molstar 3.0.0-dev.0 → 3.0.0-dev.5

package/lib/commonjs/perf-tests/state.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/perf-tests/string-builder.d.ts

@@ -1,3 +0,0 @@
-export declare namespace Test {
-    function run(): void;
-}

package/lib/commonjs/perf-tests/string-builder.js

@@ -1,57 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Test = void 0;
-var tslib_1 = require("tslib");
-var B = (0, tslib_1.__importStar)(require("benchmark"));
-var string_builder_1 = require("../mol-util/string-builder");
-var Test;
-(function (Test) {
-    function createData(n) {
-        var ret = [];
-        for (var i = 0; i < n; i++) {
-            ret[i] = '' + ((100000000 * Math.random() + 1) | 0);
-        }
-        return ret;
-    }
-    function build(data, chunkSize) {
-        var sb = string_builder_1.StringBuilder.create(chunkSize);
-        for (var i = 0, _i = data.length; i < _i; i++) {
-            string_builder_1.StringBuilder.writeSafe(sb, data[i]);
-            string_builder_1.StringBuilder.whitespace1(sb);
-        }
-        return sb;
-    }
-    function buildWS(data, chunkSize) {
-        var sb = string_builder_1.StringBuilder.create(chunkSize);
-        for (var i = 0, _i = data.length; i < _i; i++) {
-            string_builder_1.StringBuilder.writeSafe(sb, data[i] + ' ');
-        }
-        return sb;
-    }
-    // function naive(data: string[]) {
-    //     let ret = '';
-    //     for (let i = 0, _i = data.length; i < _i; i++) ret += data[i];
-    //     return ret;
-    // }
-    // function join(data: string[]) {
-    //     let ret = [];
-    //     for (let i = 0, _i = data.length; i < _i; i++) ret[i] = data[i];
-    //     return ret.join('');
-    // }
-    function run() {
-        var data = createData(26 * 100000);
-        var N = 512;
-        var suite = new B.Suite();
-        suite
-            // .add(`naive`, () => naive(data))
-            // .add(`join`, () => join(data))
-            // .add(`${N} chunks`, () => SB.getChunks(build(data, N)))
-            .add("".concat(N, " str"), function () { return string_builder_1.StringBuilder.getString(build(data, N)); })
-            .add("".concat(N, " str ws"), function () { return string_builder_1.StringBuilder.getString(buildWS(data, N)); })
-            .on('cycle', function (e) { return console.log(String(e.target)); })
-            .run();
-    }
-    Test.run = run;
-})(Test = exports.Test || (exports.Test = {}));
-Test.run();
-//# sourceMappingURL=string-builder.js.map

package/lib/commonjs/perf-tests/string-builder.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/perf-tests/structure.d.ts

@@ -1,24 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { Structure } from '../mol-model/structure';
-export declare function readCIF(path: string): Promise<{
-    mmcif: unknown;
-    models: import("../mol-model/structure").Trajectory;
-    structures: Structure[];
-}>;
-export declare function getBcif(pdbId: string): Promise<{
-    mmcif: unknown;
-    models: import("../mol-model/structure").Trajectory;
-    structures: Structure[];
-}>;
-export declare namespace PropertyAccess {
-    function write(s: Structure): void;
-    function testAssembly(id: string, s: Structure): Promise<void>;
-    function testSymmetry(id: string, s: Structure): Promise<void>;
-    function testIncludeSurroundings(id: string, s: Structure): Promise<void>;
-    function runBonds(): Promise<void>;
-    function run(): Promise<void>;
-}

package/lib/commonjs/perf-tests/structure.js

@@ -1,529 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.PropertyAccess = exports.getBcif = exports.readCIF = void 0;
-var tslib_1 = require("tslib");
-var B = (0, tslib_1.__importStar)(require("benchmark"));
-var util = (0, tslib_1.__importStar)(require("util"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
-var cif_1 = require("../mol-io/reader/cif");
-var structure_1 = require("../mol-model/structure");
-// import { Segmentation, OrderedSet } from '../mol-data/int'
-var mmcif_1 = require("../mol-model/structure/export/mmcif");
-var linear_algebra_1 = require("../mol-math/linear-algebra");
-var mmcif_2 = require("../mol-model-formats/structure/mmcif");
-// import { printUnits } from '../apps/structure-info/model';
-// import { EquivalenceClasses } from '../mol-data/util';
-require('util.promisify').shim();
-var readFileAsync = util.promisify(fs.readFile);
-var writeFileAsync = util.promisify(fs.writeFile);
-function readData(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var input, data, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    if (!path.match(/\.bcif$/)) return [3 /*break*/, 2];
-                    return [4 /*yield*/, readFileAsync(path)];
-                case 1:
-                    input = _a.sent();
-                    data = new Uint8Array(input.byteLength);
-                    for (i = 0; i < input.byteLength; i++)
-                        data[i] = input[i];
-                    return [2 /*return*/, data];
-                case 2: return [2 /*return*/, readFileAsync(path, 'utf8')];
-            }
-        });
-    });
-}
-// (Symbol as any).asyncIterator = (Symbol as any).asyncIterator || Symbol.for('Symbol.asyncIterator');
-// interface ProgressGenerator<T> extends AsyncIterableIterator<number | T> {
-//     next(cont?: boolean): Promise<IteratorResult<number | T>>
-// }
-// async function *test(): ProgressGenerator<boolean> {
-//     const r = yield await new Promise<number>(res => res(10));
-//     return r;
-// }
-// async function runIt(itP: () => ProgressGenerator<boolean>) {
-//     const it = itP();
-//     while (true) {
-//         const { value, done } = await it.next(true);
-//         if (done) return value;
-//     }
-// }
-// runIt(test).then(r => console.log('rerdasdasda', r))
-function readCIF(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var input, comp, parsed, data, models, structures;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    console.time('readData');
-                    return [4 /*yield*/, readData(path)];
-                case 1:
-                    input = _a.sent();
-                    console.timeEnd('readData');
-                    console.time('parse');
-                    comp = typeof input === 'string' ? cif_1.CIF.parseText(input) : cif_1.CIF.parseBinary(input);
-                    return [4 /*yield*/, comp.run()];
-                case 2:
-                    parsed = _a.sent();
-                    console.timeEnd('parse');
-                    if (parsed.isError) {
-                        throw parsed;
-                    }
-                    data = parsed.result.blocks[0];
-                    console.time('buildModels');
-                    return [4 /*yield*/, (0, mmcif_2.trajectoryFromMmCIF)(data).run()];
-                case 3:
-                    models = _a.sent();
-                    console.timeEnd('buildModels');
-                    structures = [structure_1.Structure.ofModel(models.representative)];
-                    return [2 /*return*/, { mmcif: models.representative.sourceData.data, models: models, structures: structures }];
-            }
-        });
-    });
-}
-exports.readCIF = readCIF;
-var DATA_DIR = './build/data';
-if (!fs.existsSync(DATA_DIR))
-    fs.mkdirSync(DATA_DIR);
-function getBcifUrl(pdbId) {
-    return "http://www.ebi.ac.uk/pdbe/coordinates/".concat(pdbId.toLowerCase(), "/full?encoding=bcif");
-}
-function getBcifPath(pdbId) {
-    return "".concat(DATA_DIR, "/").concat(pdbId.toLowerCase(), "_full.bcif");
-}
-function ensureBcifAvailable(pdbId) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var bcifPath, data, _a, _b;
-        return (0, tslib_1.__generator)(this, function (_c) {
-            switch (_c.label) {
-                case 0:
-                    bcifPath = getBcifPath(pdbId);
-                    if (!!fs.existsSync(bcifPath)) return [3 /*break*/, 4];
-                    console.log("downloading ".concat(pdbId, " bcif..."));
-                    return [4 /*yield*/, (0, node_fetch_1.default)(getBcifUrl(pdbId))];
-                case 1:
-                    data = _c.sent();
-                    _a = writeFileAsync;
-                    _b = [bcifPath];
-                    return [4 /*yield*/, data.buffer()];
-                case 2: return [4 /*yield*/, _a.apply(void 0, _b.concat([_c.sent()]))];
-                case 3:
-                    _c.sent();
-                    console.log("done downloading ".concat(pdbId, " bcif"));
-                    _c.label = 4;
-                case 4: return [2 /*return*/];
-            }
-        });
-    });
-}
-function getBcif(pdbId) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, ensureBcifAvailable(pdbId)];
-                case 1:
-                    _a.sent();
-                    return [4 /*yield*/, readCIF(getBcifPath(pdbId))];
-                case 2: return [2 /*return*/, _a.sent()];
-            }
-        });
-    });
-}
-exports.getBcif = getBcif;
-var PropertyAccess;
-(function (PropertyAccess) {
-    function baseline(model) {
-        if (!mmcif_2.MmcifFormat.is(model.sourceData))
-            throw new Error('Model must be mmCIF');
-        var atom_site = model.sourceData.data.db.atom_site;
-        var id = atom_site.id.value;
-        var s = 0;
-        for (var i = 0, _i = atom_site._rowCount; i < _i; i++) {
-            s += id(i);
-        }
-        return s;
-    }
-    function sumProperty(structure, p) {
-        var l = structure_1.StructureElement.Location.create(structure);
-        var s = 0;
-        for (var _a = 0, _b = structure.units; _a < _b.length; _a++) {
-            var unit = _b[_a];
-            l.unit = unit;
-            var elements = unit.elements;
-            for (var j = 0, _j = elements.length; j < _j; j++) {
-                l.element = elements[j];
-                s += p(l);
-            }
-        }
-        return s;
-    }
-    // function sumPropertySegmented(structure: Structure, p: Element.Property<number>) {
-    //     const { elements, units } = structure;
-    //     const unitIds = ElementSet.unitIndices(elements);
-    //     const l = Element.Location();
-    //     let s = 0;
-    //     let vA = 0, cC = 0, rC = 0;
-    //     for (let i = 0, _i = unitIds.length; i < _i; i++) {
-    //         const unit = units[unitIds[i]] as Unit.Atomic;
-    //         l.unit = unit;
-    //         const set = ElementSet.groupAt(elements, i);
-    //         const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set.elements);
-    //         const residues = unit.hierarchy.residueSegments;
-    //         while (chainsIt.hasNext) {
-    //             cC++;
-    //             const chainSegment = chainsIt.move();
-    //             const residuesIt = Segmentation.transientSegments(residues, set.elements, chainSegment);
-    //             while (residuesIt.hasNext) {
-    //                 rC++;
-    //                 const residueSegment = residuesIt.move();
-    //                 // l.element= OrdSet.getAt(set, residueSegment.start);
-    //                 // console.log(unit.hierarchy.residues.auth_comp_id.value(unit.residueIndex[l.atom]), l.atom, OrdSet.getAt(set, residueSegment.end))
-    //                 for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
-    //                     l.element= ElementGroup.getAt(set, j);
-    //                     vA++;
-    //                     s += p(l);
-    //                 }
-    //             }
-    //         }
-    //     }
-    //     console.log('seg atom count', vA, cC, rC);
-    //     return s;
-    // }
-    // function sumPropertyResidue(structure: Structure, p: Element.Property<number>) {
-    //     const { atoms, units } = structure;
-    //     const unitIds = ElementSet.unitIds(atoms);
-    //     const l = Element.Location();
-    //     let s = 0;
-    //     for (let i = 0, _i = unitIds.length; i < _i; i++) {
-    //         const unit = units[unitIds[i]];
-    //         l.unit = unit;
-    //         const set = ElementSet.unitGetByIndex(atoms, i);
-    //         const residuesIt = Segmentation.transientSegments(unit.hierarchy.residueSegments, set.atoms);
-    //         while (residuesIt.hasNext) {
-    //             l.element= ElementGroup.getAt(set, residuesIt.move().start);
-    //             s += p(l);
-    //         }
-    //     }
-    //     return s;
-    // }
-    // function sumPropertyAtomSetIt(structure: Structure, p: Element.Property<number>) {
-    //     const { elements, units } = structure;
-    //     let s = 0;
-    //     const atomsIt = ElementSet.elements(elements);
-    //     const l = Element.Location();
-    //     while (atomsIt.hasNext) {
-    //         const a = atomsIt.move();
-    //         l.unit = units[Element.unit(a)];
-    //         l.element= Element.index(a);
-    //         s += p(l);
-    //     }
-    //     return s;
-    // }
-    // function sumPropertySegmentedMutable(structure: Structure, p: Property<number>) {
-    //     const { atoms, units } = structure;
-    //     const unitIds = ElementSet.unitIds(atoms);
-    //     const l = Property.createLocation();
-    //     let s = 0;
-    //     for (let i = 0, _i = unitIds.length; i < _i; i++) {
-    //         const unit = units[unitIds[i]];
-    //         l.unit = unit;
-    //         const set = ElementSet.unitGetByIndex(atoms, i);
-    //         const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set);
-    //         const residuesIt = Segmentation.transientSegments(unit.hierarchy.residueSegments, set);
-    //         while (chainsIt.hasNext) {
-    //             const chainSegment = chainsIt.move();
-    //             residuesIt.updateRange(chainSegment);
-    //             while (residuesIt.hasNext) {
-    //                 const residueSegment = residuesIt.move();
-    //                 for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
-    //                     l.element= OrdSet.getAt(set, j);
-    //                     s += p(l);
-    //                 }
-    //             }
-    //         }
-    //     }
-    //     return s;
-    // }
-    // function sumDirect(structure: Structure) {
-    //     const { atoms, units } = structure;
-    //     const unitIds = ElementSet.unitIds(atoms);
-    //     let s = 0;
-    //     for (let i = 0, _i = unitIds.length; i < _i; i++) {
-    //         const unitId = unitIds[i];
-    //         const unit = units[unitId];
-    //         const set = ElementSet.unitGetByIndex(atoms, i);
-    //         //const { residueIndex, chainIndex } = unit;
-    //         const p = unit.conformation.atomId.value;
-    //         for (let j = 0, _j = ElementGroup.size(set); j < _j; j++) {
-    //             const aI = ElementGroup.getAt(set, j);
-    //             s += p(aI);
-    //         }
-    //     }
-    //     return s;
-    // }
-    // function concatProperty(structure: Structure, p: Property<string>) {
-    //     const { atoms, units } = structure;
-    //     const unitIds = ElementSet.unitIds(atoms);
-    //     const l = Property.createLocation(structure);
-    //     let s = [];
-    //     for (let i = 0, _i = unitIds.length; i < _i; i++) {
-    //         const unitId = unitIds[i];
-    //         l.unit = units[unitId];
-    //         const set = ElementSet.unitGetByIndex(atoms, i);
-    //         const { residueIndex, chainIndex } = l.unit;
-    //         for (let j = 0, _j = OrdSet.size(set); j < _j; j++) {
-    //             const aI = OrdSet.getAt(set, j);
-    //             l.element= aI;
-    //             l.residueIndex = residueIndex[aI];
-    //             l.chainIndex = chainIndex[aI];
-    //             s[s.length] = p(l);
-    //         }
-    //     }
-    //     return s;
-    // }
-    function write(s) {
-        console.log((0, mmcif_1.to_mmCIF)('test', s));
-    }
-    PropertyAccess.write = write;
-    function testAssembly(id, s) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var a;
-            return (0, tslib_1.__generator)(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        console.time('assembly');
-                        return [4 /*yield*/, structure_1.StructureSymmetry.buildAssembly(s, '1').run()];
-                    case 1:
-                        a = _a.sent();
-                        // const auth_comp_id = SP.residue.auth_comp_id;
-                        // const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
-                        // const alas = await query(q1, a);
-                        console.timeEnd('assembly');
-                        fs.writeFileSync("".concat(DATA_DIR, "/").concat(id, "_assembly.bcif"), (0, mmcif_1.to_mmCIF)(id, a, true));
-                        // fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, Selection.unionStructure(alas), true));
-                        console.log('exported');
-                        return [2 /*return*/];
-                }
-            });
-        });
-    }
-    PropertyAccess.testAssembly = testAssembly;
-    function testSymmetry(id, s) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var a;
-            return (0, tslib_1.__generator)(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        console.time('symmetry');
-                        return [4 /*yield*/, structure_1.StructureSymmetry.buildSymmetryRange(s, linear_algebra_1.Vec3.create(-1, -1, -1), linear_algebra_1.Vec3.create(1, 1, 1)).run()];
-                    case 1:
-                        a = _a.sent();
-                        // const auth_comp_id = SP.residue.auth_comp_id;
-                        // const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
-                        // const alas = await query(q1, a);
-                        console.timeEnd('symmetry');
-                        fs.writeFileSync("".concat(DATA_DIR, "/").concat(id, "_symm.bcif"), (0, mmcif_1.to_mmCIF)(id, a, true));
-                        // fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, Selection.unionStructure(alas), true));
-                        console.log('exported');
-                        return [2 /*return*/];
-                }
-            });
-        });
-    }
-    PropertyAccess.testSymmetry = testSymmetry;
-    function testIncludeSurroundings(id, s) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var a, auth_comp_id, op, q1, surr;
-            return (0, tslib_1.__generator)(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        // const a = s;
-                        console.time('symmetry');
-                        return [4 /*yield*/, structure_1.StructureSymmetry.buildSymmetryRange(s, linear_algebra_1.Vec3.create(-2, -2, -2), linear_algebra_1.Vec3.create(2, 2, 2)).run()];
-                    case 1:
-                        a = _a.sent();
-                        auth_comp_id = structure_1.StructureProperties.atom.auth_comp_id, op = structure_1.StructureProperties.unit.operator_name;
-                        q1 = structure_1.Queries.modifiers.includeSurroundings(structure_1.Queries.generators.atoms({
-                            chainTest: function (l) { return op(l.element) === '1_555'; },
-                            atomTest: function (l) { return auth_comp_id(l.element) === 'REA'; }
-                        }), {
-                            radius: 5,
-                            wholeResidues: true
-                        });
-                        surr = structure_1.StructureSelection.unionStructure(structure_1.StructureQuery.run(q1, a));
-                        console.timeEnd('symmetry');
-                        // for (const u of surr.units) {
-                        //     const { atomId } = u.model.atomicConformation;
-                        //     console.log(`${u.id}, ${u.conformation.operator.name}`);
-                        //     for (let i = 0; i < u.elements.length; i++) {
-                        //         console.log(`  ${atomId.value(u.elements[i])}`);
-                        //     }
-                        // }
-                        // const it = surr.elementLocations();
-                        // while (it.hasNext) {
-                        //     const e = it.move();
-                        //     console.log(`${SP.unit.operator_name(e)} ${SP.atom.id(e)}`);
-                        // }
-                        // fs.writeFileSync(`${DATA_DIR}/${id}_surr.bcif`, to_mmCIF(id, a, true));
-                        fs.writeFileSync("".concat(DATA_DIR, "/").concat(id, "_surr.cif"), (0, mmcif_1.to_mmCIF)(id, surr, false));
-                        console.log('exported');
-                        return [2 /*return*/];
-                }
-            });
-        });
-    }
-    PropertyAccess.testIncludeSurroundings = testIncludeSurroundings;
-    // export async function testGrouping(structure: Structure) {
-    //     const { elements, units } = await Run(Symmetry.buildAssembly(structure, '1'));
-    //     console.log('grouping', units.length);
-    //     console.log('built asm');
-    //     const uniqueGroups = EquivalenceClasses<number, { unit: Unit, group: ElementGroup }>(
-    //         ({ unit, group }) => ElementGroup.hashCode(group),
-    //         (a, b) => a.unit.model.id === b.unit.model.id && (a.group.key === b.group.key && OrderedSet.areEqual(a.group.elements, b.group.elements))
-    //     );
-    //     for (let i = 0, _i = ElementSet.groupCount(elements); i < _i; i++) {
-    //         const group = ElementSet.groupAt(elements, i);
-    //         const unitId = ElementSet.groupUnitIndex(elements, i);
-    //         uniqueGroups.add(unitId, { unit: units[unitId], group });
-    //     }
-    //     console.log('group count', uniqueGroups.groups.length);
-    // }
-    function query(q, s) {
-        return structure_1.StructureQuery.run(q, s);
-    }
-    function runBonds() {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var structures;
-            return (0, tslib_1.__generator)(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, readCIF('e:/test/quick/3j3q_full.bcif')];
-                    case 1:
-                        structures = (_a.sent()).structures;
-                        console.time('bonds');
-                        structures[0].interUnitBonds;
-                        console.timeEnd('bonds');
-                        return [2 /*return*/];
-                }
-            });
-        });
-    }
-    PropertyAccess.runBonds = runBonds;
-    function run() {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var _a, structures, models /* , mmcif */, auth_comp_id, q, P, q1, q2, q3, q2r, col, suite;
-            var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, readCIF('e:/test/quick/1cbs_updated.cif')];
-                    case 1:
-                        _a = _b.sent(), structures = _a.structures, models = _a.models;
-                        // const { structures: s1, /* , mmcif */ } = await readCIF('e:/test/quick/1tqn_updated.cif');
-                        // testGrouping(structures[0]);
-                        // console.log('------');
-                        // testGrouping(s1[0]);
-                        // const { structures, models/*, mmcif*/ } = await readCIF('e:/test/quick/5j7v_updated.cif');
-                        // console.log(mmcif.pdbx_struct_oper_list.matrix.toArray());
-                        // console.log(mmcif.pdbx_struct_oper_list.vector.toArray());
-                        // await testAssembly('1hrv', structures[0]);
-                        // await testSymmetry('1cbs', structures[0]);
-                        return [4 /*yield*/, testIncludeSurroundings('1cbs', structures[0])];
-                    case 2:
-                        // const { structures: s1, /* , mmcif */ } = await readCIF('e:/test/quick/1tqn_updated.cif');
-                        // testGrouping(structures[0]);
-                        // console.log('------');
-                        // testGrouping(s1[0]);
-                        // const { structures, models/*, mmcif*/ } = await readCIF('e:/test/quick/5j7v_updated.cif');
-                        // console.log(mmcif.pdbx_struct_oper_list.matrix.toArray());
-                        // console.log(mmcif.pdbx_struct_oper_list.vector.toArray());
-                        // await testAssembly('1hrv', structures[0]);
-                        // await testSymmetry('1cbs', structures[0]);
-                        _b.sent();
-                        // throw '';
-                        // console.log(models[0].symmetry.assemblies);
-                        // const { structures, models } = await readCIF('e:/test/molstar/3j3q.bcif');
-                        // fs.writeFileSync('e:/test/molstar/3j3q.bcif', to_mmCIF('test', structures[0], true));
-                        // return;
-                        // console.log(toMmCIFString('test', structures[0]));
-                        // return;
-                        console.log('bs', baseline(models.representative));
-                        console.log('sp', sumProperty(structures[0], function (l) { return l.unit.model.atomicConformation.atomId.value(l.element); }));
-                        // console.log(sumPropertySegmented(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
-                        // console.log(sumPropertySegmentedMutable(structures[0], l => l.unit.model.conformation.atomId.value(l.element));
-                        // console.log(sumPropertyAtomSetIt(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
-                        // console.log(sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)));
-                        // console.log(sumDirect(structures[0]));
-                        // console.log('r', sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])));
-                        console.time('atom.x');
-                        console.log('atom.x', sumProperty(structures[0], structure_1.StructureProperties.atom.x));
-                        console.timeEnd('atom.x');
-                        console.time('__x');
-                        // console.log('__x', sumProperty(structures[0], l => l.unit.conformation.x[l.atom]));
-                        console.timeEnd('__x');
-                        auth_comp_id = structure_1.StructureProperties.atom.auth_comp_id;
-                        q = structure_1.Queries.generators.atoms({ atomTest: structure_1.Queries.pred.eq(function (l) { return structure_1.StructureProperties.atom.auth_comp_id(l.element); }, 'ALA') });
-                        P = structure_1.StructureProperties;
-                        q1 = (structure_1.Queries.generators.atoms({ atomTest: function (l) { return auth_comp_id(l.element) === 'ALA'; } }));
-                        q2 = (structure_1.Queries.generators.atoms({ atomTest: function (l) { return auth_comp_id(l.element) === 'ALA'; }, groupBy: function (l) { return structure_1.StructureProperties.residue.key(l.element); } }));
-                        q3 = (structure_1.Queries.generators.atoms({
-                            chainTest: structure_1.Queries.pred.inSet(function (l) { return P.chain.auth_asym_id(l.element); }, ['A', 'B', 'C', 'D']),
-                            atomTest: structure_1.Queries.pred.eq(function (l) { return P.atom.auth_comp_id(l.element); }, 'ALA')
-                        }));
-                        return [4 /*yield*/, query(q, structures[0])];
-                    case 3:
-                        _b.sent();
-                        // console.log(to_mmCIF('test', Selection.union(q0r)));
-                        console.time('q1');
-                        query(q1, structures[0]);
-                        console.timeEnd('q1');
-                        console.time('q1');
-                        query(q1, structures[0]);
-                        console.timeEnd('q1');
-                        console.time('q2');
-                        q2r = query(q2, structures[0]);
-                        console.timeEnd('q2');
-                        console.log(structure_1.StructureSelection.structureCount(q2r));
-                        col = models.representative.atomicConformation.atomId.value;
-                        suite = new B.Suite();
-                        suite
-                            // .add('test q', () => q1(structures[0]))
-                            // .add('test q', () => q(structures[0]))
-                            .add('test int', function () { return sumProperty(structures[0], function (l) { return col(l.element); }); })
-                            .add('test q1', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-                            return [2 /*return*/, query(q1, structures[0])];
-                        }); }); })
-                            .add('test q3', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-                            return [2 /*return*/, query(q3, structures[0])];
-                        }); }); })
-                            // .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))
-                            // .add('baseline', () =>  baseline(models[0]))
-                            // .add('direct', () =>  sumDirect(structures[0]))
-                            // .add('normal int', () => sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.element))
-                            // .add('atom set it int', () => sumPropertyAtomSetIt(structures[0], l => l.unit.conformation.atomId.value(l.element))
-                            // .add('segmented faster int', () => sumPropertySegmented(structures[0], l => l.unit.conformation.atomId.value(l.element))
-                            // .add('faster int', () => sumProperty(structures[0], l => l.unit.conformation.atomId.value(l.element))
-                            // .add('segmented faster _x', () => sumPropertySegmented(structures[0], l => l.unit.conformation.__x[l.atom]))
-                            // .add('faster _x', () => sumProperty(structures[0], l => l.unit.conformation.__x[l.atom] +  l.unit.conformation.__y[l.atom] +  l.unit.conformation.__z[l.atom]))
-                            // .add('segmented mut faster int', () => sumPropertySegmentedMutable(structures[0], l => l.unit.conformation.atomId.value(l.element))
-                            // .add('normal shortcut int', () => sumProperty(structures[0], l => l.conformation.atomId.value(l.element))
-                            // .add('cached int', () => sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)))
-                            // .add('concat str', () => concatProperty(structures[0], l => l.unit.model.hierarchy.atoms.auth_atom_id.value(l.element))
-                            // .add('cached concat str', () => concatProperty(structures[0], Property.cachedAtomColumn(m => m.hierarchy.atoms.auth_atom_id)))
-                            .on('cycle', function (e) { return console.log(String(e.target)); })
-                            .run();
-                        return [2 /*return*/];
-                }
-            });
-        });
-    }
-    PropertyAccess.run = run;
-})(PropertyAccess = exports.PropertyAccess || (exports.PropertyAccess = {}));
-PropertyAccess.runBonds();
-//# sourceMappingURL=structure.js.map