@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

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

@@ -1,30 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.GroupPropertyCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-class GroupPropertyCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const result = yield this.rcsbFvQuery.requestGroupInfo(requestConfig);
-                return GroupPropertyCollector.getGroupProperties(result);
-            }
-            catch (error) {
-                console.log(error);
-                throw error;
-            }
-        });
-    }
-    static getGroupProperties(r) {
-        var _a, _b;
-        return {
-            groupName: (_a = r.rcsb_group_info.group_name) !== null && _a !== void 0 ? _a : "NA",
-            groupDescription: (_b = r.rcsb_group_info.group_description) !== null && _b !== void 0 ? _b : "NA"
-        };
-    }
-}
-exports.GroupPropertyCollector = GroupPropertyCollector;

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

@@ -1,12 +0,0 @@
-import { QueryInterfacesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-export interface InterfaceInstanceInterface {
-    rcsbId: string;
-    assemblyId: string;
-    interfaceId: string;
-    asymIds: [string, string];
-    operatorIds: [Array<Array<string>>, Array<Array<string>>];
-}
-export declare class InterfaceInstanceCollector {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryInterfacesArgs): Promise<Array<InterfaceInstanceInterface>>;
-}

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

@@ -1,45 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.InterfaceInstanceCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-var assertDefined = Assertions_1.Assertions.assertDefined;
-var assertElementMatrixDefined = Assertions_1.Assertions.assertElementMatrixDefined;
-class InterfaceInstanceCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const result = yield this.rcsbFvQuery.requestInterfaceInstances(requestConfig);
-                return result.map(r => parseInterfaceInstances(r));
-            }
-            catch (error) {
-                console.log(error);
-                throw error;
-            }
-        });
-    }
-}
-exports.InterfaceInstanceCollector = InterfaceInstanceCollector;
-function parseInterfaceInstances(coreInterface) {
-    var _a, _b, _c, _d;
-    assertElementMatrixDefined(coreInterface.rcsb_interface_operator[0]);
-    assertElementMatrixDefined(coreInterface.rcsb_interface_operator[1]);
-    assertElementListDefined(coreInterface.rcsb_interface_partner);
-    assertDefined((_a = coreInterface.rcsb_interface_partner[0].interface_partner_identifier) === null || _a === void 0 ? void 0 : _a.asym_id);
-    assertDefined((_b = coreInterface.rcsb_interface_partner[1].interface_partner_identifier) === null || _b === void 0 ? void 0 : _b.asym_id);
-    return {
-        rcsbId: coreInterface.rcsb_interface_container_identifiers.rcsb_id,
-        assemblyId: coreInterface.rcsb_interface_container_identifiers.assembly_id,
-        interfaceId: coreInterface.rcsb_interface_container_identifiers.interface_id,
-        asymIds: [
-            (_c = coreInterface.rcsb_interface_partner[0].interface_partner_identifier) === null || _c === void 0 ? void 0 : _c.asym_id,
-            (_d = coreInterface.rcsb_interface_partner[1].interface_partner_identifier) === null || _d === void 0 ? void 0 : _d.asym_id
-        ],
-        operatorIds: [coreInterface.rcsb_interface_operator[0], coreInterface.rcsb_interface_operator[1]]
-    };
-}

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

@@ -1,8 +0,0 @@
-import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
-import { MultipleDocumentPropertyCollectorInterface } from "./DataCollectorInterface";
-export declare class MultipleEntityInstancesCollector implements MultipleDocumentPropertyCollectorInterface<"entity_ids", PolymerEntityInstanceInterface> {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<PolymerEntityInstanceInterface>>;
-    private static getEntityInstances;
-}

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

@@ -1,36 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultipleEntityInstancesCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const PolymerEntityInstancesCollector_1 = require("./PolymerEntityInstancesCollector");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-class MultipleEntityInstancesCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const result = yield this.rcsbFvQuery.requestMultipleEntityInstances(requestConfig);
-                return MultipleEntityInstancesCollector.getEntityInstances(result);
-            }
-            catch (error) {
-                console.log(error);
-                throw error;
-            }
-        });
-    }
-    static getEntityInstances(polymer_entities) {
-        const out = new Array();
-        polymer_entities === null || polymer_entities === void 0 ? void 0 : polymer_entities.forEach(entity => {
-            if (Array.isArray(entity.polymer_entity_instances)) {
-                assertElementListDefined(entity.polymer_entity_instances);
-                PolymerEntityInstancesCollector_1.PolymerEntityInstancesCollector.parsePolymerEntityInstances(entity.polymer_entity_instances, out);
-            }
-        });
-        return out;
-    }
-}
-exports.MultipleEntityInstancesCollector = MultipleEntityInstancesCollector;

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

@@ -1,23 +0,0 @@
-import { QueryEntriesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-export interface EntryPropertyInterface {
-    rcsbId: string;
-    entryId: string;
-    experimentalMethod: string;
-    resolution?: number;
-    name: string;
-    taxNames: Array<string>;
-    entryMolecularWeight?: number;
-    description: Array<string>;
-    entityToInstance: Map<string, Array<string>>;
-    structureDeterminationMethodology: StructureDeterminationMethodology;
-    nonPolymerEntityToInstance: Map<string, Array<string>>;
-    instanceToOperator: Map<string, Map<string, Array<string>>>;
-    entityToPrd: Map<string, string>;
-}
-export declare class MultipleEntryPropertyCollector {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryEntriesArgs): Promise<Array<EntryPropertyInterface>>;
-    private static getEntryProperties;
-    private static instanceToOperator;
-}

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

@@ -1,57 +0,0 @@
-"use strict";
-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;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const result = yield this.rcsbFvQuery.requestMultipleEntriesProperties(requestConfig);
-            return result.map(r => MultipleEntryPropertyCollector.getEntryProperties(r));
-        });
-    }
-    static getEntryProperties(r) {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r;
-        return {
-            rcsbId: r.rcsb_id,
-            entryId: r.rcsb_id,
-            experimentalMethod: (_a = r.rcsb_entry_info.experimental_method) !== null && _a !== void 0 ? _a : "NA",
-            resolution: (_c = (_b = r.rcsb_entry_info.resolution_combined) === null || _b === void 0 ? void 0 : _b[0]) !== null && _c !== void 0 ? _c : undefined,
-            name: (_e = (_d = r.struct) === null || _d === void 0 ? void 0 : _d.title) !== null && _e !== void 0 ? _e : "NA",
-            description: (_g = (_f = r.pdbx_molecule_features) === null || _f === void 0 ? void 0 : _f.map(mf => mf === null || mf === void 0 ? void 0 : mf.details).filter((x) => x != null)) !== null && _g !== void 0 ? _g : [],
-            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,
-            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),
-            entityToPrd: (_r = (_q = r.polymer_entities) === null || _q === void 0 ? void 0 : _q.filter((pe) => typeof pe != "undefined").map(pe => { var _a, _b, _c; return [(_a = pe === null || pe === void 0 ? void 0 : pe.rcsb_id) !== null && _a !== void 0 ? _a : "", (_c = (_b = pe === null || pe === void 0 ? void 0 : pe.entity_poly) === null || _b === void 0 ? void 0 : _b.rcsb_prd_id) !== null && _c !== void 0 ? _c : ""]; }).reduce((map, pair) => map.set(pair[0], pair[1]), new Map())) !== null && _r !== void 0 ? _r : new Map()
-        };
-    }
-    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/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector.d.ts

@@ -1,11 +0,0 @@
-import { MultipleDocumentPropertyCollectorInterface } from "./DataCollectorInterface";
-export interface InstanceSequenceInterface {
-    rcsbId: string;
-    sequence: string;
-}
-export declare class MultipleInstanceSequencesCollector implements MultipleDocumentPropertyCollectorInterface<"instance_ids", InstanceSequenceInterface> {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: {
-        instance_ids: string[];
-    }): Promise<InstanceSequenceInterface[]>;
-}

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

@@ -1,26 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultipleInstanceSequencesCollector = 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;
-class MultipleInstanceSequencesCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const result = yield this.rcsbFvQuery.requestMultipleInstanceSequences(requestConfig);
-            return result.map(r => {
-                var _a, _b, _c, _d;
-                assertDefined(r.rcsb_id), assertDefined((_b = (_a = r.polymer_entity) === null || _a === void 0 ? void 0 : _a.entity_poly) === null || _b === void 0 ? void 0 : _b.pdbx_seq_one_letter_code_can);
-                return {
-                    rcsbId: r.rcsb_id,
-                    sequence: (_d = (_c = r.polymer_entity) === null || _c === void 0 ? void 0 : _c.entity_poly) === null || _d === void 0 ? void 0 : _d.pdbx_seq_one_letter_code_can
-                };
-            });
-        });
-    }
-}
-exports.MultipleInstanceSequencesCollector = MultipleInstanceSequencesCollector;

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

@@ -1,12 +0,0 @@
-import { QueryPolymer_EntitiesArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { PolymerEntityInstanceInterface } from "./PolymerEntityInstancesCollector";
-export interface PolymerEntityInterface {
-    rcsbId: string;
-    entityId: string;
-    entryId: string;
-    instances: PolymerEntityInstanceInterface[];
-}
-export declare class MultiplePolymerEntityCollector {
-    private readonly multipleEntityInstanceCollector;
-    collect(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<PolymerEntityInterface>>;
-}

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

@@ -1,30 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultiplePolymerEntityCollector = void 0;
-const tslib_1 = require("tslib");
-const MultipleEntityInstancesCollector_1 = require("./MultipleEntityInstancesCollector");
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
-class MultiplePolymerEntityCollector {
-    constructor() {
-        this.multipleEntityInstanceCollector = new MultipleEntityInstancesCollector_1.MultipleEntityInstancesCollector();
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const results = yield this.multipleEntityInstanceCollector.collect(requestConfig);
-            const map = new Map();
-            results.forEach(r => {
-                var _a;
-                if (!map.has(`${r.entryId}${TagDelimiter_1.TagDelimiter.entity}${r.entityId}`))
-                    map.set(`${r.entryId}${TagDelimiter_1.TagDelimiter.entity}${r.entityId}`, []);
-                (_a = map.get(`${r.entryId}${TagDelimiter_1.TagDelimiter.entity}${r.entityId}`)) === null || _a === void 0 ? void 0 : _a.push(r);
-            });
-            return Array.from(map.entries()).map(([k, v]) => ({
-                rcsbId: v[0].rcsbId,
-                entityId: v[0].entityId,
-                entryId: v[0].entryId,
-                instances: v
-            }));
-        });
-    }
-}
-exports.MultiplePolymerEntityCollector = MultiplePolymerEntityCollector;

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

@@ -1,5 +0,0 @@
-export declare class PolymerEntityChromosomeCollector {
-    private readonly rcsbFvQuery;
-    collect(entityIds: Array<string>): Promise<Map<string, Array<string>>>;
-    private entityChromosomes;
-}

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

@@ -1,43 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PolymerEntityChromosomeCollector = void 0;
-const tslib_1 = require("tslib");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-class PolymerEntityChromosomeCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(entityIds) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const entityMap = new Map();
-            const result = yield Promise.all(entityIds.map(e => {
-                return this.entityChromosomes(e);
-            }));
-            result.forEach((alignment, n) => {
-                var _a;
-                (_a = alignment.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
-                    var _a, _b, _c;
-                    if (((_b = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0) {
-                        if (!entityMap.has(entityIds[n]))
-                            entityMap.set(entityIds[n], new Array());
-                        if (ta === null || ta === void 0 ? void 0 : ta.target_id)
-                            (_c = entityMap.get(entityIds[n])) === null || _c === void 0 ? void 0 : _c.push(ta.target_id);
-                    }
-                });
-            });
-            return entityMap;
-        });
-    }
-    entityChromosomes(entityId) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            const request = {
-                from: GqlTypes_1.SequenceReference.PdbEntity,
-                to: GqlTypes_1.SequenceReference.NcbiGenome,
-                queryId: entityId
-            };
-            return yield this.rcsbFvQuery.requestAlignment(request);
-        });
-    }
-}
-exports.PolymerEntityChromosomeCollector = PolymerEntityChromosomeCollector;

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

@@ -1,24 +0,0 @@
-import { CorePolymerEntityInstance, QueryEntryArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { StructureDeterminationMethodology } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-export interface PolymerEntityInstanceInterface {
-    rcsbId: string;
-    entityId: string;
-    entryId: string;
-    asymId: string;
-    authId: string;
-    authResId: Array<string>;
-    name: string;
-    taxNames: Array<string>;
-    experimentalMethod: string;
-    resolution?: number;
-    sequenceLength: number;
-    entityMolecularWeight?: number;
-    entryMolecularWeight?: number;
-    structureDeterminationMethodology: StructureDeterminationMethodology;
-}
-export declare class PolymerEntityInstancesCollector {
-    private readonly rcsbFvQuery;
-    collect(requestConfig: QueryEntryArgs): Promise<Array<PolymerEntityInstanceInterface>>;
-    private static getEntryInstances;
-    static parsePolymerEntityInstances(polymerEntityInstances: Array<CorePolymerEntityInstance>, out: Array<PolymerEntityInstanceInterface>): void;
-}

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

@@ -1,71 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PolymerEntityInstancesCollector = void 0;
-const tslib_1 = require("tslib");
-const RcsbClient_1 = require("../../RcsbGraphQL/RcsbClient");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertElementListDefined = Assertions_1.Assertions.assertElementListDefined;
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class PolymerEntityInstancesCollector {
-    constructor() {
-        this.rcsbFvQuery = RcsbClient_1.rcsbClient;
-    }
-    collect(requestConfig) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            try {
-                const result = yield this.rcsbFvQuery.requestEntityInstances(requestConfig);
-                return PolymerEntityInstancesCollector.getEntryInstances(result);
-            }
-            catch (error) {
-                console.log(error);
-                throw error;
-            }
-        });
-    }
-    static getEntryInstances(entry) {
-        const out = new Array();
-        if ((entry === null || entry === void 0 ? void 0 : entry.polymer_entities) instanceof Array) {
-            entry.polymer_entities.forEach(entity => {
-                if (entity && Array.isArray(entity === null || entity === void 0 ? void 0 : entity.polymer_entity_instances)) {
-                    assertElementListDefined(entity.polymer_entity_instances);
-                    PolymerEntityInstancesCollector.parsePolymerEntityInstances(entity.polymer_entity_instances, out);
-                }
-            });
-        }
-        return out;
-    }
-    static parsePolymerEntityInstances(polymerEntityInstances, out) {
-        polymerEntityInstances.forEach(instance => {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s, _t, _u, _v, _w, _x;
-            const taxIds = new Set();
-            if (((_a = instance === null || instance === void 0 ? void 0 : instance.polymer_entity) === null || _a === void 0 ? void 0 : _a.rcsb_entity_source_organism) instanceof Array)
-                instance.polymer_entity.rcsb_entity_source_organism.forEach(sO => {
-                    if (typeof (sO === null || sO === void 0 ? void 0 : sO.ncbi_scientific_name) === "string" && sO.ncbi_scientific_name.length > 0)
-                        taxIds.add(sO.ncbi_scientific_name);
-                });
-            const o = instance.rcsb_polymer_entity_instance_container_identifiers;
-            const p = (_b = instance.polymer_entity) === null || _b === void 0 ? void 0 : _b.entry;
-            assertDefined(o), assertDefined(o === null || o === void 0 ? void 0 : o.entity_id), assertDefined(o.auth_asym_id), assertElementListDefined(o === null || o === void 0 ? void 0 : o.auth_to_entity_poly_seq_mapping);
-            assertDefined(p);
-            assertDefined((_d = (_c = instance.polymer_entity) === null || _c === void 0 ? void 0 : _c.entity_poly) === null || _d === void 0 ? void 0 : _d.rcsb_sample_sequence_length);
-            assertDefined((_e = instance.polymer_entity.entry) === null || _e === void 0 ? void 0 : _e.rcsb_entry_info.structure_determination_methodology);
-            out.push({
-                rcsbId: instance.rcsb_id,
-                entryId: o.entry_id,
-                entityId: o.entity_id,
-                asymId: o.asym_id,
-                authId: o.auth_asym_id,
-                authResId: o.auth_to_entity_poly_seq_mapping,
-                name: (_o = ((_k = (_j = (_h = (_g = (_f = instance.polymer_entity) === null || _f === void 0 ? void 0 : _f.rcsb_polymer_entity) === null || _g === void 0 ? void 0 : _g.rcsb_polymer_name_combined) === null || _h === void 0 ? void 0 : _h.names) === null || _j === void 0 ? void 0 : _j.join(", ")) !== null && _k !== void 0 ? _k : (_m = (_l = instance === null || instance === void 0 ? void 0 : instance.polymer_entity) === null || _l === void 0 ? void 0 : _l.rcsb_polymer_entity) === null || _m === void 0 ? void 0 : _m.pdbx_description)) !== null && _o !== void 0 ? _o : "NA",
-                taxNames: Array.from(taxIds),
-                experimentalMethod: (_p = p.rcsb_entry_info.experimental_method) !== null && _p !== void 0 ? _p : "NA",
-                resolution: (_t = (_s = (_r = (_q = instance.polymer_entity) === null || _q === void 0 ? void 0 : _q.entry) === null || _r === void 0 ? void 0 : _r.rcsb_entry_info.resolution_combined) === null || _s === void 0 ? void 0 : _s[0]) !== null && _t !== void 0 ? _t : undefined,
-                sequenceLength: instance.polymer_entity.entity_poly.rcsb_sample_sequence_length,
-                entityMolecularWeight: (_v = (_u = instance.polymer_entity.rcsb_polymer_entity) === null || _u === void 0 ? void 0 : _u.formula_weight) !== null && _v !== void 0 ? _v : undefined,
-                entryMolecularWeight: (_x = (_w = instance.polymer_entity.entry) === null || _w === void 0 ? void 0 : _w.rcsb_entry_info.molecular_weight) !== null && _x !== void 0 ? _x : undefined,
-                structureDeterminationMethodology: instance.polymer_entity.entry.rcsb_entry_info.structure_determination_methodology
-            });
-        });
-    }
-}
-exports.PolymerEntityInstancesCollector = PolymerEntityInstancesCollector;

package/lib/commonjs/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -1,23 +0,0 @@
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
-export interface ExternalTrackBuilderInterface {
-    processAlignmentAndFeatures?(data: {
-        annotations?: Array<AnnotationFeatures>;
-        alignments?: AlignmentResponse;
-        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<void>;
-    filterAlignments?(data: {
-        alignments: AlignmentResponse;
-        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<AlignmentResponse>;
-    filterFeatures?(data: {
-        annotations: Array<AnnotationFeatures>;
-        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<AnnotationFeatures>>;
-    addTo?(tracks: {
-        alignmentTracks?: Array<RcsbFvRowConfigInterface>;
-        annotationTracks?: Array<RcsbFvRowConfigInterface>;
-        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<void>;
-}

package/lib/commonjs/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/lib/commonjs/RcsbCollectTools/FeatureTools/FeatureTools.d.ts

@@ -1,9 +0,0 @@
-import { RcsbFvLink } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { ExternalTrackBuilderInterface } from "./ExternalTrackBuilderInterface";
-import { RcsbFvTrackDataAnnotationInterface } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface";
-export declare class FeatureTools {
-    private static readonly rcsbLigand;
-    static mergeBlocks(blocks: Array<RcsbFvTrackDataAnnotationInterface>): void;
-    static parseLink(title: string): RcsbFvLink;
-    static mergeTrackBuilders(builderA: ExternalTrackBuilderInterface, builderB?: ExternalTrackBuilderInterface): ExternalTrackBuilderInterface;
-}

package/lib/commonjs/RcsbCollectTools/FeatureTools/FeatureTools.js

@@ -1,89 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.FeatureTools = void 0;
-const tslib_1 = require("tslib");
-const web_resources_json_1 = tslib_1.__importDefault(require("../../RcsbServerConfig/web.resources.json"));
-const RcsbAnnotationConstants_1 = require("../../RcsbAnnotationConfig/RcsbAnnotationConstants");
-class FeatureTools {
-    static mergeBlocks(blocks) {
-        var _a, _b;
-        let merged = false;
-        do {
-            merged = false;
-            for (let n = 0; n < (blocks.length - 1); n++) {
-                const end = blocks[n].end;
-                if (!end)
-                    return;
-                if (((_a = blocks[n].oriEnd) !== null && _a !== void 0 ? _a : Number.MIN_SAFE_INTEGER) + 1 == blocks[n + 1].oriBegin && blocks[n].color === blocks[n + 1].color) {
-                    if (blocks[n].gaps == null)
-                        blocks[n].gaps = [];
-                    (_b = blocks[n].gaps) === null || _b === void 0 ? void 0 : _b.push({ begin: end, end: blocks[n + 1].begin, isConnected: true });
-                    blocks[n].end = blocks[n + 1].end;
-                    blocks[n].oriEnd = blocks[n + 1].oriEnd;
-                    blocks.splice((n + 1), 1);
-                    merged = true;
-                    break;
-                }
-            }
-        } while (merged);
-    }
-    static parseLink(title) {
-        let match = FeatureTools.rcsbLigand.exec(title);
-        if (match) {
-            return {
-                visibleTex: match[3],
-                url: web_resources_json_1.default.rcsb_ligand.url + match[3],
-                style: {
-                    color: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbLink,
-                    fontWeight: "bold"
-                }
-            };
-        }
-        else if (title == "binding_site") {
-            return { visibleTex: "", style: { fontWeight: "bold" } };
-        }
-        return { visibleTex: title, style: { fontWeight: "bold" } };
-    }
-    static mergeTrackBuilders(builderA, builderB) {
-        return {
-            addTo(tracks) {
-                return tslib_1.__awaiter(this, void 0, void 0, function* () {
-                    var _a, _b;
-                    yield ((_a = builderA.addTo) === null || _a === void 0 ? void 0 : _a.call(builderA, tracks));
-                    yield ((_b = builderB === null || builderB === void 0 ? void 0 : builderB.addTo) === null || _b === void 0 ? void 0 : _b.call(builderB, tracks));
-                });
-            },
-            processAlignmentAndFeatures(data) {
-                return tslib_1.__awaiter(this, void 0, void 0, function* () {
-                    var _a, _b;
-                    yield ((_a = builderA.processAlignmentAndFeatures) === null || _a === void 0 ? void 0 : _a.call(builderA, data));
-                    yield ((_b = builderB === null || builderB === void 0 ? void 0 : builderB.processAlignmentAndFeatures) === null || _b === void 0 ? void 0 : _b.call(builderB, data));
-                });
-            },
-            filterFeatures(data) {
-                return tslib_1.__awaiter(this, void 0, void 0, function* () {
-                    let annotations = data.annotations;
-                    const rcsbContext = data.rcsbContext;
-                    if (builderA.filterFeatures)
-                        annotations = yield builderA.filterFeatures({ annotations, rcsbContext });
-                    if (builderB === null || builderB === void 0 ? void 0 : builderB.filterFeatures)
-                        annotations = yield builderB.filterFeatures({ annotations, rcsbContext });
-                    return annotations;
-                });
-            },
-            filterAlignments(data) {
-                return tslib_1.__awaiter(this, void 0, void 0, function* () {
-                    let alignments = data.alignments;
-                    const rcsbContext = data.rcsbContext;
-                    if (builderA.filterAlignments)
-                        alignments = yield builderA.filterAlignments({ alignments, rcsbContext });
-                    if (builderB === null || builderB === void 0 ? void 0 : builderB.filterAlignments)
-                        alignments = yield builderB.filterAlignments({ alignments, rcsbContext });
-                    return alignments;
-                });
-            }
-        };
-    }
-}
-exports.FeatureTools = FeatureTools;
-FeatureTools.rcsbLigand = new RegExp(/^(ligand)(\s)(\w{1,3})$/);

package/lib/commonjs/RcsbExport/FeatureType.d.ts

@@ -1,10 +0,0 @@
-import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-declare const ExtendedTypes: {
-    BurialFraction: Type;
-    BuriedResidues: Type;
-};
-type MergedType = typeof Type & typeof ExtendedTypes;
-declare const MergedType: MergedType;
-type FeatureType = typeof MergedType;
-export declare const FeatureType: FeatureType;
-export {};

package/lib/commonjs/RcsbExport/FeatureType.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.FeatureType = void 0;
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const BURIAL_FRACTION = "BURIAL_FRACTION";
-const BURIED_RESIDUES = "BURIED_RESIDUES";
-const ExtendedTypes = {
-    BurialFraction: BURIAL_FRACTION,
-    BuriedResidues: BURIED_RESIDUES
-};
-const MergedType = Object.assign(Object.assign({}, GqlTypes_1.Type), ExtendedTypes);
-exports.FeatureType = MergedType;

package/lib/commonjs/RcsbExport/RcsbFvUI.d.ts

@@ -1,7 +0,0 @@
-import { GroupedOptionsInterface, SelectOptionInterface } from "../RcsbFvWeb/RcsbFvComponents/SelectButton";
-import { SelectButtonConfigInterface } from "../RcsbFvWeb/RcsbFvComponents/ComponentsManager";
-export declare class RcsbFvUI {
-    static clearSelectButton(elementFvId: string, selectButtonId: string): void;
-    static createSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface> | Array<GroupedOptionsInterface>, config?: SelectButtonConfigInterface): void;
-    static addSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface>, config?: SelectButtonConfigInterface): void;
-}

package/lib/commonjs/RcsbExport/RcsbFvUI.js

@@ -1,16 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvUI = void 0;
-const RcsbFvCoreBuilder_1 = require("../RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder");
-class RcsbFvUI {
-    static clearSelectButton(elementFvId, selectButtonId) {
-        RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.clearAdditionalSelectButton(elementFvId, selectButtonId);
-    }
-    static createSelectButton(elementFvId, selectButtonId, options, config) {
-        RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.buildSelectButton(elementFvId, selectButtonId, options, config);
-    }
-    static addSelectButton(elementFvId, selectButtonId, options, config) {
-        RcsbFvCoreBuilder_1.RcsbFvCoreBuilder.addSelectButton(elementFvId, selectButtonId, options, config);
-    }
-}
-exports.RcsbFvUI = RcsbFvUI;

package/lib/commonjs/RcsbFvExamples/ChromosomeFv.d.ts

@@ -1 +0,0 @@
-export {};