molstar
Version:
A comprehensive macromolecular library.
114 lines • 5.29 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Adapted from NGL.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseCube = void 0;
var tslib_1 = require("tslib");
var linear_algebra_1 = require("../../../mol-math/linear-algebra");
var tokenizer_1 = require("../common/text/tokenizer");
var db_1 = require("../../../mol-data/db");
var mol_task_1 = require("../../../mol-task");
var result_1 = require("../result");
var number_parser_1 = require("../common/text/number-parser");
var bohrToAngstromFactor = 0.529177210859;
function readHeader(tokenizer) {
var headerLines = tokenizer_1.Tokenizer.readLines(tokenizer, 6);
var h = function (k, l) {
var field = +headerLines[k].trim().split(/\s+/g)[l];
return Number.isNaN(field) ? 0 : field;
};
var basis = function (i) {
var n = h(i + 2, 0);
var s = bohrToAngstromFactor;
return [Math.abs(n), linear_algebra_1.Vec3.create(h(i + 2, 1) * s, h(i + 2, 2) * s, h(i + 2, 3) * s), n];
};
var comment1 = headerLines[0].trim();
var comment2 = headerLines[1].trim();
var _a = basis(0), atomCount = _a[0], origin = _a[1], rawAtomCount = _a[2];
var _b = basis(1), NVX = _b[0], basisX = _b[1];
var _c = basis(2), NVY = _c[0], basisY = _c[1];
var _d = basis(3), NVZ = _d[0], basisZ = _d[1];
var atoms = readAtoms(tokenizer, atomCount, bohrToAngstromFactor);
var dataSetIds = [];
if (rawAtomCount >= 0) {
var nVal = h(2, 4);
if (nVal === 0)
nVal = 1;
for (var i = 0; i < nVal; i++)
dataSetIds.push(i);
}
else {
var counts = tokenizer_1.Tokenizer.readLine(tokenizer).trim().split(/\s+/g);
for (var i = 0, _i = +counts[0]; i < _i; i++)
dataSetIds.push(+counts[i + 1]);
}
var header = { orbitals: rawAtomCount < 0, comment1: comment1, comment2: comment2, atomCount: atomCount, origin: origin, dim: linear_algebra_1.Vec3.create(NVX, NVY, NVZ), basisX: basisX, basisY: basisY, basisZ: basisZ, dataSetIds: dataSetIds };
return { header: header, atoms: atoms };
}
function readAtoms(tokenizer, count, scaleFactor) {
var number = new Int32Array(count);
var value = new Float64Array(count);
var x = new Float32Array(count);
var y = new Float32Array(count);
var z = new Float32Array(count);
for (var i = 0; i < count; i++) {
var fields = tokenizer_1.Tokenizer.readLine(tokenizer).trim().split(/\s+/g);
number[i] = +fields[0];
value[i] = +fields[1];
x[i] = +fields[2] * scaleFactor;
y[i] = +fields[3] * scaleFactor;
z[i] = +fields[4] * scaleFactor;
}
return {
count: count,
number: db_1.Column.ofArray({ array: number, schema: db_1.Column.Schema.int }),
nuclearCharge: db_1.Column.ofArray({ array: value, schema: db_1.Column.Schema.float }),
x: db_1.Column.ofArray({ array: x, schema: db_1.Column.Schema.float }),
y: db_1.Column.ofArray({ array: y, schema: db_1.Column.Schema.float }),
z: db_1.Column.ofArray({ array: z, schema: db_1.Column.Schema.float })
};
}
function readValues(ctx, tokenizer, header) {
var N = header.dim[0] * header.dim[1] * header.dim[2] * header.dataSetIds.length;
var chunkSize = 100 * 100 * 100;
var data = new Float64Array(N);
var offset = 0;
return (0, mol_task_1.chunkedSubtask)(ctx, chunkSize, data, function (count, data) {
var max = Math.min(N, offset + count);
for (var i = offset; i < max; i++) {
tokenizer_1.Tokenizer.skipWhitespace(tokenizer);
tokenizer.tokenStart = tokenizer.position;
tokenizer_1.Tokenizer.eatValue(tokenizer);
data[i] = (0, number_parser_1.parseFloat)(tokenizer.data, tokenizer.tokenStart, tokenizer.tokenEnd);
}
offset = max;
return max === N ? 0 : chunkSize;
}, function (ctx, _, i) { return ctx.update({ current: Math.min(i, N), max: N }); });
}
function parseCube(data, name) {
var _this = this;
return mol_task_1.Task.create('Parse Cube', function (taskCtx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var tokenizer, _a, header, atoms, values;
return (0, tslib_1.__generator)(this, function (_b) {
switch (_b.label) {
case 0: return [4 /*yield*/, taskCtx.update('Reading header...')];
case 1:
_b.sent();
tokenizer = (0, tokenizer_1.Tokenizer)(data);
_a = readHeader(tokenizer), header = _a.header, atoms = _a.atoms;
return [4 /*yield*/, readValues(taskCtx, tokenizer, header)];
case 2:
values = _b.sent();
return [2 /*return*/, result_1.ReaderResult.success({ header: header, atoms: atoms, values: values, name: name })];
}
});
}); });
}
exports.parseCube = parseCube;
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