename}.molj`);
             const data = yield this.plugin.runTask(this.plugin.fetch({ url, type: 'string' }));
-            return data;
+            return string_like_1.StringLike.toString(data);
         });
     }
     /** Get MOLJ state for the image (get from cache or fetch from API) */
     getSnapshot(filename) {
-        var _a;
-        var _b;
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            var _a;
+            var _b;
             return (_a = (_b = this.cache)[filename]) !== null && _a !== void 0 ? _a : (_b[filename] = yield this.fetchSnapshot(filename));
         });
     }

package/lib/extensions/state-gallery/ui.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StateGalleryTitleBox = exports.StateGalleryManagerControls = exports.StateGalleryControls = void 0;
+exports.StateGalleryControls = void 0;
+exports.StateGalleryManagerControls = StateGalleryManagerControls;
+exports.StateGalleryTitleBox = StateGalleryTitleBox;
 const tslib_1 = require("tslib");
 const jsx_runtime_1 = require("react/jsx-runtime");
 const base_1 = require("molstar/lib/mol-plugin-ui/base");
@@ -69,7 +71,7 @@ class StateGalleryControls extends base_1.CollapsableControls {
     }
     renderControls() {
         return (0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(parameters_1.ParameterControls, { params: Params, values: this.values, onChangeValues: this.onChangeValues, onEnter: this.load }), (!this.state.manager || this.state.manager.entryId !== this.state.entryId) &&
-                    (0, jsx_runtime_1.jsx)(common_1.Button, Object.assign({ icon: this.state.isLoading ? undefined : icons_1.CheckSvg, title: 'Load', disabled: this.loadDisabled(), onClick: this.load, className: 'msp-btn-block' }, { children: this.state.isLoading ? 'Loading...' : 'Load' })), this.state.manager &&
+                    (0, jsx_runtime_1.jsx)(common_1.Button, { icon: this.state.isLoading ? undefined : icons_1.CheckSvg, title: 'Load', disabled: this.loadDisabled(), onClick: this.load, className: 'msp-btn-block', children: this.state.isLoading ? 'Loading...' : 'Load' }), this.state.manager &&
                     (0, jsx_runtime_1.jsx)(StateGalleryManagerControls, { manager: this.state.manager })] });
     }
 }
@@ -102,21 +104,20 @@ function StateGalleryManagerControls(props) {
         return () => subs.forEach(sub => sub.unsubscribe());
     }, [props.manager]);
     if (nImages === 0) {
-        return (0, jsx_runtime_1.jsxs)("div", Object.assign({ style: { margin: 8 } }, { children: ["No data available for ", props.manager.entryId, "."] }));
+        return (0, jsx_runtime_1.jsxs)("div", { style: { margin: 8 }, children: ["No data available for ", props.manager.entryId, "."] });
     }
-    return (0, jsx_runtime_1.jsxs)("div", Object.assign({ className: 'pdbemolstar-state-gallery-controls', onKeyDown: handleKeyDown, tabIndex: -1, ref: keyDownTargetRef }, { children: [(0, jsx_runtime_1.jsx)(common_1.ExpandGroup, Object.assign({ header: 'States', initiallyExpanded: true }, { children: (0, jsx_runtime_1.jsx)("div", Object.assign({ style: { marginBottom: 8 } }, { children: categories.groups.map(cat => {
+    return (0, jsx_runtime_1.jsxs)("div", { className: 'pdbemolstar-state-gallery-controls', onKeyDown: handleKeyDown, tabIndex: -1, ref: keyDownTargetRef, children: [(0, jsx_runtime_1.jsx)(common_1.ExpandGroup, { header: 'States', initiallyExpanded: true, children: (0, jsx_runtime_1.jsx)("div", { style: { marginBottom: 8 }, children: categories.groups.map(cat => {
                         var _a;
-                        return (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, Object.assign({ header: cat, initiallyExpanded: true }, { children: (_a = categories.members.get(cat)) === null || _a === void 0 ? void 0 : _a.map(img => (0, jsx_runtime_1.jsx)(ImageButton, { img: img, isSelected: img === selected, status: status, onClick: () => props.manager.load(img) }, img.filename)) }), cat);
-                    }) })) }), 'states'), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, Object.assign({ header: 'Description', initiallyExpanded: true }, { children: (0, jsx_runtime_1.jsx)("div", Object.assign({ className: 'pdbemolstar-state-gallery-legend' }, { children: (0, jsx_runtime_1.jsx)("div", { dangerouslySetInnerHTML: { __html: (_a = selected === null || selected === void 0 ? void 0 : selected.description) !== null && _a !== void 0 ? _a : '' } }) })) }), 'description')] }));
+                        return (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, { header: cat, initiallyExpanded: true, children: (_a = categories.members.get(cat)) === null || _a === void 0 ? void 0 : _a.map(img => (0, jsx_runtime_1.jsx)(ImageButton, { img: img, isSelected: img === selected, status: status, onClick: () => props.manager.load(img) }, img.filename)) }, cat);
+                    }) }) }, 'states'), (0, jsx_runtime_1.jsx)(common_1.ExpandGroup, { header: 'Description', initiallyExpanded: true, children: (0, jsx_runtime_1.jsx)("div", { className: 'pdbemolstar-state-gallery-legend', children: (0, jsx_runtime_1.jsx)("div", { dangerouslySetInnerHTML: { __html: (_a = selected === null || selected === void 0 ? void 0 : selected.description) !== null && _a !== void 0 ? _a : '' } }) }) }, 'description')] });
 }
-exports.StateGalleryManagerControls = StateGalleryManagerControls;
 /** Button with image title */
 function ImageButton(props) {
     var _a;
     const { img, isSelected, status, onClick } = props;
     const icon = !isSelected ? icons_2.EmptyIconSvg : (status === 'loading') ? icons_2.HourglassBottomSvg : (status === 'error') ? icons_1.ErrorSvg : icons_1.CheckSvg;
     const tooltip = imageTooltip(img, isSelected ? status : 'ready');
-    return (0, jsx_runtime_1.jsxs)(common_1.Button, Object.assign({ className: 'msp-action-menu-button pdbemolstar-state-gallery-state-button', icon: icon, onClick: onClick, title: tooltip, style: { fontWeight: isSelected ? 'bold' : undefined } }, { children: [(_a = img.title) !== null && _a !== void 0 ? _a : img.filename, img.subtitle && (0, jsx_runtime_1.jsxs)("small", { children: ["\u2002 ", img.subtitle] })] }));
+    return (0, jsx_runtime_1.jsxs)(common_1.Button, { className: 'msp-action-menu-button pdbemolstar-state-gallery-state-button', icon: icon, onClick: onClick, title: tooltip, style: { fontWeight: isSelected ? 'bold' : undefined }, children: [(_a = img.title) !== null && _a !== void 0 ? _a : img.filename, img.subtitle && (0, jsx_runtime_1.jsxs)("small", { children: ["\u2002 ", img.subtitle] })] });
 }
 /** Box in viewport with image title and arrows to move between images (3D states) */
 function StateGalleryTitleBox() {
@@ -147,11 +148,10 @@ function StateGalleryTitleBox() {
     }, [plugin]);
     if (image === undefined)
         return null;
-    return (0, jsx_runtime_1.jsxs)("div", Object.assign({ className: 'pdbemolstar-state-gallery-title-box' }, { children: [manager &&
-                (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(common_1.Button, { className: 'msp-btn-icon', title: 'Previous state', icon: icons_2.ChevronLeftSvg, onClick: () => manager.loadPrevious() }) }), (0, jsx_runtime_1.jsxs)("div", Object.assign({ className: 'pdbemolstar-state-gallery-title', title: imageTooltip(image, status) }, { children: [(0, jsx_runtime_1.jsx)("div", Object.assign({ className: 'pdbemolstar-state-gallery-title-icon' }, { children: (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: status === 'error' ? icons_1.ErrorSvg : status === 'loading' ? icons_2.HourglassBottomSvg : icons_2.EmptyIconSvg }) })), (0, jsx_runtime_1.jsxs)("div", Object.assign({ className: 'pdbemolstar-state-gallery-title-text' }, { children: [(_a = image.title) !== null && _a !== void 0 ? _a : image.filename, (0, jsx_runtime_1.jsx)("br", {}), (0, jsx_runtime_1.jsx)("small", { children: image.subtitle })] }))] })), manager &&
-                (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(common_1.Button, { className: 'msp-btn-icon', title: 'Next state', icon: icons_2.ChevronRightSvg, onClick: () => manager === null || manager === void 0 ? void 0 : manager.loadNext() }) })] }));
+    return (0, jsx_runtime_1.jsxs)("div", { className: 'pdbemolstar-state-gallery-title-box', children: [manager &&
+                (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(common_1.Button, { className: 'msp-btn-icon', title: 'Previous state', icon: icons_2.ChevronLeftSvg, onClick: () => manager.loadPrevious() }) }), (0, jsx_runtime_1.jsxs)("div", { className: 'pdbemolstar-state-gallery-title', title: imageTooltip(image, status), children: [(0, jsx_runtime_1.jsx)("div", { className: 'pdbemolstar-state-gallery-title-icon', children: (0, jsx_runtime_1.jsx)(icons_1.Icon, { svg: status === 'error' ? icons_1.ErrorSvg : status === 'loading' ? icons_2.HourglassBottomSvg : icons_2.EmptyIconSvg }) }), (0, jsx_runtime_1.jsxs)("div", { className: 'pdbemolstar-state-gallery-title-text', children: [(_a = image.title) !== null && _a !== void 0 ? _a : image.filename, (0, jsx_runtime_1.jsx)("br", {}), (0, jsx_runtime_1.jsx)("small", { children: image.subtitle })] })] }), manager &&
+                (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(common_1.Button, { className: 'msp-btn-icon', title: 'Next state', icon: icons_2.ChevronRightSvg, onClick: () => manager === null || manager === void 0 ? void 0 : manager.loadNext() }) })] });
 }
-exports.StateGalleryTitleBox = StateGalleryTitleBox;
 /** Return tooltip text for an image */
 function imageTooltip(img, status) {
     var _a;

package/lib/helpers.d.ts

@@ -1,8 +1,11 @@
+import { ComponentExpressionT } from 'molstar/lib/extensions/mvs/tree/mvs/param-types';
+import { Mat3, Mat4 } from 'molstar/lib/mol-math/linear-algebra';
 import { Model, Structure } from 'molstar/lib/mol-model/structure';
 import { BuiltInTrajectoryFormat } from 'molstar/lib/mol-plugin-state/formats/trajectory';
 import { StructureRef } from 'molstar/lib/mol-plugin-state/manager/structure/hierarchy-state';
 import { PluginConfigItem } from 'molstar/lib/mol-plugin/config';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { PluginLayoutStateProps } from 'molstar/lib/mol-plugin/layout';
 import { Expression } from 'molstar/lib/mol-script/language/expression';
 import { Overpaint } from 'molstar/lib/mol-theme/overpaint';
 import { Color } from 'molstar/lib/mol-util/color';
@@ -76,7 +79,9 @@ export interface QueryParam {
     representationColor?: any;
     focus?: boolean;
     tooltip?: string;
+    /** @deprecated I don't know what this is */
     start?: any;
+    /** @deprecated I don't know what this is */
     end?: any;
     atom_id?: number[];
     uniprot_accession?: string;
@@ -84,6 +89,7 @@ export interface QueryParam {
     start_uniprot_residue_number?: number;
     end_uniprot_residue_number?: number;
 }
+export declare function queryParamsToMvsComponentExpressions(params: QueryParam[]): ComponentExpressionT[];
 export declare namespace QueryHelper {
     function getQueryObject(params: QueryParam[], contextData: Structure): Expression;
     function getInteractivityLoci(params: QueryParam[], contextData: Structure): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
@@ -188,4 +194,6 @@ export declare namespace PluginConfigUtils {
     /** Retrieve config values for items in `configItems` from the current plugin config */
     function getConfigValues<T extends object>(plugin: PluginContext | undefined, configItems: ConfigFor<T>, defaults: T): T;
 }
+export declare function pluginLayoutStateFromInitParams(initParams: InitParams): PluginLayoutStateProps;
+export declare function getRotationMat4(view: 'front' | 'back' | 'right' | 'left' | 'top' | 'bottom' | Mat3): Mat4;
 export {};

package/lib/helpers.js

@@ -1,13 +1,29 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PluginConfigUtils = exports.PreemptiveQueue = exports.nonnegativeModulo = exports.createIndex = exports.groupElements = exports.distinct = exports.getComponentTypeFromTags = exports.StructureComponentTags = exports.Tags = exports.applyOverpaint = exports.normalizeColor = exports.addDefaults = exports.combineUrl = exports.getStructureUrl = exports.runWithProgressMessage = exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
+exports.PluginConfigUtils = exports.PreemptiveQueue = exports.StructureComponentTags = exports.Tags = exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
+exports.queryParamsToMvsComponentExpressions = queryParamsToMvsComponentExpressions;
+exports.runWithProgressMessage = runWithProgressMessage;
+exports.getStructureUrl = getStructureUrl;
+exports.combineUrl = combineUrl;
+exports.addDefaults = addDefaults;
+exports.normalizeColor = normalizeColor;
+exports.applyOverpaint = applyOverpaint;
+exports.getComponentTypeFromTags = getComponentTypeFromTags;
+exports.distinct = distinct;
+exports.groupElements = groupElements;
+exports.createIndex = createIndex;
+exports.nonnegativeModulo = nonnegativeModulo;
+exports.pluginLayoutStateFromInitParams = pluginLayoutStateFromInitParams;
+exports.getRotationMat4 = getRotationMat4;
 const tslib_1 = require("tslib");
 const prop_1 = require("molstar/lib/extensions/model-archive/quality-assessment/prop");
+const linear_algebra_1 = require("molstar/lib/mol-math/linear-algebra");
 const structure_1 = require("molstar/lib/mol-model/structure");
 const query_1 = require("molstar/lib/mol-model/structure/query/query");
 const transforms_1 = require("molstar/lib/mol-plugin-state/transforms");
 const transformers_1 = require("molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers");
 const commands_1 = require("molstar/lib/mol-plugin/commands");
+const layout_1 = require("molstar/lib/mol-plugin/layout");
 const builder_1 = require("molstar/lib/mol-script/language/builder");
 const compiler_1 = require("molstar/lib/mol-script/runtime/query/compiler");
 const mol_state_1 = require("molstar/lib/mol-state");
@@ -50,7 +66,7 @@ var PDBeVolumes;
         }
     }
     PDBeVolumes.toggle = toggle;
-})(PDBeVolumes = exports.PDBeVolumes || (exports.PDBeVolumes = {}));
+})(PDBeVolumes || (exports.PDBeVolumes = PDBeVolumes = {}));
 var AlphafoldView;
 (function (AlphafoldView) {
     function getLociByPLDDT(score, contextData) {
@@ -69,7 +85,7 @@ var AlphafoldView;
         return structure_1.StructureSelection.toLociWithSourceUnits(sel);
     }
     AlphafoldView.getLociByPLDDT = getLociByPLDDT;
-})(AlphafoldView = exports.AlphafoldView || (exports.AlphafoldView = {}));
+})(AlphafoldView || (exports.AlphafoldView = AlphafoldView = {}));
 var LigandView;
 (function (LigandView) {
     function query(ligandViewParams) {
@@ -134,95 +150,156 @@ var LigandView;
         };
     }
     LigandView.branchedQuery = branchedQuery;
-})(LigandView = exports.LigandView || (exports.LigandView = {}));
+})(LigandView || (exports.LigandView = LigandView = {}));
+function queryParamsToMvsComponentExpressions(params) {
+    const broadcasted = broadcast(params, ['atoms', 'atom_id']);
+    return broadcasted.map(item => {
+        var _a;
+        return ({
+            label_entity_id: item.entity_id,
+            label_asym_id: item.struct_asym_id,
+            auth_asym_id: item.auth_asym_id,
+            label_seq_id: item.residue_number,
+            auth_seq_id: (_a = item.auth_seq_id) !== null && _a !== void 0 ? _a : item.auth_residue_number,
+            pdbx_PDB_ins_code: item.auth_ins_code_id,
+            beg_label_seq_id: item.start_residue_number,
+            end_label_seq_id: item.end_residue_number,
+            beg_auth_seq_id: item.start_auth_residue_number,
+            end_auth_seq_id: item.end_auth_residue_number,
+            label_atom_id: item.atoms,
+            auth_atom_id: undefined,
+            type_symbol: undefined,
+            atom_id: item.atom_id,
+            atom_index: undefined,
+            label_comp_id: item.label_comp_id,
+            auth_comp_id: undefined,
+        });
+    });
+}
+/** `broadcastSingleKey([{chain: 'A', residue: 5, atom: ['C', 'O']}], 'atom')`
+ * -> `[{chain: 'A', residue: 5, atom: 'C'}], {chain: 'A', residue: 5, atom: 'O'}` */
+function broadcastSingleKey(objs, key) {
+    const out = [];
+    for (const obj of objs) {
+        if (obj[key] === undefined) {
+            out.push(obj);
+        }
+        else {
+            for (const value of obj[key]) {
+                out.push(Object.assign(Object.assign({}, obj), { [key]: value }));
+            }
+        }
+    }
+    return out;
+}
+/** `broadcast([{chain: 'A', residue: [5, 6], atom: ['C', 'O']}], ['residue', 'atom'])`
+ * -> `[{chain: 'A', residue: 5, atom: 'C'}], {chain: 'A', residue: 5, atom: 'O', {chain: 'A', residue: 6, atom: 'C'}], {chain: 'A', residue: 6, atom: 'O'}` */
+function broadcast(objs, keys) {
+    return keys.reduce((list, key) => broadcastSingleKey(list, key), objs);
+}
 var QueryHelper;
 (function (QueryHelper) {
     function getQueryObject(params, contextData) {
         const selections = [];
-        let siftMappings;
-        let currentAccession;
-        params.forEach(param => {
-            const selection = {};
+        /** `undefined` means SIFTSMappingMapping has not been retrieved yet. `null` means SIFTSMappingMapping has been retrieved unsuccessfully.  */
+        let _siftMappings;
+        function getSiftsMappings() {
+            var _a;
+            if (_siftMappings === undefined)
+                _siftMappings = (_a = sifts_mapping_1.SIFTSMapping.Provider.get(contextData.models[0]).value) !== null && _a !== void 0 ? _a : null;
+            return _siftMappings;
+        }
+        for (const param of params) {
+            const predicates = {
+                entity: [],
+                chain: [],
+                residue: [],
+                atom: [],
+            };
             // entity
-            if (param.entity_id)
-                selection['entityTest'] = l => structure_1.StructureProperties.entity.id(l.element) === param.entity_id;
+            if (param.entity_id !== undefined) {
+                predicates.entity.push(l => structure_1.StructureProperties.entity.id(l.element) === param.entity_id);
+            }
             // chain
-            if (param.struct_asym_id) {
-                selection['chainTest'] = l => structure_1.StructureProperties.chain.label_asym_id(l.element) === param.struct_asym_id;
+            if (param.struct_asym_id !== undefined) {
+                predicates.chain.push(l => structure_1.StructureProperties.chain.label_asym_id(l.element) === param.struct_asym_id);
             }
-            else if (param.auth_asym_id) {
-                selection['chainTest'] = l => structure_1.StructureProperties.chain.auth_asym_id(l.element) === param.auth_asym_id;
+            if (param.auth_asym_id !== undefined) {
+                predicates.chain.push(l => structure_1.StructureProperties.chain.auth_asym_id(l.element) === param.auth_asym_id);
             }
-            // residues
-            if (param.label_comp_id) {
-                selection['residueTest'] = l => structure_1.StructureProperties.atom.label_comp_id(l.element) === param.label_comp_id;
+            // residue
+            if (param.label_comp_id !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.atom.label_comp_id(l.element) === param.label_comp_id);
             }
-            else if (param.uniprot_accession && param.uniprot_residue_number !== undefined) {
-                selection['residueTest'] = l => {
-                    if (!siftMappings || currentAccession !== param.uniprot_accession) {
-                        siftMappings = sifts_mapping_1.SIFTSMapping.Provider.get(contextData.models[0]).value;
-                        currentAccession = param.uniprot_accession;
-                    }
-                    const rI = structure_1.StructureProperties.residue.key(l.element);
-                    return !!siftMappings && param.uniprot_accession === siftMappings.accession[rI] && param.uniprot_residue_number === +siftMappings.num[rI];
-                };
+            if (param.residue_number !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.label_seq_id(l.element) === param.residue_number);
             }
-            else if (param.uniprot_accession && param.start_uniprot_residue_number !== undefined && param.end_uniprot_residue_number !== undefined) {
-                selection['residueTest'] = l => {
-                    if (!siftMappings || currentAccession !== param.uniprot_accession) {
-                        siftMappings = sifts_mapping_1.SIFTSMapping.Provider.get(contextData.models[0]).value;
-                        currentAccession = param.uniprot_accession;
-                    }
-                    const rI = structure_1.StructureProperties.residue.key(l.element);
-                    return !!siftMappings && param.uniprot_accession === siftMappings.accession[rI] && (param.start_uniprot_residue_number <= +siftMappings.num[rI] && param.end_uniprot_residue_number >= +siftMappings.num[rI]);
-                };
+            if (param.start_residue_number !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.label_seq_id(l.element) >= param.start_residue_number);
             }
-            else if (param.residue_number !== undefined) {
-                selection['residueTest'] = l => structure_1.StructureProperties.residue.label_seq_id(l.element) === param.residue_number;
+            if (param.end_residue_number !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.label_seq_id(l.element) <= param.end_residue_number);
             }
-            else if (param.start_residue_number !== undefined && param.end_residue_number !== undefined && param.end_residue_number > param.start_residue_number) {
-                selection['residueTest'] = l => {
-                    const labelSeqId = structure_1.StructureProperties.residue.label_seq_id(l.element);
-                    return labelSeqId >= param.start_residue_number && labelSeqId <= param.end_residue_number;
-                };
+            if (param.auth_seq_id !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_seq_id);
             }
-            else if (param.start_residue_number !== undefined && param.end_residue_number !== undefined && param.end_residue_number === param.start_residue_number) {
-                selection['residueTest'] = l => structure_1.StructureProperties.residue.label_seq_id(l.element) === param.start_residue_number;
+            if (param.auth_residue_number !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number);
             }
-            else if (param.auth_seq_id !== undefined) {
-                selection['residueTest'] = l => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_seq_id;
+            if (param.auth_ins_code_id !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.pdbx_PDB_ins_code(l.element) === param.auth_ins_code_id);
             }
-            else if (param.auth_residue_number !== undefined && !param.auth_ins_code_id) {
-                selection['residueTest'] = l => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number;
+            if (param.start_auth_residue_number !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.auth_seq_id(l.element) >= param.start_auth_residue_number);
+                if (param.start_auth_ins_code_id !== undefined) {
+                    // This assumes insertion code come in alphabetical order, which is not always true (e.g. 1ucy chain A [auth L]). However, authors of such monstrosities do not deserve their structures to be displayed correctly.
+                    predicates.residue.push(l => structure_1.StructureProperties.residue.auth_seq_id(l.element) > param.start_auth_residue_number || structure_1.StructureProperties.residue.pdbx_PDB_ins_code(l.element) >= param.start_auth_ins_code_id);
+                }
+            }
+            if (param.end_auth_residue_number !== undefined) {
+                predicates.residue.push(l => structure_1.StructureProperties.residue.auth_seq_id(l.element) <= param.end_auth_residue_number);
+                if (param.end_auth_ins_code_id !== undefined) {
+                    // This assumes insertion code come in alphabetical order, which is not always true (e.g. 1ucy chain A [auth L]). However, authors of such monstrosities do not deserve their structures to be displayed correctly.
+                    predicates.residue.push(l => structure_1.StructureProperties.residue.auth_seq_id(l.element) < param.end_auth_residue_number || structure_1.StructureProperties.residue.pdbx_PDB_ins_code(l.element) <= param.end_auth_ins_code_id);
+                }
+            }
+            if (param.uniprot_accession !== undefined) {
+                predicates.residue.push(l => { var _a; return ((_a = getSiftsMappings()) === null || _a === void 0 ? void 0 : _a.accession[structure_1.StructureProperties.residue.key(l.element)]) === param.uniprot_accession; });
             }
-            else if (param.auth_residue_number !== undefined && param.auth_ins_code_id) {
-                selection['residueTest'] = l => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number;
+            if (param.uniprot_residue_number !== undefined) {
+                predicates.residue.push(l => { var _a; return Number((_a = getSiftsMappings()) === null || _a === void 0 ? void 0 : _a.num[structure_1.StructureProperties.residue.key(l.element)]) === param.uniprot_residue_number; });
             }
-            else if (param.start_auth_residue_number !== undefined && param.end_auth_residue_number !== undefined && param.end_auth_residue_number > param.start_auth_residue_number) {
-                selection['residueTest'] = l => {
-                    const authSeqId = structure_1.StructureProperties.residue.auth_seq_id(l.element);
-                    return authSeqId >= param.start_auth_residue_number && authSeqId <= param.end_auth_residue_number;
-                };
+            if (param.start_uniprot_residue_number !== undefined) {
+                predicates.residue.push(l => { var _a; return Number((_a = getSiftsMappings()) === null || _a === void 0 ? void 0 : _a.num[structure_1.StructureProperties.residue.key(l.element)]) >= param.start_uniprot_residue_number; });
             }
-            else if (param.start_auth_residue_number !== undefined && param.end_auth_residue_number !== undefined && param.end_auth_residue_number === param.start_auth_residue_number) {
-                selection['residueTest'] = l => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.start_auth_residue_number;
+            if (param.end_uniprot_residue_number !== undefined) {
+                predicates.residue.push(l => { var _a; return Number((_a = getSiftsMappings()) === null || _a === void 0 ? void 0 : _a.num[structure_1.StructureProperties.residue.key(l.element)]) <= param.end_uniprot_residue_number; });
             }
-            // atoms
+            // atom
             if (param.atoms) {
-                selection['atomTest'] = l => param.atoms.includes(structure_1.StructureProperties.atom.label_atom_id(l.element));
+                predicates.atom.push(l => param.atoms.includes(structure_1.StructureProperties.atom.label_atom_id(l.element)));
             }
             if (param.atom_id) {
-                selection['atomTest'] = l => param.atom_id.includes(structure_1.StructureProperties.atom.id(l.element));
+                predicates.atom.push(l => param.atom_id.includes(structure_1.StructureProperties.atom.id(l.element)));
             }
-            selections.push(selection);
-        });
-        const atmGroupsQueries = [];
-        selections.forEach(selection => {
-            atmGroupsQueries.push(structure_1.Queries.generators.atoms(selection));
-        });
+            selections.push({
+                entityTest: predicateConjunction(predicates.entity),
+                chainTest: predicateConjunction(predicates.chain),
+                residueTest: predicateConjunction(predicates.residue),
+                atomTest: predicateConjunction(predicates.atom),
+            });
+        }
+        const atmGroupsQueries = selections.map(selection => structure_1.Queries.generators.atoms(selection));
         return structure_1.Queries.combinators.merge(atmGroupsQueries);
     }
     QueryHelper.getQueryObject = getQueryObject;
+    function predicateConjunction(predicates) {
+        if (predicates.length === 0)
+            return undefined;
+        if (predicates.length === 1)
+            return predicates[0];
+        return (x => predicates.every(pred => pred(x)));
+    }
     function getInteractivityLoci(params, contextData) {
         const sel = query_1.StructureQuery.run(QueryHelper.getQueryObject(params, contextData), contextData);
         return structure_1.StructureSelection.toLociWithSourceUnits(sel);
@@ -234,7 +311,7 @@ var QueryHelper;
         return structure_1.StructureSelection.toLociWithSourceUnits(sel);
     }
     QueryHelper.getHetLoci = getHetLoci;
-})(QueryHelper = exports.QueryHelper || (exports.QueryHelper = {}));
+})(QueryHelper || (exports.QueryHelper = QueryHelper = {}));
 var ModelInfo;
 (function (ModelInfo) {
     function get(model, structures) {
@@ -267,7 +344,7 @@ var ModelInfo;
         });
     }
     ModelInfo.get = get;
-})(ModelInfo = exports.ModelInfo || (exports.ModelInfo = {}));
+})(ModelInfo || (exports.ModelInfo = ModelInfo = {}));
 /** Run `action` with showing a message in the bottom-left corner of the plugin UI */
 function runWithProgressMessage(plugin, progressMessage, action) {
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
@@ -287,7 +364,6 @@ function runWithProgressMessage(plugin, progressMessage, action) {
         yield plugin.runTask(task);
     });
 }
-exports.runWithProgressMessage = runWithProgressMessage;
 /** Return URL for a ModelServer request.
  * If `queryType` is 'full' and `lowPrecisionCoords` is false, return URL of the static file instead (updated mmCIF or bCIF). */
 function getStructureUrl(initParams, request) {
@@ -304,7 +380,6 @@ function getStructureUrl(initParams, request) {
         return (queryString !== '') ? `${url}?${queryString}` : url;
     }
 }
-exports.getStructureUrl = getStructureUrl;
 /** Combine URL parts into one URL while avoiding double slashes. Examples:
  * combineUrl('https://example.org', '1tqn') -> 'https://example.org/1tqn';
  * combineUrl('https://example.org/', '1tqn') -> 'https://example.org/1tqn'; */
@@ -315,7 +390,6 @@ function combineUrl(firstPart, ...moreParts) {
     }
     return result;
 }
-exports.combineUrl = combineUrl;
 /** Create a copy of object `object`, fill in missing/undefined keys using `defaults`.
  * This is similar to {...defaults,...object} but `undefined` in `object` will not override a value from `defaults`. */
 function addDefaults(object, defaults) {
@@ -326,7 +400,6 @@ function addDefaults(object, defaults) {
     }
     return result;
 }
-exports.addDefaults = addDefaults;
 /** Convert `colorVal` from any of supported color formats (e.g. 'yellow', '#ffff00', {r:255,g:255,b:0}) to `Color`.
  * Return default color (gray) if `colorVal` is undefined or null.
 */
@@ -349,12 +422,11 @@ function normalizeColor(colorVal, defaultColor = color_1.Color.fromRgb(170, 170,
     }
     return defaultColor;
 }
-exports.normalizeColor = normalizeColor;
 /** Apply overpaint to every representation of every component in a structure.
  * Excludes representations created as "added representations" by `PDBeMolstarPlugin.visual.select`. */
 function applyOverpaint(plugin, structRef, overpaintLayers) {
-    var _a;
     return tslib_1.__awaiter(this, void 0, void 0, function* () {
+        var _a;
         if (overpaintLayers.length === 0)
             return;
         const update = plugin.build();
@@ -378,7 +450,6 @@ function applyOverpaint(plugin, structRef, overpaintLayers) {
         yield update.commit();
     });
 }
-exports.applyOverpaint = applyOverpaint;
 exports.Tags = {
     /** Tag needed for `clearStructureOverpaint`; defined in src/mol-plugin-state/helpers/structure-overpaint.ts but private */
     Overpaint: 'overpaint-controls',
@@ -405,7 +476,6 @@ function getComponentTypeFromTags(tags) {
     }
     return undefined;
 }
-exports.getComponentTypeFromTags = getComponentTypeFromTags;
 /** Return a new array containing `values` without duplicates (only first occurrence will be kept).
  * Values v1, v2 are considered duplicates when `key(v1)===key(v2)`. */
 function distinct(values, key = (value => value)) {
@@ -420,7 +490,6 @@ function distinct(values, key = (value => value)) {
     }
     return out;
 }
-exports.distinct = distinct;
 /** Group elements by result of `groupFunction` applied to them */
 function groupElements(elements, groupFunction) {
     const groups = [];
@@ -442,20 +511,17 @@ function groupElements(elements, groupFunction) {
         members,
     };
 }
-exports.groupElements = groupElements;
 /** Return a mapping of elements to their index in the `elements` array */
 function createIndex(elements) {
     const index = new Map();
     elements.forEach((elem, i) => index.set(elem, i));
     return index;
 }
-exports.createIndex = createIndex;
 /** Return modulo of two numbers (a % b) within range [0, b) */
 function nonnegativeModulo(a, b) {
     const modulo = a % b;
     return (modulo < 0) ? modulo + b : modulo;
 }
-exports.nonnegativeModulo = nonnegativeModulo;
 /** Queue for running jobs where enqueued jobs get discarded when a new job is enqueued.
  * (Discarded jobs may or may not actually be executed, but their result is not accessible anyway.) */
 class PreemptiveQueue {
@@ -520,4 +586,32 @@ var PluginConfigUtils;
         return values;
     }
     PluginConfigUtils.getConfigValues = getConfigValues;
-})(PluginConfigUtils = exports.PluginConfigUtils || (exports.PluginConfigUtils = {}));
+})(PluginConfigUtils || (exports.PluginConfigUtils = PluginConfigUtils = {}));
+function pluginLayoutStateFromInitParams(initParams) {
+    return {
+        isExpanded: initParams.expanded,
+        showControls: !initParams.hideControls,
+        regionState: {
+            left: initParams.leftPanel ? 'full' : 'hidden',
+            right: initParams.rightPanel ? 'full' : 'hidden',
+            top: initParams.sequencePanel ? 'full' : 'hidden',
+            bottom: initParams.logPanel ? 'full' : 'hidden',
+        },
+        controlsDisplay: initParams.reactive ? 'reactive' : initParams.landscape ? 'landscape' : layout_1.PluginLayoutStateParams.controlsDisplay.defaultValue,
+    };
+}
+function getRotationMat4(view) {
+    switch (view) {
+        case 'front': return linear_algebra_1.Mat4.identity();
+        case 'back': return [-1, 0, 0, 0, 0, 1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1];
+        case 'right': return [0, 0, -1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1];
+        case 'left': return [0, 0, 1, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1];
+        case 'top': return [1, 0, 0, 0, 0, 0, -1, 0, 0, 1, 0, 0, 0, 0, 0, 1];
+        case 'bottom': return [1, 0, 0, 0, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 1];
+        default: {
+            const out = linear_algebra_1.Mat4.fromMat3((0, linear_algebra_1.Mat4)(), view);
+            out[15] = 1;
+            return out;
+        }
+    }
+}

package/lib/labels.d.ts

@@ -1,2 +1,2 @@
 import { PluginBehavior } from 'molstar/lib/mol-plugin/behavior';
-export declare const PDBeLociLabelProvider: import("molstar/lib/mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
+export declare const PDBeLociLabelProvider: import("molstar/lib/mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/loci-details.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports._bundleLabel = exports.bondLabel = exports.lociDetails = void 0;
+exports.lociDetails = lociDetails;
+exports.bondLabel = bondLabel;
+exports._bundleLabel = _bundleLabel;
 const int_1 = require("molstar/lib/mol-data/int");
 const sifts_mapping_1 = require("molstar/lib/mol-model-props/sequence/sifts-mapping");
 const structure_1 = require("molstar/lib/mol-model/structure");
@@ -12,13 +14,12 @@ function lociDetails(loci) {
             return structureElementStatsDetail(structure_1.StructureElement.Stats.ofLoci(loci));
         case 'bond-loci': {
             const bond = loci.bonds[0];
-            return bond ? bondLabel(bond, 'element') : '';
+            return bond ? bondLabel(bond, 'element') : {};
         }
         default:
             return undefined;
     }
 }
-exports.lociDetails = lociDetails;
 function structureElementStatsDetail(stats) {
     const { chainCount, residueCount, elementCount } = stats;
     if (elementCount === 1 && residueCount === 0 && chainCount === 0) {
@@ -100,7 +101,6 @@ function bondLabel(bond, granularity) {
         ],
     }, granularity);
 }
-exports.bondLabel = bondLabel;
 function _bundleLabel(bundle, granularity) {
     let isSingleElements = true;
     for (const l of bundle.loci) {
@@ -125,4 +125,3 @@ function _bundleLabel(bundle, granularity) {
         return elementDetails;
     }
 }
-exports._bundleLabel = _bundleLabel;

package/lib/plugin-custom-state.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PluginCustomControls = exports.ExtensionCustomState = exports.PluginCustomState = void 0;
+exports.PluginCustomControls = exports.ExtensionCustomState = void 0;
+exports.PluginCustomState = PluginCustomState;
 ;
 ;
 /** Access `plugin.customState` only through this function to get proper typing.
@@ -9,7 +10,6 @@ function PluginCustomState(plugin) {
     var _a;
     return (_a = plugin.customState) !== null && _a !== void 0 ? _a : (plugin.customState = {});
 }
-exports.PluginCustomState = PluginCustomState;
 /** Functions for accessing plugin-bound custom state for extensions. */
 exports.ExtensionCustomState = {
     /** Get plugin-bound custom state for a specific extension. If not present, initialize with empty object. */