molstar
Version:
A comprehensive macromolecular library.
89 lines • 4.3 kB
JavaScript
;
Object.defineProperty(exports, "__esModule", { value: true });
exports.test = exports.readCIF = void 0;
var tslib_1 = require("tslib");
var util = (0, tslib_1.__importStar)(require("util"));
var fs = (0, tslib_1.__importStar)(require("fs"));
var cif_1 = require("../mol-io/reader/cif");
var structure_1 = require("../mol-model/structure");
var geometry_1 = require("../mol-math/geometry");
// import { sortArray } from 'mol-data/util';
var int_1 = require("../mol-data/int");
var mmcif_1 = require("../mol-model-formats/structure/mmcif");
var boundary_1 = require("../mol-math/geometry/boundary");
require('util.promisify').shim();
var readFileAsync = util.promisify(fs.readFile);
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')];
}
});
});
}
function readCIF(path) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var input, comp, parsed, models, structures;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, readData(path)];
case 1:
input = _a.sent();
comp = typeof input === 'string' ? cif_1.CIF.parseText(input) : cif_1.CIF.parseBinary(input);
return [4 /*yield*/, comp.run()];
case 2:
parsed = _a.sent();
if (parsed.isError) {
throw parsed;
}
return [4 /*yield*/, (0, mmcif_1.trajectoryFromMmCIF)(parsed.result.blocks[0]).run()];
case 3:
models = _a.sent();
structures = [structure_1.Structure.ofModel(models.representative)];
return [2 /*return*/, { mmcif: models.representative.sourceData.data, models: models, structures: structures }];
}
});
});
}
exports.readCIF = readCIF;
function test() {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var _a, mmcif, structures, position, lookup, result;
return (0, tslib_1.__generator)(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, readCIF('e:/test/quick/1tqn_updated.cif')];
case 1:
_a = _b.sent(), mmcif = _a.mmcif, structures = _a.structures;
position = { x: mmcif.db.atom_site.Cartn_x.toArray(), y: mmcif.db.atom_site.Cartn_y.toArray(), z: mmcif.db.atom_site.Cartn_z.toArray(),
indices: int_1.OrderedSet.ofBounds(0, mmcif.db.atom_site._rowCount),
// radius: [1, 1, 1, 1]
// indices: [1]
};
lookup = (0, geometry_1.GridLookup3D)(position, (0, boundary_1.getBoundary)(position));
console.log(lookup.boundary.box, lookup.boundary.sphere);
result = lookup.find(-30.07, 8.178, -13.897, 10);
console.log(result.count); // , sortArray(result.indices));
// const sl = structures[0].lookup3d;
// const result1 = sl.find(-30.07, 8.178, -13.897, 10);
// console.log(result1.count);//, result1.indices);
console.log(structures[0].boundary);
console.log(lookup.boundary);
return [2 /*return*/];
}
});
});
}
exports.test = test;
test();
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