@rcsb/rcsb-saguaro-app 6.0.0-development.8 → 6.0.0

package/lib/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.d.ts

@@ -11,9 +11,12 @@ export interface EntryPropertyIntreface {
     description: Array<string>;
     entityToInstance: Map<string, Array<string>>;
     structureDeterminationMethodology: StructureDeterminationMethodology;
+    nonPolymerEntityToInstance: Map<string, Array<string>>;
+    instanceToOperator: Map<string, Map<string, Array<string>>>;
 }
 export declare class MultipleEntryPropertyCollector {
     private readonly rcsbFvQuery;
     collect(requestConfig: QueryEntriesArgs): Promise<Array<EntryPropertyIntreface>>;
     private static getEntryProperties;
+    private static instanceToOperator;
 }

package/lib/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.js

@@ -1,5 +1,8 @@
 import { __awaiter } from "tslib";
 import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
+import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
+var assertDefined = Assertions.assertDefined;
+var assertElementListDefined = Assertions.assertElementListDefined;
 export class MultipleEntryPropertyCollector {
     constructor() {
         this.rcsbFvQuery = rcsbClient;
@@ -11,7 +14,7 @@ export class MultipleEntryPropertyCollector {
         });
     }
     static getEntryProperties(r) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m;
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p;
         return {
             rcsbId: r.rcsb_id,
             entryId: r.rcsb_id,
@@ -22,7 +25,28 @@ export class MultipleEntryPropertyCollector {
             taxNames: (_j = (_h = r.polymer_entities) === null || _h === void 0 ? void 0 : _h.map((entity) => { var _a; return ((_a = entity === null || entity === void 0 ? void 0 : entity.rcsb_entity_source_organism) === null || _a === void 0 ? void 0 : _a.map((so) => (so === null || so === void 0 ? void 0 : so.ncbi_scientific_name))); }).flat().filter((x) => x != null)) !== null && _j !== void 0 ? _j : [],
             entryMolecularWeight: (_k = r.rcsb_entry_info.molecular_weight) !== null && _k !== void 0 ? _k : undefined,
             entityToInstance: (_m = (_l = r.polymer_entities) === null || _l === void 0 ? void 0 : _l.map(pe => { var _a; return [pe === null || pe === void 0 ? void 0 : pe.rcsb_id, (_a = pe === null || pe === void 0 ? void 0 : pe.polymer_entity_instances) === null || _a === void 0 ? void 0 : _a.map(pei => pei === null || pei === void 0 ? void 0 : pei.rcsb_id)]; }).reduce((r, x) => r.set(x[0], x[1]), new Map())) !== null && _m !== void 0 ? _m : new Map(),
-            structureDeterminationMethodology: r.rcsb_entry_info.structure_determination_methodology
+            structureDeterminationMethodology: r.rcsb_entry_info.structure_determination_methodology,
+            nonPolymerEntityToInstance: (_p = (_o = r.nonpolymer_entities) === null || _o === void 0 ? void 0 : _o.map(pe => { var _a; return [pe === null || pe === void 0 ? void 0 : pe.rcsb_id, (_a = pe === null || pe === void 0 ? void 0 : pe.nonpolymer_entity_instances) === null || _a === void 0 ? void 0 : _a.map(pei => pei === null || pei === void 0 ? void 0 : pei.rcsb_id)]; }).reduce((r, x) => r.set(x[0], x[1]), new Map())) !== null && _p !== void 0 ? _p : new Map(),
+            instanceToOperator: MultipleEntryPropertyCollector.instanceToOperator(r)
         };
     }
+    static instanceToOperator(r) {
+        const out = new Map();
+        assertDefined(r.assemblies);
+        r.assemblies.forEach(assembly => {
+            assertDefined(assembly === null || assembly === void 0 ? void 0 : assembly.rcsb_id), assertDefined(assembly === null || assembly === void 0 ? void 0 : assembly.pdbx_struct_assembly_gen);
+            out.set(assembly.rcsb_id, new Map());
+            assembly.pdbx_struct_assembly_gen.forEach(assemblyGen => {
+                assertDefined(assemblyGen === null || assemblyGen === void 0 ? void 0 : assemblyGen.oper_expression), assertElementListDefined(assemblyGen.asym_id_list);
+                const operators = assemblyGen.oper_expression.split(",");
+                const instances = assemblyGen.asym_id_list;
+                instances.forEach(asymId => {
+                    var _a, _b, _c;
+                    const instanceId = `${r.rcsb_id}.${asymId}`;
+                    (_a = out.get(assembly.rcsb_id)) === null || _a === void 0 ? void 0 : _a.set(instanceId, [...operators, ...(_c = (_b = out.get(assembly.rcsb_id)) === null || _b === void 0 ? void 0 : _b.get(instanceId)) !== null && _c !== void 0 ? _c : []]);
+                });
+            });
+        });
+        return out;
+    }
 }

package/lib/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js

@@ -13,7 +13,7 @@ class UiComponent extends React.Component {
 }
 buildSequenceIdentityAlignmentFv("pfv", "5_30", undefined, {
     boardConfig: {
-        selectionChangeCallBack: (selection) => {
+        selectionChangeCallback: (selection) => {
             console.log(selection);
         }
     },

package/lib/RcsbFvExamples/UniprotEntityInstanceFv.js

@@ -1,7 +1,7 @@
 import { buildUniprotEntityInstanceFv } from "../RcsbFvWeb/RcsbFvBuilder";
 buildUniprotEntityInstanceFv("pfv", "P01112", "2UZI_3", "2UZI.C", { boardConfig: {
         trackWidth: 600,
-        elementClickCallBack: (d) => {
+        elementClickCallback: (d) => {
             const div = document.getElementById("myDiv");
             if (!div)
                 return;

package/lib/RcsbFvExamples/UniprotFv.js

@@ -1,7 +1,7 @@
 import { buildMultipleAlignmentSequenceFv } from "../RcsbFvWeb/RcsbFvBuilder";
 buildMultipleAlignmentSequenceFv("pfv", "select", "P01112", {}, {
     boardConfig: {
-        selectionChangeCallBack: (s) => {
+        selectionChangeCallback: (s) => {
             console.log(">", s);
         }
     }

package/lib/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js

@@ -52,7 +52,8 @@ export class SequenceTrackFactory {
                 source: TrackUtils.transformSourceFromTarget(id, c),
                 provenanceName: TrackUtils.getProvenanceConfigFormTarget(id, c).name,
                 provenanceColor: TrackUtils.getProvenanceConfigFormTarget(id, c).color,
-                label: s
+                label: s,
+                name: `RES ${s}`
             };
             sequenceData.push(this.addAuthorResIds(o, {
                 from: config.from,

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts

@@ -83,6 +83,7 @@ export interface RcsbFvModuleInterface extends RcsbFvModulePublicInterface {
     display(): void;
     build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
+    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
 }
 export interface RcsbFvModulePublicInterface<P extends {
     [k: string]: any;
@@ -99,5 +100,4 @@ export interface RcsbFvModulePublicInterface<P extends {
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface<P, S, R, M>>>;
     getFv(): RcsbFv<P, S, R, M>;
     wait(): Promise<void>;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
 }

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.d.ts

@@ -21,6 +21,7 @@ export interface ItemFeaturesInterface {
 }
 export declare class GroupMemberItem extends React.Component<GroupMemberItemInterface, {}> {
     private static readonly SEQUENCE_ALIGNMENT_3D_LINK;
+    private static readonly ICON_PROPS;
     render(): import("react/jsx-runtime").JSX.Element;
 }
 export {};

package/lib/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js

@@ -3,15 +3,21 @@ import React from "react";
 import resource from "../../../RcsbServerConfig/web.resources.json";
 import { GroupProvenanceId, StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
 import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
+import BxCube from "boxicons/svg/solid/bxs-cube.svg";
 const NA = "N/A";
 export class GroupMemberItem extends React.Component {
     render() {
         var _a;
         return (_jsxs("div", { children: [_jsxs("div", { style: { position: "relative", minHeight: 358 }, children: [imageIcon(this.props.item), _jsx("img", { src: memberImgUrl(this.props.item, this.props.groupProvenanceId), alt: "image", style: { width: "100%" } })] }), _jsxs("div", { className: "bg-light border-top p-md-4", children: [hasGroup3D(this.props.groupProvenanceId) ?
-                            _jsxs("div", { children: [_jsxs("strong", { children: [_jsx("i", { className: "bx bxs-cube" }), " Explore in 3D"] }), ": ", _jsx("a", { href: alignment1d3dUrl(this.props.groupId, this.props.searchQuery), children: GroupMemberItem.SEQUENCE_ALIGNMENT_3D_LINK })] }) : null, _jsxs("div", { children: [_jsx("strong", { children: memberSummaryUrlText(this.props.item, this.props.groupProvenanceId) }), _jsx("span", { children: " - " }), _jsx("a", { href: memberSummaryUrl(this.props.item, this.props.groupProvenanceId), children: "Summary" }), _jsx("span", { children: " | " }), _jsx("a", { href: member3DViewUrl(this.props.item, this.props.groupProvenanceId), children: "Structure" })] }), _jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.name, children: [_jsx("strong", { children: "Name: " }), this.props.item.name] }), _jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [_jsx("strong", { children: "Organism: " }), this.props.item.taxNames.join(", ")] }), _jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.experimentalMethod, children: [_jsx("strong", { children: "Experimental Method: " }), (_a = this.props.item.experimentalMethod) !== null && _a !== void 0 ? _a : NA] }), (_jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [_jsx("strong", { children: "Resolution: " }), this.props.item.resolution ? `${this.props.item.resolution} Å` : NA] })), this.props.item.molecularWeight ? (_jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [_jsx("strong", { children: "Molecular Weight: " }), `${this.props.item.molecularWeight} kDa`] })) : null] })] }));
+                            _jsxs("div", { children: [_jsx(BxCube, Object.assign({}, GroupMemberItem.ICON_PROPS)), " ", _jsx("strong", { children: "Explore in 3D" }), ": ", _jsx("a", { href: alignment1d3dUrl(this.props.groupId, this.props.searchQuery), children: GroupMemberItem.SEQUENCE_ALIGNMENT_3D_LINK })] }) : null, _jsxs("div", { children: [_jsx("strong", { children: memberSummaryUrlText(this.props.item, this.props.groupProvenanceId) }), _jsx("span", { children: " - " }), _jsx("a", { href: memberSummaryUrl(this.props.item, this.props.groupProvenanceId), children: "Summary" }), _jsx("span", { children: " | " }), _jsx("a", { href: member3DViewUrl(this.props.item, this.props.groupProvenanceId), children: "Structure" })] }), _jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.name, children: [_jsx("strong", { children: "Name: " }), this.props.item.name] }), _jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [_jsx("strong", { children: "Organism: " }), this.props.item.taxNames.join(", ")] }), _jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.experimentalMethod, children: [_jsx("strong", { children: "Experimental Method: " }), (_a = this.props.item.experimentalMethod) !== null && _a !== void 0 ? _a : NA] }), (_jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [_jsx("strong", { children: "Resolution: " }), this.props.item.resolution ? `${this.props.item.resolution} Å` : NA] })), this.props.item.molecularWeight ? (_jsxs("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [_jsx("strong", { children: "Molecular Weight: " }), `${this.props.item.molecularWeight} kDa`] })) : null] })] }));
     }
 }
 GroupMemberItem.SEQUENCE_ALIGNMENT_3D_LINK = "Sequence Alignments";
+GroupMemberItem.ICON_PROPS = {
+    width: 15,
+    height: 15,
+    viewBox: "0 0 24 24"
+};
 function memberImgUrl(ei, groupProvenanceId) {
     if (groupProvenanceId === GroupProvenanceId.ProvenanceMatchingDepositGroupId)
         return resource.rcsb_cdn.url + ei.entryId.toLowerCase().substring(1, 3) + "/" + ei.entryId.toLowerCase() + "/" + ei.entryId.toLowerCase() + "_model-1.jpeg";

package/lib/RcsbQueries/Yosemite/QueryMultipleEntriesProperties.graphql

@@ -17,6 +17,19 @@ query multiple_entries_properties($entry_ids: [String!]!){
                 rcsb_id
             }
         }
+        nonpolymer_entities {
+            rcsb_id
+            rcsb_nonpolymer_entity_container_identifiers {
+                entity_id
+                rcsb_id
+            }
+            nonpolymer_entity_instances {
+                rcsb_nonpolymer_entity_instance_container_identifiers {
+                    asym_id
+                }
+                rcsb_id
+            }
+        }
         rcsb_entry_info{
             experimental_method
             resolution_combined
@@ -26,5 +39,12 @@ query multiple_entries_properties($entry_ids: [String!]!){
         struct {
             title
         }
+        assemblies {
+            rcsb_id
+            pdbx_struct_assembly_gen {
+                oper_expression
+                asym_id_list
+            }
+        }
     }
 }

package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js

@@ -67,7 +67,7 @@ export function groupExternalTrackBuilder() {
         const logoRowData = querySequenceLogo.map((s, n) => ({
             begin: n + 1,
             label: s.mode(),
-            description: [s.frequency().filter(s => (s.value >= 0.01)).map(s => (s.symbol.replace("-", "gap") + ": " + Math.trunc(s.value * 100) / 100)).join(", ")]
+            description: [s.frequency().filter(s => (s.value >= 0.01)).slice(0, 14).map(s => (s.symbol.replace("-", "gap") + ": " + Math.trunc(s.value * 100) / 100)).join(", ")]
         }));
         variationRowData = [{
                 trackId: "annotationTrack_ALIGNMENT_FREQ",

package/lib/commonjs/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.d.ts

@@ -11,9 +11,12 @@ export interface EntryPropertyIntreface {
     description: Array<string>;
     entityToInstance: Map<string, Array<string>>;
     structureDeterminationMethodology: StructureDeterminationMethodology;
+    nonPolymerEntityToInstance: Map<string, Array<string>>;
+    instanceToOperator: Map<string, Map<string, Array<string>>>;
 }
 export declare class MultipleEntryPropertyCollector {
     private readonly rcsbFvQuery;
     collect(requestConfig: QueryEntriesArgs): Promise<Array<EntryPropertyIntreface>>;
     private static getEntryProperties;
+    private static instanceToOperator;
 }

package/lib/commonjs/RcsbCollectTools/DataCollectors/MultipleEntryPropertyCollector.js

@@ -3,6 +3,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MultipleEntryPropertyCollector = void 0;
 const tslib_1 = require("tslib");
 const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
+const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
+var assertDefined = Assertions_1.Assertions.assertDefined;
+var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
 class MultipleEntryPropertyCollector {
     constructor() {
         this.rcsbFvQuery = RcsbClient_1.rcsbClient;
@@ -14,7 +17,7 @@ class MultipleEntryPropertyCollector {
         });
     }
     static getEntryProperties(r) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m;
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p;
         return {
             rcsbId: r.rcsb_id,
             entryId: r.rcsb_id,
@@ -25,8 +28,29 @@ class MultipleEntryPropertyCollector {
             taxNames: (_j = (_h = r.polymer_entities) === null || _h === void 0 ? void 0 : _h.map((entity) => { var _a; return ((_a = entity === null || entity === void 0 ? void 0 : entity.rcsb_entity_source_organism) === null || _a === void 0 ? void 0 : _a.map((so) => (so === null || so === void 0 ? void 0 : so.ncbi_scientific_name))); }).flat().filter((x) => x != null)) !== null && _j !== void 0 ? _j : [],
             entryMolecularWeight: (_k = r.rcsb_entry_info.molecular_weight) !== null && _k !== void 0 ? _k : undefined,
             entityToInstance: (_m = (_l = r.polymer_entities) === null || _l === void 0 ? void 0 : _l.map(pe => { var _a; return [pe === null || pe === void 0 ? void 0 : pe.rcsb_id, (_a = pe === null || pe === void 0 ? void 0 : pe.polymer_entity_instances) === null || _a === void 0 ? void 0 : _a.map(pei => pei === null || pei === void 0 ? void 0 : pei.rcsb_id)]; }).reduce((r, x) => r.set(x[0], x[1]), new Map())) !== null && _m !== void 0 ? _m : new Map(),
-            structureDeterminationMethodology: r.rcsb_entry_info.structure_determination_methodology
+            structureDeterminationMethodology: r.rcsb_entry_info.structure_determination_methodology,
+            nonPolymerEntityToInstance: (_p = (_o = r.nonpolymer_entities) === null || _o === void 0 ? void 0 : _o.map(pe => { var _a; return [pe === null || pe === void 0 ? void 0 : pe.rcsb_id, (_a = pe === null || pe === void 0 ? void 0 : pe.nonpolymer_entity_instances) === null || _a === void 0 ? void 0 : _a.map(pei => pei === null || pei === void 0 ? void 0 : pei.rcsb_id)]; }).reduce((r, x) => r.set(x[0], x[1]), new Map())) !== null && _p !== void 0 ? _p : new Map(),
+            instanceToOperator: MultipleEntryPropertyCollector.instanceToOperator(r)
         };
     }
+    static instanceToOperator(r) {
+        const out = new Map();
+        assertDefined(r.assemblies);
+        r.assemblies.forEach(assembly => {
+            assertDefined(assembly === null || assembly === void 0 ? void 0 : assembly.rcsb_id), assertDefined(assembly === null || assembly === void 0 ? void 0 : assembly.pdbx_struct_assembly_gen);
+            out.set(assembly.rcsb_id, new Map());
+            assembly.pdbx_struct_assembly_gen.forEach(assemblyGen => {
+                assertDefined(assemblyGen === null || assemblyGen === void 0 ? void 0 : assemblyGen.oper_expression), assertElementListDefined(assemblyGen.asym_id_list);
+                const operators = assemblyGen.oper_expression.split(",");
+                const instances = assemblyGen.asym_id_list;
+                instances.forEach(asymId => {
+                    var _a, _b, _c;
+                    const instanceId = `${r.rcsb_id}.${asymId}`;
+                    (_a = out.get(assembly.rcsb_id)) === null || _a === void 0 ? void 0 : _a.set(instanceId, [...operators, ...(_c = (_b = out.get(assembly.rcsb_id)) === null || _b === void 0 ? void 0 : _b.get(instanceId)) !== null && _c !== void 0 ? _c : []]);
+                });
+            });
+        });
+        return out;
+    }
 }
 exports.MultipleEntryPropertyCollector = MultipleEntryPropertyCollector;

package/lib/commonjs/RcsbFvExamples/SequenceIdentityGroupAlignmentFv.js

@@ -16,7 +16,7 @@ class UiComponent extends react_1.default.Component {
 }
 (0, RcsbFvBuilder_1.buildSequenceIdentityAlignmentFv)("pfv", "5_30", undefined, {
     boardConfig: {
-        selectionChangeCallBack: (selection) => {
+        selectionChangeCallback: (selection) => {
             console.log(selection);
         }
     },

package/lib/commonjs/RcsbFvExamples/UniprotEntityInstanceFv.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const RcsbFvBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder");
 (0, RcsbFvBuilder_1.buildUniprotEntityInstanceFv)("pfv", "P01112", "2UZI_3", "2UZI.C", { boardConfig: {
         trackWidth: 600,
-        elementClickCallBack: (d) => {
+        elementClickCallback: (d) => {
             const div = document.getElementById("myDiv");
             if (!div)
                 return;

package/lib/commonjs/RcsbFvExamples/UniprotFv.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const RcsbFvBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder");
 (0, RcsbFvBuilder_1.buildMultipleAlignmentSequenceFv)("pfv", "select", "P01112", {}, {
     boardConfig: {
-        selectionChangeCallBack: (s) => {
+        selectionChangeCallback: (s) => {
             console.log(">", s);
         }
     }

package/lib/commonjs/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory.js

@@ -55,7 +55,8 @@ class SequenceTrackFactory {
                 source: TrackUtils_1.TrackUtils.transformSourceFromTarget(id, c),
                 provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(id, c).name,
                 provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(id, c).color,
-                label: s
+                label: s,
+                name: `RES ${s}`
             };
             sequenceData.push(this.addAuthorResIds(o, {
                 from: config.from,

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts

@@ -83,6 +83,7 @@ export interface RcsbFvModuleInterface extends RcsbFvModulePublicInterface {
     display(): void;
     build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
+    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
 }
 export interface RcsbFvModulePublicInterface<P extends {
     [k: string]: any;
@@ -99,5 +100,4 @@ export interface RcsbFvModulePublicInterface<P extends {
     getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface<P, S, R, M>>>;
     getFv(): RcsbFv<P, S, R, M>;
     wait(): Promise<void>;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
 }

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.d.ts

@@ -21,6 +21,7 @@ export interface ItemFeaturesInterface {
 }
 export declare class GroupMemberItem extends React.Component<GroupMemberItemInterface, {}> {
     private static readonly SEQUENCE_ALIGNMENT_3D_LINK;
+    private static readonly ICON_PROPS;
     render(): import("react/jsx-runtime").JSX.Element;
 }
 export {};

package/lib/commonjs/RcsbGroupWeb/RcsbGroupView/RcsbGroupMembers/GroupMemberItem.js

@@ -7,16 +7,22 @@ const react_1 = tslib_1.__importDefault(require("react"));
 const web_resources_json_1 = tslib_1.__importDefault(require("../../../RcsbServerConfig/web.resources.json"));
 const DwEnums_1 = require("@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums");
 const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
+const bxs_cube_svg_1 = tslib_1.__importDefault(require("boxicons/svg/solid/bxs-cube.svg"));
 const NA = "N/A";
 class GroupMemberItem extends react_1.default.Component {
     render() {
         var _a;
         return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: { position: "relative", minHeight: 358 }, children: [imageIcon(this.props.item), (0, jsx_runtime_1.jsx)("img", { src: memberImgUrl(this.props.item, this.props.groupProvenanceId), alt: "image", style: { width: "100%" } })] }), (0, jsx_runtime_1.jsxs)("div", { className: "bg-light border-top p-md-4", children: [hasGroup3D(this.props.groupProvenanceId) ?
-                            (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("strong", { children: [(0, jsx_runtime_1.jsx)("i", { className: "bx bxs-cube" }), " Explore in 3D"] }), ": ", (0, jsx_runtime_1.jsx)("a", { href: alignment1d3dUrl(this.props.groupId, this.props.searchQuery), children: GroupMemberItem.SEQUENCE_ALIGNMENT_3D_LINK })] }) : null, (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("strong", { children: memberSummaryUrlText(this.props.item, this.props.groupProvenanceId) }), (0, jsx_runtime_1.jsx)("span", { children: " - " }), (0, jsx_runtime_1.jsx)("a", { href: memberSummaryUrl(this.props.item, this.props.groupProvenanceId), children: "Summary" }), (0, jsx_runtime_1.jsx)("span", { children: " | " }), (0, jsx_runtime_1.jsx)("a", { href: member3DViewUrl(this.props.item, this.props.groupProvenanceId), children: "Structure" })] }), (0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.name, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Name: " }), this.props.item.name] }), (0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Organism: " }), this.props.item.taxNames.join(", ")] }), (0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.experimentalMethod, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Experimental Method: " }), (_a = this.props.item.experimentalMethod) !== null && _a !== void 0 ? _a : NA] }), ((0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Resolution: " }), this.props.item.resolution ? `${this.props.item.resolution} Å` : NA] })), this.props.item.molecularWeight ? ((0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Molecular Weight: " }), `${this.props.item.molecularWeight} kDa`] })) : null] })] }));
+                            (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(bxs_cube_svg_1.default, Object.assign({}, GroupMemberItem.ICON_PROPS)), " ", (0, jsx_runtime_1.jsx)("strong", { children: "Explore in 3D" }), ": ", (0, jsx_runtime_1.jsx)("a", { href: alignment1d3dUrl(this.props.groupId, this.props.searchQuery), children: GroupMemberItem.SEQUENCE_ALIGNMENT_3D_LINK })] }) : null, (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("strong", { children: memberSummaryUrlText(this.props.item, this.props.groupProvenanceId) }), (0, jsx_runtime_1.jsx)("span", { children: " - " }), (0, jsx_runtime_1.jsx)("a", { href: memberSummaryUrl(this.props.item, this.props.groupProvenanceId), children: "Summary" }), (0, jsx_runtime_1.jsx)("span", { children: " | " }), (0, jsx_runtime_1.jsx)("a", { href: member3DViewUrl(this.props.item, this.props.groupProvenanceId), children: "Structure" })] }), (0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.name, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Name: " }), this.props.item.name] }), (0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Organism: " }), this.props.item.taxNames.join(", ")] }), (0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, title: this.props.item.experimentalMethod, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Experimental Method: " }), (_a = this.props.item.experimentalMethod) !== null && _a !== void 0 ? _a : NA] }), ((0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Resolution: " }), this.props.item.resolution ? `${this.props.item.resolution} Å` : NA] })), this.props.item.molecularWeight ? ((0, jsx_runtime_1.jsxs)("div", { style: { textOverflow: "ellipsis", whiteSpace: "nowrap", overflow: "hidden" }, children: [(0, jsx_runtime_1.jsx)("strong", { children: "Molecular Weight: " }), `${this.props.item.molecularWeight} kDa`] })) : null] })] }));
     }
 }
 exports.GroupMemberItem = GroupMemberItem;
 GroupMemberItem.SEQUENCE_ALIGNMENT_3D_LINK = "Sequence Alignments";
+GroupMemberItem.ICON_PROPS = {
+    width: 15,
+    height: 15,
+    viewBox: "0 0 24 24"
+};
 function memberImgUrl(ei, groupProvenanceId) {
     if (groupProvenanceId === DwEnums_1.GroupProvenanceId.ProvenanceMatchingDepositGroupId)
         return web_resources_json_1.default.rcsb_cdn.url + ei.entryId.toLowerCase().substring(1, 3) + "/" + ei.entryId.toLowerCase() + "/" + ei.entryId.toLowerCase() + "_model-1.jpeg";

package/lib/commonjs/RcsbQueries/Yosemite/QueryMultipleEntriesProperties.graphql

@@ -17,6 +17,19 @@ query multiple_entries_properties($entry_ids: [String!]!){
                 rcsb_id
             }
         }
+        nonpolymer_entities {
+            rcsb_id
+            rcsb_nonpolymer_entity_container_identifiers {
+                entity_id
+                rcsb_id
+            }
+            nonpolymer_entity_instances {
+                rcsb_nonpolymer_entity_instance_container_identifiers {
+                    asym_id
+                }
+                rcsb_id
+            }
+        }
         rcsb_entry_info{
             experimental_method
             resolution_combined
@@ -26,5 +39,12 @@ query multiple_entries_properties($entry_ids: [String!]!){
         struct {
             title
         }
+        assemblies {
+            rcsb_id
+            pdbx_struct_assembly_gen {
+                oper_expression
+                asym_id_list
+            }
+        }
     }
 }

package/lib/commonjs/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js

@@ -70,7 +70,7 @@ function groupExternalTrackBuilder() {
         const logoRowData = querySequenceLogo.map((s, n) => ({
             begin: n + 1,
             label: s.mode(),
-            description: [s.frequency().filter(s => (s.value >= 0.01)).map(s => (s.symbol.replace("-", "gap") + ": " + Math.trunc(s.value * 100) / 100)).join(", ")]
+            description: [s.frequency().filter(s => (s.value >= 0.01)).slice(0, 14).map(s => (s.symbol.replace("-", "gap") + ": " + Math.trunc(s.value * 100) / 100)).join(", ")]
         }));
         variationRowData = [{
                 trackId: "annotationTrack_ALIGNMENT_FREQ",

package/lib/commonjs/scss/bootstrap-group-display.module.scss

@@ -5,7 +5,6 @@
 
     @include styleVars.bootstrapRoot;
     @include meta.load-css("bootstrap/dist/css/bootstrap.min");
-    @include meta.load-css("~boxicons/css/boxicons.min");
 
     a {
         color: #337ab7;

package/lib/scss/bootstrap-group-display.module.scss

@@ -5,7 +5,6 @@
 
     @include styleVars.bootstrapRoot;
     @include meta.load-css("bootstrap/dist/css/bootstrap.min");
-    @include meta.load-css("~boxicons/css/boxicons.min");
 
     a {
         color: #337ab7;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-app",
-  "version": "6.0.0-development.8",
+  "version": "6.0.0",
   "description": "RCSB 1D Saguaro Web App",
   "main": "build/app.js",
   "files": [
@@ -24,10 +24,10 @@
     "build-tsc": "tsc",
     "build-commonjs": "tsc --build tsconfig.commonjs.json",
     "clean": "del-cli lib && del-cli build",
-    "buildDoc": "typedoc --excludeExternals --externalPattern \"**/node_modules/**\" --plugin typedoc-plugin-missing-exports ./src/app.ts && sed -i '' '/---/d' docs/index.html",
+    "buildDoc": "typedoc --excludeExternals --externalPattern \"**/node_modules/**\" --plugin typedoc-plugin-missing-exports  --plugin typedoc-theme-hierarchy --theme hierarchy --entryPointStrategy expand ./src && sed -i '' '/---/d' docs/index.html",
     "cpExamples": "ncp examples docs/examples",
     "buildAllDoc": "npm run buildDoc && npm run cpExamples",
-    "publishApp": "npm publish --tag development",
+    "publishApp": "npm publish",
     "test": "echo \"Error: no test specified\" && exit 1"
   },
   "repository": {
@@ -54,6 +54,7 @@
     "@babel/core": "^7.23.2",
     "@babel/plugin-proposal-class-properties": "^7.17.12",
     "@babel/preset-env": "^7.23.2",
+    "@svgr/webpack": "^8.1.0",
     "@types/lodash": "^4.14.200",
     "@types/lodash.range": "^3.2.8",
     "@types/object-hash": "^3.0.5",
@@ -82,6 +83,7 @@
     "ts-node": "^10.9.1",
     "typedoc": "^0.25.3",
     "typedoc-plugin-missing-exports": "^2.1.0",
+    "typedoc-theme-hierarchy": "^4.1.2",
     "typescript": "^5.2.2",
     "uniqid": "^5.4.0",
     "webpack": "^5.89.0",
@@ -95,13 +97,12 @@
     "ideogram": "^1.44.1",
     "react-bootstrap": "^2.8.0",
     "react-select": "^5.7.7",
-    "resolve-url-loader": "^5.0.0",
     "rxjs": "^7.8.1",
     "string-to-color": "^2.2.2"
   },
   "peerDependencies": {
     "@rcsb/rcsb-api-tools": "^4.1.13",
-    "@rcsb/rcsb-saguaro": "^3.0.0-development.5",
+    "@rcsb/rcsb-saguaro": "^3.0.3",
     "boxicons": "^2.1.0",
     "react": "^18.1.0",
     "react-dom": "^18.1.0"