drugflow-molstar 0.4.7 → 0.4.8

package/lib/domain-annotations/behavior.js

@@ -1,10 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PDBeDomainAnnotations = void 0;
-const prop_1 = require("./prop");
-const color_1 = require("./color");
-const param_definition_1 = require("Molstar/mol-util/param-definition");
-const behavior_1 = require("Molstar/mol-plugin/behavior");
+var tslib_1 = require("tslib");
+var prop_1 = require("./prop");
+var color_1 = require("./color");
+var param_definition_1 = require("Molstar/mol-util/param-definition");
+var behavior_1 = require("Molstar/mol-plugin/behavior");
 exports.PDBeDomainAnnotations = behavior_1.PluginBehavior.create({
     name: 'pdbe-domain-annotations-prop',
     category: 'custom-props',
@@ -12,34 +13,37 @@ exports.PDBeDomainAnnotations = behavior_1.PluginBehavior.create({
         name: 'Domain annotations',
         description: 'Data for domain annotations, obtained via PDBe.'
     },
-    ctor: class extends behavior_1.PluginBehavior.Handler {
-        constructor() {
-            super(...arguments);
-            this.provider = prop_1.DomainAnnotationsProvider;
-            this.labelDomainAnnotations = {
-                label: (loci) => void 0
+    ctor: /** @class */ (function (_super) {
+        tslib_1.__extends(class_1, _super);
+        function class_1() {
+            var _this = _super.apply(this, tslib_1.__spreadArray([], tslib_1.__read(arguments), false)) || this;
+            _this.provider = prop_1.DomainAnnotationsProvider;
+            _this.labelDomainAnnotations = {
+                label: function (loci) { return void 0; }
             };
+            return _this;
         }
-        register() {
+        class_1.prototype.register = function () {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
             this.ctx.managers.lociLabels.addProvider(this.labelDomainAnnotations);
             this.ctx.representation.structure.themes.colorThemeRegistry.add(color_1.DomainAnnotationsColorThemeProvider);
-        }
-        update(p) {
-            let updated = this.params.autoAttach !== p.autoAttach;
+        };
+        class_1.prototype.update = function (p) {
+            var updated = this.params.autoAttach !== p.autoAttach;
             this.params.autoAttach = p.autoAttach;
             this.params.showTooltip = p.showTooltip;
             this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
             return updated;
-        }
-        unregister() {
+        };
+        class_1.prototype.unregister = function () {
             this.ctx.customModelProperties.unregister(prop_1.DomainAnnotationsProvider.descriptor.name);
             this.ctx.managers.lociLabels.removeProvider(this.labelDomainAnnotations);
             this.ctx.representation.structure.themes.colorThemeRegistry.remove(color_1.DomainAnnotationsColorThemeProvider);
-        }
-    },
-    params: () => ({
+        };
+        return class_1;
+    }(behavior_1.PluginBehavior.Handler)),
+    params: function () { return ({
         autoAttach: param_definition_1.ParamDefinition.Boolean(false),
         showTooltip: param_definition_1.ParamDefinition.Boolean(true)
-    })
+    }); }
 });

package/lib/domain-annotations/color.js

@@ -1,12 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DomainAnnotationsColorThemeProvider = exports.DomainAnnotationsColorTheme = exports.DomainAnnotationsColorThemeParams = void 0;
-const prop_1 = require("./prop");
-const structure_1 = require("Molstar/mol-model/structure");
-const color_1 = require("Molstar/mol-theme/color");
-const color_2 = require("Molstar/mol-util/color");
-const param_definition_1 = require("Molstar/mol-util/param-definition");
-const DomainColors = [
+exports.DomainAnnotationsColorThemeProvider = exports.DomainAnnotationsColorThemeParams = void 0;
+exports.DomainAnnotationsColorTheme = DomainAnnotationsColorTheme;
+var prop_1 = require("./prop");
+var structure_1 = require("Molstar/mol-model/structure");
+var color_1 = require("Molstar/mol-theme/color");
+var color_2 = require("Molstar/mol-util/color");
+var param_definition_1 = require("Molstar/mol-util/param-definition");
+var DomainColors = [
     color_2.Color.fromRgb(170, 170, 170), // not applicable
     color_2.Color.fromRgb(255, 112, 3)
 ];
@@ -16,19 +17,19 @@ exports.DomainAnnotationsColorThemeParams = {
     })
 };
 function DomainAnnotationsColorTheme(ctx, props) {
-    let color;
+    var color;
     if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(prop_1.DomainAnnotationsProvider.descriptor)) {
-        const getDomains = prop_1.DomainAnnotations.getDomains;
-        const issue = props.type.params.kind;
-        color = (location) => {
-            if (structure_1.StructureElement.Location.is(location) && getDomains(location).indexOf(issue) >= 0) {
+        var getDomains_1 = prop_1.DomainAnnotations.getDomains;
+        var issue_1 = props.type.params.kind;
+        color = function (location) {
+            if (structure_1.StructureElement.Location.is(location) && getDomains_1(location).indexOf(issue_1) >= 0) {
                 return DomainColors[1];
             }
             return DomainColors[0];
         };
     }
     else {
-        color = () => DomainColors[0];
+        color = function () { return DomainColors[0]; };
     }
     return {
         factory: DomainAnnotationsColorTheme,
@@ -38,17 +39,16 @@ function DomainAnnotationsColorTheme(ctx, props) {
         description: 'Highlights Sequnece and Structure Domain Annotations. Data obtained via PDBe.',
     };
 }
-exports.DomainAnnotationsColorTheme = DomainAnnotationsColorTheme;
 exports.DomainAnnotationsColorThemeProvider = {
     name: 'pdbe-domain-annotations',
     label: 'Domain annotations',
     category: color_1.ColorTheme.Category.Misc,
     factory: DomainAnnotationsColorTheme,
-    getParams: ctx => {
-        const domainNames = prop_1.DomainAnnotations.getDomainNames(ctx.structure);
-        const domainTypes = prop_1.DomainAnnotations.getDomainTypes(ctx.structure);
-        const optionObj = {};
-        domainTypes.forEach((tp, index) => {
+    getParams: function (ctx) {
+        var domainNames = prop_1.DomainAnnotations.getDomainNames(ctx.structure);
+        var domainTypes = prop_1.DomainAnnotations.getDomainTypes(ctx.structure);
+        var optionObj = {};
+        domainTypes.forEach(function (tp, index) {
             if (domainNames[index].length > 0) {
                 optionObj[tp] = param_definition_1.ParamDefinition.Group({
                     kind: param_definition_1.ParamDefinition.Select(domainNames[index][0], param_definition_1.ParamDefinition.arrayToOptions(domainNames[index]))
@@ -69,11 +69,11 @@ exports.DomainAnnotationsColorThemeProvider = {
         }
     },
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.DomainAnnotationsColorThemeParams),
-    isApplicable: (ctx) => prop_1.DomainAnnotations.isApplicable(ctx.structure?.models[0]),
+    isApplicable: function (ctx) { var _a; return prop_1.DomainAnnotations.isApplicable((_a = ctx.structure) === null || _a === void 0 ? void 0 : _a.models[0]); },
     ensureCustomProperties: {
-        attach: (ctx, data) => {
+        attach: function (ctx, data) {
             return data.structure ? prop_1.DomainAnnotationsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve();
         },
-        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(prop_1.DomainAnnotationsProvider.descriptor, false)
+        detach: function (data) { return data.structure && data.structure.models[0].customProperties.reference(prop_1.DomainAnnotationsProvider.descriptor, false); }
     }
 };

package/lib/domain-annotations/prop.js

@@ -1,18 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DomainAnnotationsProvider = exports.DomainAnnotationsParams = exports.DomainAnnotations = void 0;
-const structure_1 = require("Molstar/mol-model/structure");
-const wrapper_1 = require("Molstar/mol-model-props/common/wrapper");
-const custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
-const param_definition_1 = require("Molstar/mol-util/param-definition");
-const array_1 = require("Molstar/mol-util/array");
-const assets_1 = require("Molstar/mol-util/assets");
-const custom_property_1 = require("Molstar/mol-model/custom-property");
+var tslib_1 = require("tslib");
+var structure_1 = require("Molstar/mol-model/structure");
+var wrapper_1 = require("Molstar/mol-model-props/common/wrapper");
+var custom_model_property_1 = require("Molstar/mol-model-props/common/custom-model-property");
+var param_definition_1 = require("Molstar/mol-util/param-definition");
+var array_1 = require("Molstar/mol-util/array");
+var assets_1 = require("Molstar/mol-util/assets");
+var custom_property_1 = require("Molstar/mol-model/custom-property");
 var DomainAnnotations;
 (function (DomainAnnotations) {
     DomainAnnotations.DefaultServerUrl = 'https://www.ebi.ac.uk/pdbe/api/mappings';
     function getEntryUrl(pdbId, serverUrl) {
-        return `${serverUrl}/${pdbId.toLowerCase()}`;
+        return "".concat(serverUrl, "/").concat(pdbId.toLowerCase());
     }
     DomainAnnotations.getEntryUrl = getEntryUrl;
     function isApplicable(model) {
@@ -20,35 +21,45 @@ var DomainAnnotations;
     }
     DomainAnnotations.isApplicable = isApplicable;
     function fromJson(model, data) {
-        const info = wrapper_1.PropertyWrapper.createInfo();
-        const domainMap = createdomainMapFromJson(model, data);
-        return { info, data: domainMap };
+        var info = wrapper_1.PropertyWrapper.createInfo();
+        var domainMap = createdomainMapFromJson(model, data);
+        return { info: info, data: domainMap };
     }
     DomainAnnotations.fromJson = fromJson;
-    async function fromServer(ctx, model, props) {
-        const url = assets_1.Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
-        const json = await ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime);
-        const data = json.data[model.entryId.toLowerCase()];
-        if (!data)
-            throw new Error('missing data');
-        return { value: fromJson(model, data), assets: [json] };
+    function fromServer(ctx, model, props) {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
+            var url, json, data;
+            return tslib_1.__generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        url = assets_1.Asset.getUrlAsset(ctx.assetManager, getEntryUrl(model.entryId, props.serverUrl));
+                        return [4 /*yield*/, ctx.assetManager.resolve(url, 'json').runInContext(ctx.runtime)];
+                    case 1:
+                        json = _a.sent();
+                        data = json.data[model.entryId.toLowerCase()];
+                        if (!data)
+                            throw new Error('missing data');
+                        return [2 /*return*/, { value: fromJson(model, data), assets: [json] }];
+                }
+            });
+        });
     }
     DomainAnnotations.fromServer = fromServer;
-    const _emptyArray = [];
+    var _emptyArray = [];
     function getDomains(e) {
         if (!structure_1.Unit.isAtomic(e.unit))
             return _emptyArray;
-        const prop = exports.DomainAnnotationsProvider.get(e.unit.model).value;
+        var prop = exports.DomainAnnotationsProvider.get(e.unit.model).value;
         if (!prop || !prop.data)
             return _emptyArray;
-        const rI = e.unit.residueIndex[e.element];
+        var rI = e.unit.residueIndex[e.element];
         return prop.data.domains.has(rI) ? prop.data.domains.get(rI) : _emptyArray;
     }
     DomainAnnotations.getDomains = getDomains;
     function getDomainTypes(structure) {
         if (!structure)
             return _emptyArray;
-        const prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
+        var prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
         if (!prop || !prop.data)
             return _emptyArray;
         return prop.data.domainTypes;
@@ -57,7 +68,7 @@ var DomainAnnotations;
     function getDomainNames(structure) {
         if (!structure)
             return _emptyArray;
-        const prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
+        var prop = exports.DomainAnnotationsProvider.get(structure.models[0]).value;
         if (!prop || !prop.data)
             return _emptyArray;
         return prop.data.domainNames;
@@ -74,65 +85,103 @@ exports.DomainAnnotationsProvider = custom_model_property_1.CustomModelProperty.
     }),
     type: 'static',
     defaultParams: exports.DomainAnnotationsParams,
-    getParams: (data) => exports.DomainAnnotationsParams,
-    isApplicable: (data) => DomainAnnotations.isApplicable(data),
-    obtain: async (ctx, data, props) => {
-        const p = { ...param_definition_1.ParamDefinition.getDefaultValues(exports.DomainAnnotationsParams), ...props };
-        return await DomainAnnotations.fromServer(ctx, data, p);
-    }
+    getParams: function (data) { return exports.DomainAnnotationsParams; },
+    isApplicable: function (data) { return DomainAnnotations.isApplicable(data); },
+    obtain: function (ctx, data, props) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
+        var p;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    p = tslib_1.__assign(tslib_1.__assign({}, param_definition_1.ParamDefinition.getDefaultValues(exports.DomainAnnotationsParams)), props);
+                    return [4 /*yield*/, DomainAnnotations.fromServer(ctx, data, p)];
+                case 1: return [2 /*return*/, _a.sent()];
+            }
+        });
+    }); }
 });
 function findChainLabel(map, label_entity_id, label_asym_id) {
-    const entityIndex = map.entities.getEntityIndex;
-    const eI = entityIndex(label_entity_id);
+    var entityIndex = map.entities.getEntityIndex;
+    var eI = entityIndex(label_entity_id);
     if (eI < 0 || !map.entity_index_label_asym_id.has(eI))
         return -1;
-    const cm = map.entity_index_label_asym_id.get(eI);
+    var cm = map.entity_index_label_asym_id.get(eI);
     if (!cm)
         return -1;
     return cm.has(label_asym_id) ? cm.get(label_asym_id) : -1;
 }
 function findResidue(modelData, map, label_entity_id, label_asym_id, label_seq_id) {
-    const cI = findChainLabel(map, label_entity_id, label_asym_id);
+    var cI = findChainLabel(map, label_entity_id, label_asym_id);
     if (cI < 0)
         return -1;
-    const rm = map.chain_index_auth_seq_id.get(cI);
+    var rm = map.chain_index_auth_seq_id.get(cI);
     return rm.has(label_seq_id) ? rm.get(label_seq_id) : -1;
 }
 function createdomainMapFromJson(modelData, data) {
-    const domainTypes = [];
-    const domainNames = [];
-    const ret = new Map();
-    const defaultDomains = ['Pfam', 'InterPro', 'CATH', 'SCOP'];
-    for (const db_name of Object.keys(data)) {
-        if (defaultDomains.indexOf(db_name) === -1)
-            continue;
-        const tempDomains = [];
-        domainTypes.push(db_name);
-        const db = data[db_name];
-        for (const db_code of Object.keys(db)) {
-            const domain = db[db_code];
-            for (const map of domain.mappings) {
-                (0, array_1.arraySetAdd)(tempDomains, domain.identifier);
-                const indexData = modelData.atomicHierarchy.index;
-                const indexMap = indexData.map;
-                for (let i = map.start.residue_number; i <= map.end.residue_number; i++) {
-                    const seq_id = i;
-                    const idx = findResidue(modelData, indexMap, map.entity_id + '', map.chain_id, seq_id);
-                    let addVal = [domain.identifier];
-                    const prevVal = ret.get(idx);
-                    if (prevVal) {
-                        prevVal.push(domain.identifier);
-                        addVal = prevVal;
+    var e_1, _a, e_2, _b, e_3, _c;
+    var domainTypes = [];
+    var domainNames = [];
+    var ret = new Map();
+    var defaultDomains = ['Pfam', 'InterPro', 'CATH', 'SCOP'];
+    try {
+        for (var _d = tslib_1.__values(Object.keys(data)), _e = _d.next(); !_e.done; _e = _d.next()) {
+            var db_name = _e.value;
+            if (defaultDomains.indexOf(db_name) === -1)
+                continue;
+            var tempDomains = [];
+            domainTypes.push(db_name);
+            var db = data[db_name];
+            try {
+                for (var _f = (e_2 = void 0, tslib_1.__values(Object.keys(db))), _g = _f.next(); !_g.done; _g = _f.next()) {
+                    var db_code = _g.value;
+                    var domain = db[db_code];
+                    try {
+                        for (var _h = (e_3 = void 0, tslib_1.__values(domain.mappings)), _j = _h.next(); !_j.done; _j = _h.next()) {
+                            var map = _j.value;
+                            (0, array_1.arraySetAdd)(tempDomains, domain.identifier);
+                            var indexData = modelData.atomicHierarchy.index;
+                            var indexMap = indexData.map;
+                            for (var i = map.start.residue_number; i <= map.end.residue_number; i++) {
+                                var seq_id = i;
+                                var idx = findResidue(modelData, indexMap, map.entity_id + '', map.chain_id, seq_id);
+                                var addVal = [domain.identifier];
+                                var prevVal = ret.get(idx);
+                                if (prevVal) {
+                                    prevVal.push(domain.identifier);
+                                    addVal = prevVal;
+                                }
+                                ret.set(idx, addVal);
+                            }
+                        }
+                    }
+                    catch (e_3_1) { e_3 = { error: e_3_1 }; }
+                    finally {
+                        try {
+                            if (_j && !_j.done && (_c = _h.return)) _c.call(_h);
+                        }
+                        finally { if (e_3) throw e_3.error; }
                     }
-                    ret.set(idx, addVal);
                 }
             }
+            catch (e_2_1) { e_2 = { error: e_2_1 }; }
+            finally {
+                try {
+                    if (_g && !_g.done && (_b = _f.return)) _b.call(_f);
+                }
+                finally { if (e_2) throw e_2.error; }
+            }
+            domainNames.push(tempDomains);
+        }
+    }
+    catch (e_1_1) { e_1 = { error: e_1_1 }; }
+    finally {
+        try {
+            if (_e && !_e.done && (_a = _d.return)) _a.call(_d);
         }
-        domainNames.push(tempDomains);
+        finally { if (e_1) throw e_1.error; }
     }
     return {
         domains: structure_1.IndexedCustomProperty.fromResidueMap(ret),
-        domainNames,
-        domainTypes
+        domainNames: domainNames,
+        domainTypes: domainTypes
     };
 }

package/lib/drugflow-molstar-component-build-0.4.8.js

@@ -0,0 +1,2 @@
+/*! For license information please see drugflow-molstar-component-build-0.4.8.js.LICENSE.txt */
+(()=>{"use strict";const t="undefined"!=typeof window&&null!=window.customElements&&void 0!==window.customElements.polyfillWrapFlushCallback,e=(t,e,s=null)=>{for(;e!==s;){const s=e.nextSibling;t.removeChild(e),e=s}},s=`{{lit-${String(Math.random()).slice(2)}}}`,i=`\x3c!--${s}--\x3e`,n=new RegExp(`${s}|${i}`),r="$lit$";class o{constructor(t,e){this.parts=[],this.element=e;const i=[],o=[],l=document.createTreeWalker(e.content,133,null,!1);let c=0,p=-1,u=0;const{strings:_,values:{length:m}}=t;for(;u<m;){const t=l.nextNode();if(null!==t){if(p++,1===t.nodeType){if(t.hasAttributes()){const e=t.attributes,{length:s}=e;let i=0;for(let t=0;t<s;t++)a(e[t].name,r)&&i++;for(;i-- >0;){const e=_[u],s=d.exec(e)[2],i=s.toLowerCase()+r,o=t.getAttribute(i);t.removeAttribute(i);const a=o.split(n);this.parts.push({type:"attribute",index:p,name:s,strings:a}),u+=a.length-1}}"TEMPLATE"===t.tagName&&(o.push(t),l.currentNode=t.content)}else if(3===t.nodeType){const e=t.data;if(e.indexOf(s)>=0){const s=t.parentNode,o=e.split(n),l=o.length-1;for(let e=0;e<l;e++){let i,n=o[e];if(""===n)i=h();else{const t=d.exec(n);null!==t&&a(t[2],r)&&(n=n.slice(0,t.index)+t[1]+t[2].slice(0,-5)+t[3]),i=document.createTextNode(n)}s.insertBefore(i,t),this.parts.push({type:"node",index:++p})}""===o[l]?(s.insertBefore(h(),t),i.push(t)):t.data=o[l],u+=l}}else if(8===t.nodeType)if(t.data===s){const e=t.parentNode;null!==t.previousSibling&&p!==c||(p++,e.insertBefore(h(),t)),c=p,this.parts.push({type:"node",index:p}),null===t.nextSibling?t.data="":(i.push(t),p--),u++}else{let e=-1;for(;-1!==(e=t.data.indexOf(s,e+1));)this.parts.push({type:"node",index:-1}),u++}}else l.currentNode=o.pop()}for(const t of i)t.parentNode.removeChild(t)}}const a=(t,e)=>{const s=t.length-e.length;return s>=0&&t.slice(s)===e},l=t=>-1!==t.index,h=()=>document.createComment(""),d=/([ \x09\x0a\x0c\x0d])([^\0-\x1F\x7F-\x9F "'>=/]+)([ \x09\x0a\x0c\x0d]*=[ \x09\x0a\x0c\x0d]*(?:[^ \x09\x0a\x0c\x0d"'`<>=]*|"[^"]*|'[^']*))$/;function c(t,e){const{element:{content:s},parts:i}=t,n=document.createTreeWalker(s,133,null,!1);let r=u(i),o=i[r],a=-1,l=0;const h=[];let d=null;for(;n.nextNode();){a++;const t=n.currentNode;for(t.previousSibling===d&&(d=null),e.has(t)&&(h.push(t),null===d&&(d=t)),null!==d&&l++;void 0!==o&&o.index===a;)o.index=null!==d?-1:o.index-l,r=u(i,r),o=i[r]}h.forEach(t=>t.parentNode.removeChild(t))}const p=t=>{let e=11===t.nodeType?0:1;const s=document.createTreeWalker(t,133,null,!1);for(;s.nextNode();)e++;return e},u=(t,e=-1)=>{for(let s=e+1;s<t.length;s++){const e=t[s];if(l(e))return s}return-1},_=new WeakMap,m=t=>"function"==typeof t&&_.has(t),y={},f={};class g{constructor(t,e,s){this.__parts=[],this.template=t,this.processor=e,this.options=s}update(t){let e=0;for(const s of this.__parts)void 0!==s&&s.setValue(t[e]),e++;for(const t of this.__parts)void 0!==t&&t.commit()}_clone(){const e=t?this.template.element.content.cloneNode(!0):document.importNode(this.template.element.content,!0),s=[],i=this.template.parts,n=document.createTreeWalker(e,133,null,!1);let r,o=0,a=0,h=n.nextNode();for(;o<i.length;)if(r=i[o],l(r)){for(;a<r.index;)a++,"TEMPLATE"===h.nodeName&&(s.push(h),n.currentNode=h.content),null===(h=n.nextNode())&&(n.currentNode=s.pop(),h=n.nextNode());if("node"===r.type){const t=this.processor.handleTextExpression(this.options);t.insertAfterNode(h.previousSibling),this.__parts.push(t)}else this.__parts.push(...this.processor.handleAttributeExpressions(h,r.name,r.strings,this.options));o++}else this.__parts.push(void 0),o++;return t&&(document.adoptNode(e),customElements.upgrade(e)),e}}const S=window.trustedTypes&&trustedTypes.createPolicy("lit-html",{createHTML:t=>t}),v=` ${s} `;class w{constructor(t,e,s,i){this.strings=t,this.values=e,this.type=s,this.processor=i}getHTML(){const t=this.strings.length-1;let e="",n=!1;for(let o=0;o<t;o++){const t=this.strings[o],a=t.lastIndexOf("\x3c!--");n=(a>-1||n)&&-1===t.indexOf("--\x3e",a+1);const l=d.exec(t);e+=null===l?t+(n?v:i):t.substr(0,l.index)+l[1]+l[2]+r+l[3]+s}return e+=this.strings[t],e}getTemplateElement(){const t=document.createElement("template");let e=this.getHTML();return void 0!==S&&(e=S.createHTML(e)),t.innerHTML=e,t}}const b=t=>null===t||!("object"==typeof t||"function"==typeof t),x=t=>Array.isArray(t)||!(!t||!t[Symbol.iterator]);class P{constructor(t,e,s){this.dirty=!0,this.element=t,this.name=e,this.strings=s,this.parts=[];for(let t=0;t<s.length-1;t++)this.parts[t]=this._createPart()}_createPart(){return new N(this)}_getValue(){const t=this.strings,e=t.length-1,s=this.parts;if(1===e&&""===t[0]&&""===t[1]){const t=s[0].value;if("symbol"==typeof t)return String(t);if("string"==typeof t||!x(t))return t}let i="";for(let n=0;n<e;n++){i+=t[n];const e=s[n];if(void 0!==e){const t=e.value;if(b(t)||!x(t))i+="string"==typeof t?t:String(t);else for(const e of t)i+="string"==typeof e?e:String(e)}}return i+=t[e],i}commit(){this.dirty&&(this.dirty=!1,this.element.setAttribute(this.name,this._getValue()))}}class N{constructor(t){this.value=void 0,this.committer=t}setValue(t){t===y||b(t)&&t===this.value||(this.value=t,m(t)||(this.committer.dirty=!0))}commit(){for(;m(this.value);){const t=this.value;this.value=y,t(this)}this.value!==y&&this.committer.commit()}}class C{constructor(t){this.value=void 0,this.__pendingValue=void 0,this.options=t}appendInto(t){this.startNode=t.appendChild(h()),this.endNode=t.appendChild(h())}insertAfterNode(t){this.startNode=t,this.endNode=t.nextSibling}appendIntoPart(t){t.__insert(this.startNode=h()),t.__insert(this.endNode=h())}insertAfterPart(t){t.__insert(this.startNode=h()),this.endNode=t.endNode,t.endNode=this.startNode}setValue(t){this.__pendingValue=t}commit(){if(null===this.startNode.parentNode)return;for(;m(this.__pendingValue);){const t=this.__pendingValue;this.__pendingValue=y,t(this)}const t=this.__pendingValue;t!==y&&(b(t)?t!==this.value&&this.__commitText(t):t instanceof w?this.__commitTemplateResult(t):t instanceof Node?this.__commitNode(t):x(t)?this.__commitIterable(t):t===f?(this.value=f,this.clear()):this.__commitText(t))}__insert(t){this.endNode.parentNode.insertBefore(t,this.endNode)}__commitNode(t){this.value!==t&&(this.clear(),this.__insert(t),this.value=t)}__commitText(t){const e=this.startNode.nextSibling,s="string"==typeof(t=null==t?"":t)?t:String(t);e===this.endNode.previousSibling&&3===e.nodeType?e.data=s:this.__commitNode(document.createTextNode(s)),this.value=t}__commitTemplateResult(t){const e=this.options.templateFactory(t);if(this.value instanceof g&&this.value.template===e)this.value.update(t.values);else{const s=new g(e,t.processor,this.options),i=s._clone();s.update(t.values),this.__commitNode(i),this.value=s}}__commitIterable(t){Array.isArray(this.value)||(this.value=[],this.clear());const e=this.value;let s,i=0;for(const n of t)s=e[i],void 0===s&&(s=new C(this.options),e.push(s),0===i?s.appendIntoPart(this):s.insertAfterPart(e[i-1])),s.setValue(n),s.commit(),i++;i<e.length&&(e.length=i,this.clear(s&&s.endNode))}clear(t=this.startNode){e(this.startNode.parentNode,t.nextSibling,this.endNode)}}class T{constructor(t,e,s){if(this.value=void 0,this.__pendingValue=void 0,2!==s.length||""!==s[0]||""!==s[1])throw new Error("Boolean attributes can only contain a single expression");this.element=t,this.name=e,this.strings=s}setValue(t){this.__pendingValue=t}commit(){for(;m(this.__pendingValue);){const t=this.__pendingValue;this.__pendingValue=y,t(this)}if(this.__pendingValue===y)return;const t=!!this.__pendingValue;this.value!==t&&(t?this.element.setAttribute(this.name,""):this.element.removeAttribute(this.name),this.value=t),this.__pendingValue=y}}class A extends P{constructor(t,e,s){super(t,e,s),this.single=2===s.length&&""===s[0]&&""===s[1]}_createPart(){return new E(this)}_getValue(){return this.single?this.parts[0].value:super._getValue()}commit(){this.dirty&&(this.dirty=!1,this.element[this.name]=this._getValue())}}class E extends N{}let V=!1;(()=>{try{const t={get capture(){return V=!0,!1}};window.addEventListener("test",t,t),window.removeEventListener("test",t,t)}catch(t){}})();class U{constructor(t,e,s){this.value=void 0,this.__pendingValue=void 0,this.element=t,this.eventName=e,this.eventContext=s,this.__boundHandleEvent=t=>this.handleEvent(t)}setValue(t){this.__pendingValue=t}commit(){for(;m(this.__pendingValue);){const t=this.__pendingValue;this.__pendingValue=y,t(this)}if(this.__pendingValue===y)return;const t=this.__pendingValue,e=this.value,s=null==t||null!=e&&(t.capture!==e.capture||t.once!==e.once||t.passive!==e.passive),i=null!=t&&(null==e||s);s&&this.element.removeEventListener(this.eventName,this.__boundHandleEvent,this.__options),i&&(this.__options=O(t),this.element.addEventListener(this.eventName,this.__boundHandleEvent,this.__options)),this.value=t,this.__pendingValue=y}handleEvent(t){"function"==typeof this.value?this.value.call(this.eventContext||this.element,t):this.value.handleEvent(t)}}const O=t=>t&&(V?{capture:t.capture,passive:t.passive,once:t.once}:t.capture);function R(t){let e=k.get(t.type);void 0===e&&(e={stringsArray:new WeakMap,keyString:new Map},k.set(t.type,e));let i=e.stringsArray.get(t.strings);if(void 0!==i)return i;const n=t.strings.join(s);return i=e.keyString.get(n),void 0===i&&(i=new o(t,t.getTemplateElement()),e.keyString.set(n,i)),e.stringsArray.set(t.strings,i),i}const k=new Map,M=new WeakMap;new class{handleAttributeExpressions(t,e,s,i){const n=e[0];return"."===n?new A(t,e.slice(1),s).parts:"@"===n?[new U(t,e.slice(1),i.eventContext)]:"?"===n?[new T(t,e.slice(1),s)]:new P(t,e,s).parts}handleTextExpression(t){return new C(t)}},"undefined"!=typeof window&&(window.litHtmlVersions||(window.litHtmlVersions=[])).push("1.4.1");const q=(t,e)=>`${t}--${e}`;let I=!0;void 0===window.ShadyCSS?I=!1:void 0===window.ShadyCSS.prepareTemplateDom&&(console.warn("Incompatible ShadyCSS version detected. Please update to at least @webcomponents/webcomponentsjs@2.0.2 and @webcomponents/shadycss@1.3.1."),I=!1);const j=t=>e=>{const i=q(e.type,t);let n=k.get(i);void 0===n&&(n={stringsArray:new WeakMap,keyString:new Map},k.set(i,n));let r=n.stringsArray.get(e.strings);if(void 0!==r)return r;const a=e.strings.join(s);if(r=n.keyString.get(a),void 0===r){const s=e.getTemplateElement();I&&window.ShadyCSS.prepareTemplateDom(s,t),r=new o(e,s),n.keyString.set(a,r)}return n.stringsArray.set(e.strings,r),r},L=["html","svg"],F=new Set;window.JSCompiler_renameProperty=(t,e)=>t;const H={toAttribute(t,e){switch(e){case Boolean:return t?"":null;case Object:case Array:return null==t?t:JSON.stringify(t)}return t},fromAttribute(t,e){switch(e){case Boolean:return null!==t;case Number:return null===t?null:Number(t);case Object:case Array:return JSON.parse(t)}return t}},B=(t,e)=>e!==t&&(e==e||t==t),$={attribute:!0,type:String,converter:H,reflect:!1,hasChanged:B},z="finalized";class W extends HTMLElement{constructor(){super(),this.initialize()}static get observedAttributes(){this.finalize();const t=[];return this._classProperties.forEach((e,s)=>{const i=this._attributeNameForProperty(s,e);void 0!==i&&(this._attributeToPropertyMap.set(i,s),t.push(i))}),t}static _ensureClassProperties(){if(!this.hasOwnProperty(JSCompiler_renameProperty("_classProperties",this))){this._classProperties=new Map;const t=Object.getPrototypeOf(this)._classProperties;void 0!==t&&t.forEach((t,e)=>this._classProperties.set(e,t))}}static createProperty(t,e=$){if(this._ensureClassProperties(),this._classProperties.set(t,e),e.noAccessor||this.prototype.hasOwnProperty(t))return;const s="symbol"==typeof t?Symbol():`__${t}`,i=this.getPropertyDescriptor(t,s,e);void 0!==i&&Object.defineProperty(this.prototype,t,i)}static getPropertyDescriptor(t,e,s){return{get(){return this[e]},set(i){const n=this[t];this[e]=i,this.requestUpdateInternal(t,n,s)},configurable:!0,enumerable:!0}}static getPropertyOptions(t){return this._classProperties&&this._classProperties.get(t)||$}static finalize(){const t=Object.getPrototypeOf(this);if(t.hasOwnProperty(z)||t.finalize(),this[z]=!0,this._ensureClassProperties(),this._attributeToPropertyMap=new Map,this.hasOwnProperty(JSCompiler_renameProperty("properties",this))){const t=this.properties,e=[...Object.getOwnPropertyNames(t),..."function"==typeof Object.getOwnPropertySymbols?Object.getOwnPropertySymbols(t):[]];for(const s of e)this.createProperty(s,t[s])}}static _attributeNameForProperty(t,e){const s=e.attribute;return!1===s?void 0:"string"==typeof s?s:"string"==typeof t?t.toLowerCase():void 0}static _valueHasChanged(t,e,s=B){return s(t,e)}static _propertyValueFromAttribute(t,e){const s=e.type,i=e.converter||H,n="function"==typeof i?i:i.fromAttribute;return n?n(t,s):t}static _propertyValueToAttribute(t,e){if(void 0===e.reflect)return;const s=e.type,i=e.converter;return(i&&i.toAttribute||H.toAttribute)(t,s)}initialize(){this._updateState=0,this._updatePromise=new Promise(t=>this._enableUpdatingResolver=t),this._changedProperties=new Map,this._saveInstanceProperties(),this.requestUpdateInternal()}_saveInstanceProperties(){this.constructor._classProperties.forEach((t,e)=>{if(this.hasOwnProperty(e)){const t=this[e];delete this[e],this._instanceProperties||(this._instanceProperties=new Map),this._instanceProperties.set(e,t)}})}_applyInstanceProperties(){this._instanceProperties.forEach((t,e)=>this[e]=t),this._instanceProperties=void 0}connectedCallback(){this.enableUpdating()}enableUpdating(){void 0!==this._enableUpdatingResolver&&(this._enableUpdatingResolver(),this._enableUpdatingResolver=void 0)}disconnectedCallback(){}attributeChangedCallback(t,e,s){e!==s&&this._attributeToProperty(t,s)}_propertyToAttribute(t,e,s=$){const i=this.constructor,n=i._attributeNameForProperty(t,s);if(void 0!==n){const t=i._propertyValueToAttribute(e,s);if(void 0===t)return;this._updateState=8|this._updateState,null==t?this.removeAttribute(n):this.setAttribute(n,t),this._updateState=-9&this._updateState}}_attributeToProperty(t,e){if(8&this._updateState)return;const s=this.constructor,i=s._attributeToPropertyMap.get(t);if(void 0!==i){const t=s.getPropertyOptions(i);this._updateState=16|this._updateState,this[i]=s._propertyValueFromAttribute(e,t),this._updateState=-17&this._updateState}}requestUpdateInternal(t,e,s){let i=!0;if(void 0!==t){const n=this.constructor;s=s||n.getPropertyOptions(t),n._valueHasChanged(this[t],e,s.hasChanged)?(this._changedProperties.has(t)||this._changedProperties.set(t,e),!0!==s.reflect||16&this._updateState||(void 0===this._reflectingProperties&&(this._reflectingProperties=new Map),this._reflectingProperties.set(t,s))):i=!1}!this._hasRequestedUpdate&&i&&(this._updatePromise=this._enqueueUpdate())}requestUpdate(t,e){return this.requestUpdateInternal(t,e),this.updateComplete}async _enqueueUpdate(){this._updateState=4|this._updateState;try{await this._updatePromise}catch(t){}const t=this.performUpdate();return null!=t&&await t,!this._hasRequestedUpdate}get _hasRequestedUpdate(){return 4&this._updateState}get hasUpdated(){return 1&this._updateState}performUpdate(){if(!this._hasRequestedUpdate)return;this._instanceProperties&&this._applyInstanceProperties();let t=!1;const e=this._changedProperties;try{t=this.shouldUpdate(e),t?this.update(e):this._markUpdated()}catch(e){throw t=!1,this._markUpdated(),e}t&&(1&this._updateState||(this._updateState=1|this._updateState,this.firstUpdated(e)),this.updated(e))}_markUpdated(){this._changedProperties=new Map,this._updateState=-5&this._updateState}get updateComplete(){return this._getUpdateComplete()}_getUpdateComplete(){return this.getUpdateComplete()}getUpdateComplete(){return this._updatePromise}shouldUpdate(t){return!0}update(t){void 0!==this._reflectingProperties&&this._reflectingProperties.size>0&&(this._reflectingProperties.forEach((t,e)=>this._propertyToAttribute(e,this[e],t)),this._reflectingProperties=void 0),this._markUpdated()}updated(t){}firstUpdated(t){}}W[z]=!0;const D=Element.prototype;D.msMatchesSelector||D.webkitMatchesSelector;const J=window.ShadowRoot&&(void 0===window.ShadyCSS||window.ShadyCSS.nativeShadow)&&"adoptedStyleSheets"in Document.prototype&&"replace"in CSSStyleSheet.prototype,G=Symbol();class K{constructor(t,e){if(e!==G)throw new Error("CSSResult is not constructable. Use `unsafeCSS` or `css` instead.");this.cssText=t}get styleSheet(){return void 0===this._styleSheet&&(J?(this._styleSheet=new CSSStyleSheet,this._styleSheet.replaceSync(this.cssText)):this._styleSheet=null),this._styleSheet}toString(){return this.cssText}}(window.litElementVersions||(window.litElementVersions=[])).push("2.5.1");const Q={};class X extends W{static getStyles(){return this.styles}static _getUniqueStyles(){if(this.hasOwnProperty(JSCompiler_renameProperty("_styles",this)))return;const t=this.getStyles();if(Array.isArray(t)){const e=(t,s)=>t.reduceRight((t,s)=>Array.isArray(s)?e(s,t):(t.add(s),t),s),s=e(t,new Set),i=[];s.forEach(t=>i.unshift(t)),this._styles=i}else this._styles=void 0===t?[]:[t];this._styles=this._styles.map(t=>{if(t instanceof CSSStyleSheet&&!J){const e=Array.prototype.slice.call(t.cssRules).reduce((t,e)=>t+e.cssText,"");return new K(String(e),G)}return t})}initialize(){super.initialize(),this.constructor._getUniqueStyles(),this.renderRoot=this.createRenderRoot(),window.ShadowRoot&&this.renderRoot instanceof window.ShadowRoot&&this.adoptStyles()}createRenderRoot(){return this.attachShadow(this.constructor.shadowRootOptions)}adoptStyles(){const t=this.constructor._styles;0!==t.length&&(void 0===window.ShadyCSS||window.ShadyCSS.nativeShadow?J?this.renderRoot.adoptedStyleSheets=t.map(t=>t instanceof CSSStyleSheet?t:t.styleSheet):this._needsShimAdoptedStyleSheets=!0:window.ShadyCSS.ScopingShim.prepareAdoptedCssText(t.map(t=>t.cssText),this.localName))}connectedCallback(){super.connectedCallback(),this.hasUpdated&&void 0!==window.ShadyCSS&&window.ShadyCSS.styleElement(this)}update(t){const e=this.render();super.update(t),e!==Q&&this.constructor.render(e,this.renderRoot,{scopeName:this.localName,eventContext:this}),this._needsShimAdoptedStyleSheets&&(this._needsShimAdoptedStyleSheets=!1,this.constructor._styles.forEach(t=>{const e=document.createElement("style");e.textContent=t.cssText,this.renderRoot.appendChild(e)}))}render(){return Q}}X.finalized=!0,X.render=(t,s,i)=>{if(!i||"object"!=typeof i||!i.scopeName)throw new Error("The `scopeName` option is required.");const n=i.scopeName,r=M.has(s),o=I&&11===s.nodeType&&!!s.host,a=o&&!F.has(n),l=a?document.createDocumentFragment():s;if(((t,s,i)=>{let n=M.get(s);void 0===n&&(e(s,s.firstChild),M.set(s,n=new C(Object.assign({templateFactory:R},i))),n.appendInto(s)),n.setValue(t),n.commit()})(t,l,Object.assign({templateFactory:j(n)},i)),a){const t=M.get(l);M.delete(l);((t,e,s)=>{F.add(t);const i=s?s.element:document.createElement("template"),n=e.querySelectorAll("style"),{length:r}=n;if(0===r)return void window.ShadyCSS.prepareTemplateStyles(i,t);const o=document.createElement("style");for(let t=0;t<r;t++){const e=n[t];e.parentNode.removeChild(e),o.textContent+=e.textContent}(t=>{L.forEach(e=>{const s=k.get(q(e,t));void 0!==s&&s.keyString.forEach(t=>{const{element:{content:e}}=t,s=new Set;Array.from(e.querySelectorAll("style")).forEach(t=>{s.add(t)}),c(t,s)})})})(t);const a=i.content;s?function(t,e,s=null){const{element:{content:i},parts:n}=t;if(null==s)return void i.appendChild(e);const r=document.createTreeWalker(i,133,null,!1);let o=u(n),a=0,l=-1;for(;r.nextNode();)for(l++,r.currentNode===s&&(a=p(e),s.parentNode.insertBefore(e,s));-1!==o&&n[o].index===l;){if(a>0){for(;-1!==o;)n[o].index+=a,o=u(n,o);return}o=u(n,o)}}(s,o,a.firstChild):a.insertBefore(o,a.firstChild),window.ShadyCSS.prepareTemplateStyles(i,t);const l=a.querySelector("style");if(window.ShadyCSS.nativeShadow&&null!==l)e.insertBefore(l.cloneNode(!0),e.firstChild);else if(s){a.insertBefore(o,a.firstChild);const t=new Set;t.add(o),c(s,t)}})(n,l,t.value instanceof g?t.value.template:void 0),e(s,s.firstChild),s.appendChild(l),M.set(s,t)}!r&&o&&window.ShadyCSS.styleElement(s.host)},X.shadowRootOptions={mode:"open"}})();

package/lib/drugflow-molstar-component-build-0.4.8.js.LICENSE.txt

@@ -0,0 +1,24 @@
+/**
+ * @license
+ * Copyright (c) 2017 The Polymer Project Authors. All rights reserved.
+ * This code may only be used under the BSD style license found at
+ * http://polymer.github.io/LICENSE.txt
+ * The complete set of authors may be found at
+ * http://polymer.github.io/AUTHORS.txt
+ * The complete set of contributors may be found at
+ * http://polymer.github.io/CONTRIBUTORS.txt
+ * Code distributed by Google as part of the polymer project is also
+ * subject to an additional IP rights grant found at
+ * http://polymer.github.io/PATENTS.txt
+ */
+
+/**
+@license
+Copyright (c) 2019 The Polymer Project Authors. All rights reserved.
+This code may only be used under the BSD style license found at
+http://polymer.github.io/LICENSE.txt The complete set of authors may be found at
+http://polymer.github.io/AUTHORS.txt The complete set of contributors may be
+found at http://polymer.github.io/CONTRIBUTORS.txt Code distributed by Google as
+part of the polymer project is also subject to an additional IP rights grant
+found at http://polymer.github.io/PATENTS.txt
+*/

package/lib/helpers.d.ts

@@ -23,7 +23,7 @@ export declare namespace PDBeVolumes {
     function toggle(plugin: PluginContext): void;
 }
 export declare namespace AlphafoldView {
-    function getLociByPLDDT(score: number, contextData: any): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
+    function getLociByPLDDT(score: number, contextData: any): import("Molstar/mol-model/structure/structure/element/loci").Loci;
 }
 export type LigandQueryParam = {
     label_comp_id_list?: any;
@@ -76,8 +76,8 @@ export type QueryParam = {
 };
 export declare namespace QueryHelper {
     function getQueryObject(params: QueryParam[], contextData: any): Expression.Expression;
-    function getInteractivityLoci(params: any, contextData: any): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
-    function getHetLoci(queryExp: Expression.Expression, contextData: any): import("molstar/lib/mol-model/structure/structure/element/loci").Loci;
+    function getInteractivityLoci(params: any, contextData: any): import("Molstar/mol-model/structure/structure/element/loci").Loci;
+    function getHetLoci(queryExp: Expression.Expression, contextData: any): import("Molstar/mol-model/structure/structure/element/loci").Loci;
 }
 export interface ModelInfo {
     hetNames: string[];