molstar
Version:
A comprehensive macromolecular library.
529 lines • 29.4 kB
JavaScript
"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/" + pdbId.toLowerCase() + "/full?encoding=bcif";
}
function getBcifPath(pdbId) {
return DATA_DIR + "/" + 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 " + 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 " + 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(DATA_DIR + "/" + id + "_assembly.bcif", (0, mmcif_1.to_mmCIF)(id, a, true));
// fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, Selection.unionStructure(alas), true));
console.log('exported');
return [2 /*return*/];
}
});
});
}
PropertyAccess.testAssembly = testAssembly;
function testSymmetry(id, s) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var a;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
console.time('symmetry');
return [4 /*yield*/, structure_1.StructureSymmetry.buildSymmetryRange(s, linear_algebra_1.Vec3.create(-1, -1, -1), linear_algebra_1.Vec3.create(1, 1, 1)).run()];
case 1:
a = _a.sent();
// const auth_comp_id = SP.residue.auth_comp_id;
// const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
// const alas = await query(q1, a);
console.timeEnd('symmetry');
fs.writeFileSync(DATA_DIR + "/" + id + "_symm.bcif", (0, mmcif_1.to_mmCIF)(id, a, true));
// fs.writeFileSync(`${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(DATA_DIR + "/" + 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();
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