drugflow-molstar 0.3.77 → 0.4.1

package/lib/helpers.js

@@ -1,21 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ModelInfo = exports.QueryHelper = exports.LigandView = exports.AlphafoldView = exports.PDBeVolumes = void 0;
-var tslib_1 = require("tslib");
-var commands_1 = require("Molstar/mol-plugin/commands");
-var builder_1 = require("Molstar/mol-script/language/builder");
-var mol_state_1 = require("Molstar/mol-state");
-var structure_1 = require("Molstar/mol-model/structure");
-var transformers_1 = require("Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers");
-var compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
-var structure_2 = require("Molstar/mol-model/structure");
-var sifts_mapping_1 = require("./sifts-mapping");
-var query_1 = require("Molstar/mol-model/structure/query/query");
-var prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
+const commands_1 = require("Molstar/mol-plugin/commands");
+const builder_1 = require("Molstar/mol-script/language/builder");
+const mol_state_1 = require("Molstar/mol-state");
+const structure_1 = require("Molstar/mol-model/structure");
+const transformers_1 = require("Molstar/mol-plugin/behavior/dynamic/volume-streaming/transformers");
+const compiler_1 = require("Molstar/mol-script/runtime/query/compiler");
+const structure_2 = require("Molstar/mol-model/structure");
+const sifts_mapping_1 = require("./sifts-mapping");
+const query_1 = require("Molstar/mol-model/structure/query/query");
+const prop_1 = require("Molstar/extensions/model-archive/quality-assessment/prop");
 var PDBeVolumes;
 (function (PDBeVolumes) {
     function mapParams(defaultParams, mapParams, ref) {
-        var pdbeParams = tslib_1.__assign({}, defaultParams);
+        const pdbeParams = { ...defaultParams };
         pdbeParams.options.behaviorRef = 'volume-streaming' + '' + Math.floor(Math.random() * Math.floor(100));
         pdbeParams.options.emContourProvider = 'pdbe';
         pdbeParams.options.serverUrl = 'https://www.ebi.ac.uk/pdbe/volume-server';
@@ -48,19 +47,19 @@ var PDBeVolumes;
     }
     PDBeVolumes.displayUsibilityMessage = displayUsibilityMessage;
     function toggle(plugin) {
-        var state = plugin.state.data;
-        var streamingState = state.select(mol_state_1.StateSelection.Generators.ofTransformer(transformers_1.CreateVolumeStreamingInfo))[0];
+        const state = plugin.state.data;
+        const streamingState = state.select(mol_state_1.StateSelection.Generators.ofTransformer(transformers_1.CreateVolumeStreamingInfo))[0];
         if (streamingState) {
             commands_1.PluginCommands.State.ToggleVisibility(plugin, { state: state, ref: streamingState.transform.ref });
             return;
         }
     }
     PDBeVolumes.toggle = toggle;
-})(PDBeVolumes = exports.PDBeVolumes || (exports.PDBeVolumes = {}));
+})(PDBeVolumes || (exports.PDBeVolumes = PDBeVolumes = {}));
 var AlphafoldView;
 (function (AlphafoldView) {
     function getLociByPLDDT(score, contextData) {
-        var queryExp = builder_1.MolScriptBuilder.struct.modifier.union([
+        const queryExp = builder_1.MolScriptBuilder.struct.modifier.union([
             builder_1.MolScriptBuilder.struct.modifier.wholeResidues([
                 builder_1.MolScriptBuilder.struct.modifier.union([
                     builder_1.MolScriptBuilder.struct.generator.atomGroups({
@@ -70,20 +69,20 @@ var AlphafoldView;
                 ])
             ])
         ]);
-        var query = (0, compiler_1.compile)(queryExp);
-        var sel = query(new structure_1.QueryContext(contextData));
+        const query = (0, compiler_1.compile)(queryExp);
+        const sel = query(new structure_1.QueryContext(contextData));
         return structure_1.StructureSelection.toLociWithSourceUnits(sel);
     }
     AlphafoldView.getLociByPLDDT = getLociByPLDDT;
-})(AlphafoldView = exports.AlphafoldView || (exports.AlphafoldView = {}));
+})(AlphafoldView || (exports.AlphafoldView = AlphafoldView = {}));
 var LigandView;
 (function (LigandView) {
     function query(ligandViewParams) {
-        var atomGroupsParams = {
+        let atomGroupsParams = {
             'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()])
         };
         // Residue Param
-        var residueParam;
+        let residueParam;
         if (ligandViewParams.auth_seq_id) {
             residueParam = builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_seq_id(), ligandViewParams.auth_seq_id]);
         }
@@ -100,182 +99,178 @@ var LigandView;
             atomGroupsParams['chain-test'] = builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.label_asym_id(), ligandViewParams.struct_asym_id]);
         }
         // Construct core query
-        var core = ligandViewParams.show_all ?
+        const core = ligandViewParams.show_all ?
             builder_1.MolScriptBuilder.struct.generator.atomGroups(atomGroupsParams) :
             builder_1.MolScriptBuilder.struct.filter.first([
                 builder_1.MolScriptBuilder.struct.generator.atomGroups(atomGroupsParams)
             ]);
         // Construct surroundings query
-        var surroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
+        const surroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
         return {
-            core: core,
-            surroundings: surroundings
+            core,
+            surroundings
         };
     }
     LigandView.query = query;
     function branchedQuery(params) {
-        var entityObjArray = [];
-        params.atom_site.forEach(function (param) {
-            var qEntities = {
+        let entityObjArray = [];
+        params.atom_site.forEach((param) => {
+            let qEntities = {
                 'group-by': builder_1.MolScriptBuilder.core.str.concat([builder_1.MolScriptBuilder.struct.atomProperty.core.operatorName(), builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.residueKey()]),
                 'residue-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.struct.atomProperty.macromolecular.auth_seq_id(), param.auth_seq_id])
             };
             entityObjArray.push(qEntities);
         });
-        var atmGroupsQueries = [];
-        entityObjArray.forEach(function (entityObj) {
+        const atmGroupsQueries = [];
+        entityObjArray.forEach((entityObj) => {
             atmGroupsQueries.push(builder_1.MolScriptBuilder.struct.generator.atomGroups(entityObj));
         });
-        var core = builder_1.MolScriptBuilder.struct.modifier.union([
+        const core = builder_1.MolScriptBuilder.struct.modifier.union([
             atmGroupsQueries.length === 1
                 ? atmGroupsQueries[0]
                 // Need to union before merge for fast performance
-                : builder_1.MolScriptBuilder.struct.combinator.merge(atmGroupsQueries.map(function (q) { return builder_1.MolScriptBuilder.struct.modifier.union([q]); }))
+                : builder_1.MolScriptBuilder.struct.combinator.merge(atmGroupsQueries.map(q => builder_1.MolScriptBuilder.struct.modifier.union([q])))
         ]);
         // Construct surroundings query
-        var surroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
+        const surroundings = builder_1.MolScriptBuilder.struct.modifier.includeSurroundings({ 0: core, radius: 5, 'as-whole-residues': true });
         return {
-            core: core,
-            surroundings: surroundings
+            core,
+            surroundings
         };
     }
     LigandView.branchedQuery = branchedQuery;
-})(LigandView = exports.LigandView || (exports.LigandView = {}));
+})(LigandView || (exports.LigandView = LigandView = {}));
 var QueryHelper;
 (function (QueryHelper) {
     function getQueryObject(params, contextData) {
-        var selections = [];
-        var siftMappings;
-        var currentAccession;
-        params.forEach(function (param) {
-            var selection = {};
+        let selections = [];
+        let siftMappings;
+        let currentAccession;
+        params.forEach(param => {
+            let selection = {};
             // entity
             if (param.entity_id)
-                selection['entityTest'] = function (l) { return structure_1.StructureProperties.entity.id(l.element) === param.entity_id; };
+                selection['entityTest'] = (l) => structure_1.StructureProperties.entity.id(l.element) === param.entity_id;
             // chain
             if (param.struct_asym_id) {
-                selection['chainTest'] = function (l) { return structure_1.StructureProperties.chain.label_asym_id(l.element) === param.struct_asym_id; };
+                selection['chainTest'] = (l) => structure_1.StructureProperties.chain.label_asym_id(l.element) === param.struct_asym_id;
             }
             else if (param.auth_asym_id) {
-                selection['chainTest'] = function (l) { return structure_1.StructureProperties.chain.auth_asym_id(l.element) === param.auth_asym_id; };
+                selection['chainTest'] = (l) => structure_1.StructureProperties.chain.auth_asym_id(l.element) === param.auth_asym_id;
             }
             if (param.group_PDB) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.group_PDB(l.element) === param.group_PDB; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.group_PDB(l.element) === param.group_PDB;
             }
             // residues
             if (param.label_comp_id) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.atom.label_comp_id(l.element) === param.label_comp_id; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.atom.label_comp_id(l.element) === param.label_comp_id;
             }
             else if (param.uniprot_accession && param.uniprot_residue_number) {
-                selection['residueTest'] = function (l) {
+                selection['residueTest'] = (l) => {
                     if (!siftMappings || currentAccession !== param.uniprot_accession) {
                         siftMappings = sifts_mapping_1.SIFTSMapping.Provider.get(contextData.models[0]).value;
                         currentAccession = param.uniprot_accession;
                     }
-                    var rI = structure_1.StructureProperties.residue.key(l.element);
+                    const rI = structure_1.StructureProperties.residue.key(l.element);
                     return param.uniprot_accession === siftMappings.accession[rI] && param.uniprot_residue_number === +siftMappings.num[rI];
                 };
             }
             else if (param.uniprot_accession && param.start_uniprot_residue_number && param.end_uniprot_residue_number) {
-                selection['residueTest'] = function (l) {
+                selection['residueTest'] = (l) => {
                     if (!siftMappings || currentAccession !== param.uniprot_accession) {
                         siftMappings = sifts_mapping_1.SIFTSMapping.Provider.get(contextData.models[0]).value;
                         currentAccession = param.uniprot_accession;
                     }
-                    var rI = structure_1.StructureProperties.residue.key(l.element);
+                    const rI = structure_1.StructureProperties.residue.key(l.element);
                     return param.uniprot_accession === siftMappings.accession[rI] && (param.start_uniprot_residue_number <= +siftMappings.num[rI] && param.end_uniprot_residue_number >= +siftMappings.num[rI]);
                 };
             }
             else if (param.residue_number) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.label_seq_id(l.element) === param.residue_number; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.label_seq_id(l.element) === param.residue_number;
             }
             else if ((param.start_residue_number && param.end_residue_number) && (param.end_residue_number > param.start_residue_number)) {
-                selection['residueTest'] = function (l) {
-                    var labelSeqId = structure_1.StructureProperties.residue.label_seq_id(l.element);
+                selection['residueTest'] = (l) => {
+                    const labelSeqId = structure_1.StructureProperties.residue.label_seq_id(l.element);
                     return labelSeqId >= param.start_residue_number && labelSeqId <= param.end_residue_number;
                 };
             }
             else if ((param.start_residue_number && param.end_residue_number) && (param.end_residue_number === param.start_residue_number)) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.label_seq_id(l.element) === param.start_residue_number; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.label_seq_id(l.element) === param.start_residue_number;
             }
             else if (param.auth_seq_id) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_seq_id; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_seq_id;
             }
             else if (param.auth_residue_number && !param.auth_ins_code_id) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number;
             }
             else if (param.auth_residue_number && param.auth_ins_code_id) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.auth_residue_number;
             }
             else if ((param.start_auth_residue_number && param.end_auth_residue_number) && (param.end_auth_residue_number > param.start_auth_residue_number)) {
-                selection['residueTest'] = function (l) {
-                    var authSeqId = structure_1.StructureProperties.residue.auth_seq_id(l.element);
+                selection['residueTest'] = (l) => {
+                    const authSeqId = structure_1.StructureProperties.residue.auth_seq_id(l.element);
                     return authSeqId >= param.start_auth_residue_number && authSeqId <= param.end_auth_residue_number;
                 };
             }
             else if ((param.start_auth_residue_number && param.end_auth_residue_number) && (param.end_auth_residue_number === param.start_auth_residue_number)) {
-                selection['residueTest'] = function (l) { return structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.start_auth_residue_number; };
+                selection['residueTest'] = (l) => structure_1.StructureProperties.residue.auth_seq_id(l.element) === param.start_auth_residue_number;
             }
             // atoms
             if (param.atoms) {
-                selection['atomTest'] = function (l) { return param.atoms.includes(structure_1.StructureProperties.atom.label_atom_id(l.element)); };
+                selection['atomTest'] = (l) => param.atoms.includes(structure_1.StructureProperties.atom.label_atom_id(l.element));
             }
             if (param.atom_id) {
-                selection['atomTest'] = function (l) { return param.atom_id.includes(structure_1.StructureProperties.atom.id(l.element)); };
+                selection['atomTest'] = (l) => param.atom_id.includes(structure_1.StructureProperties.atom.id(l.element));
             }
             selections.push(selection);
         });
-        var atmGroupsQueries = [];
-        selections.forEach(function (selection) {
+        let atmGroupsQueries = [];
+        selections.forEach((selection) => {
             atmGroupsQueries.push(structure_2.Queries.generators.atoms(selection));
         });
         return structure_2.Queries.combinators.merge(atmGroupsQueries);
     }
     QueryHelper.getQueryObject = getQueryObject;
     function getInteractivityLoci(params, contextData) {
-        var sel = query_1.StructureQuery.run(QueryHelper.getQueryObject(params, contextData), contextData);
+        const sel = query_1.StructureQuery.run(QueryHelper.getQueryObject(params, contextData), contextData);
         return structure_1.StructureSelection.toLociWithSourceUnits(sel);
     }
     QueryHelper.getInteractivityLoci = getInteractivityLoci;
     function getHetLoci(queryExp, contextData) {
-        var query = (0, compiler_1.compile)(queryExp);
-        var sel = query(new structure_1.QueryContext(contextData));
+        const query = (0, compiler_1.compile)(queryExp);
+        const sel = query(new structure_1.QueryContext(contextData));
         return structure_1.StructureSelection.toLociWithSourceUnits(sel);
     }
     QueryHelper.getHetLoci = getHetLoci;
-})(QueryHelper = exports.QueryHelper || (exports.QueryHelper = {}));
+})(QueryHelper || (exports.QueryHelper = QueryHelper = {}));
 var ModelInfo;
 (function (ModelInfo) {
-    function get(model, structures) {
-        return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var residueCount, residueOffsets, chainIndex, hetNames, carbEntityCount, rI, cI, eI, entityType, comp_id;
-            return tslib_1.__generator(this, function (_a) {
-                residueCount = model.atomicHierarchy.residues._rowCount;
-                residueOffsets = model.atomicHierarchy.residueAtomSegments.offsets;
-                chainIndex = model.atomicHierarchy.chainAtomSegments.index;
-                hetNames = [];
-                carbEntityCount = 0;
-                for (rI = 0; rI < residueCount; rI++) {
-                    cI = chainIndex[residueOffsets[rI]];
-                    eI = model.atomicHierarchy.index.getEntityFromChain(cI);
-                    entityType = model.entities.data.type.value(eI);
-                    if (entityType !== 'non-polymer' && entityType !== 'branched')
-                        continue;
-                    comp_id = model.atomicHierarchy.atoms.label_comp_id.value(residueOffsets[rI]);
-                    if (entityType === 'branched') {
-                        carbEntityCount++;
-                    }
-                    else {
-                        if (hetNames.indexOf(comp_id) === -1)
-                            hetNames.push(comp_id);
-                    }
-                }
-                return [2 /*return*/, {
-                        hetNames: hetNames,
-                        carbEntityCount: carbEntityCount
-                    }];
-            });
-        });
+    async function get(model, structures) {
+        const { _rowCount: residueCount } = model.atomicHierarchy.residues;
+        const { offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
+        const chainIndex = model.atomicHierarchy.chainAtomSegments.index;
+        const hetNames = [];
+        let carbEntityCount = 0;
+        for (let rI = 0; rI < residueCount; rI++) {
+            const cI = chainIndex[residueOffsets[rI]];
+            const eI = model.atomicHierarchy.index.getEntityFromChain(cI);
+            const entityType = model.entities.data.type.value(eI);
+            if (entityType !== 'non-polymer' && entityType !== 'branched')
+                continue;
+            // const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(rI);
+            const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(residueOffsets[rI]);
+            if (entityType === 'branched') {
+                carbEntityCount++;
+            }
+            else {
+                if (hetNames.indexOf(comp_id) === -1)
+                    hetNames.push(comp_id);
+            }
+        }
+        return {
+            hetNames,
+            carbEntityCount
+        };
     }
     ModelInfo.get = get;
-})(ModelInfo = exports.ModelInfo || (exports.ModelInfo = {}));
+})(ModelInfo || (exports.ModelInfo = ModelInfo = {}));