molstar 3.0.0-dev.0 → 3.0.0-dev.5

package/lib/mol-io/reader/_spec/column.spec.js

@@ -1,72 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { FixedColumnProvider as FixedColumn } from '../common/text/column/fixed';
-import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
-import { Column, ColumnHelpers } from '../../../mol-data/db';
-var lines = [
-    '1.123 abc',
-    '1.00  a',
-    '1.1    bcd   ',
-    '',
-    ' 5'
-];
-var linesData = lines.join('\n');
-var linesTokens = (function () {
-    var tokens = [];
-    var last = 0;
-    for (var _i = 0, lines_1 = lines; _i < lines_1.length; _i++) {
-        var l = lines_1[_i];
-        tokens.push(last, last + l.length);
-        last += l.length + 1;
-    }
-    if (tokens[tokens.length - 1] > linesData.length)
-        tokens[tokens.length - 1] = linesData.length;
-    return tokens;
-}());
-describe('fixed text column', function () {
-    var col = FixedColumn({ data: linesData, indices: linesTokens, count: lines.length });
-    var col1 = col(0, 5, Column.Schema.float);
-    var col2 = col(5, 4, Column.Schema.str);
-    it('number', function () {
-        expect(col1.value(0)).toBe(1.123);
-        expect(col1.value(1)).toBe(1.0);
-        expect(col1.value(2)).toBe(1.1);
-        expect(col1.value(3)).toBe(0);
-        expect(col1.value(4)).toBe(5);
-    });
-    it('str', function () {
-        expect(col2.value(0)).toBe('abc');
-        expect(col2.value(1)).toBe('a');
-        expect(col2.value(2)).toBe('bc');
-        expect(col2.value(3)).toBe('');
-        expect(col2.value(4)).toBe('');
-    });
-});
-describe('token text column', function () {
-    var tokensData = '321';
-    var col = TokenColumn({ data: tokensData, indices: [0, 1, 1, 2, 2, 3], count: 3 });
-    var col1 = col(Column.Schema.int);
-    it('number', function () {
-        expect(col1.value(0)).toBe(3);
-        expect(col1.value(1)).toBe(2);
-        expect(col1.value(2)).toBe(1);
-    });
-});
-describe('binary column', function () {
-    it('window works', function () {
-        var xs = new Float64Array([1, 2, 3, 4]);
-        var w1 = ColumnHelpers.typedArrayWindow(xs, { start: 1 });
-        var w2 = ColumnHelpers.typedArrayWindow(xs, { start: 2, end: 4 });
-        expect(w1.length).toBe(3);
-        for (var i = 0; i < w1.length; i++)
-            expect(w1[i]).toBe(xs[i + 1]);
-        expect(w2.length).toBe(2);
-        for (var i = 0; i < w2.length; i++)
-            expect(w2[i]).toBe(xs[i + 2]);
-    });
-});
-//# sourceMappingURL=column.spec.js.map

package/lib/mol-io/reader/_spec/column.spec.js.map

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package/lib/mol-io/reader/_spec/common.spec.d.ts

@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export {};

package/lib/mol-io/reader/_spec/common.spec.js

@@ -1,37 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { parseFloat as fastParseFloat, parseInt as fastParseInt, getNumberType } from '../../../mol-io/reader/common/text/number-parser';
-describe('common', function () {
-    it('number-parser fastParseFloat', function () {
-        // ignore suffix numbers in parentheses
-        expect(fastParseFloat('11.0829(23)', 0, 11)).toBe(11.0829);
-        // scientific with no space between consecutive values
-        expect(fastParseFloat('-5.1E-01-6.1E-01', 0, 11)).toBe(-0.51);
-        // ignore plus sign
-        expect(fastParseFloat('+0.149', 0, 6)).toBe(0.149);
-    });
-    it('number-parser fastParseInt', function () {
-        // ignore suffix numbers in parentheses
-        expect(fastParseInt('11(23)', 0, 11)).toBe(11);
-        // ignore plus sign
-        expect(fastParseFloat('+10149', 0, 6)).toBe(10149);
-    });
-    it('number-parser getNumberType', function () {
-        expect(getNumberType('11')).toBe(0 /* Int */);
-        expect(getNumberType('5E93')).toBe(2 /* Scientific */);
-        expect(getNumberType('0.42')).toBe(1 /* Float */);
-        expect(getNumberType('Foo123')).toBe(3 /* NaN */);
-        expect(getNumberType('11.0829(23)')).toBe(3 /* NaN */);
-        expect(getNumberType('1..2')).toBe(3 /* NaN */);
-        expect(getNumberType('.')).toBe(3 /* NaN */);
-        expect(getNumberType('-.')).toBe(3 /* NaN */);
-        expect(getNumberType('e')).toBe(3 /* NaN */);
-        expect(getNumberType('-e')).toBe(3 /* NaN */);
-        expect(getNumberType('1e')).toBe(2 /* Scientific */);
-        expect(getNumberType('-1e')).toBe(2 /* Scientific */);
-    });
-});
-//# sourceMappingURL=common.spec.js.map

package/lib/mol-io/reader/_spec/common.spec.js.map

@@ -1 +0,0 @@
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package/lib/mol-io/reader/_spec/csv.spec.d.ts

@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export {};

package/lib/mol-io/reader/_spec/csv.spec.js

@@ -1,85 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { __awaiter, __generator } from "tslib";
-import { parseCsv } from '../csv/parser';
-var csvStringBasic = "StrCol,IntCol,FloatCol\n# comment\nstring1,-1,-0.34e3\nstring2,42,2.44";
-var csvStringAdvanced = "StrCol,\"Int Col\",FloatCol\n string1  \t , -1,  -0.34e3\n    # comment\n   \" stri\nng2\" ,42, 2.44 ";
-var tabString = "StrCol\tIntCol\tFloatCol\nstring1\t-1\t-0.34e3\nstring2\t42\t2.44";
-describe('csv reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, csvFile, strCol, intCol, floatCol;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseCsv(csvStringBasic).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    csvFile = parsed.result;
-                    strCol = csvFile.table.getColumn('StrCol');
-                    if (strCol)
-                        expect(strCol.toStringArray()).toEqual(['string1', 'string2']);
-                    intCol = csvFile.table.getColumn('IntCol');
-                    if (intCol)
-                        expect(intCol.toIntArray()).toEqual([-1, 42]);
-                    floatCol = csvFile.table.getColumn('FloatCol');
-                    if (floatCol)
-                        expect(floatCol.toFloatArray()).toEqual([-340.0, 2.44]);
-                    expect.assertions(3);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('advanced', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, csvFile, strCol, intCol, floatCol;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseCsv(csvStringAdvanced).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    csvFile = parsed.result;
-                    strCol = csvFile.table.getColumn('StrCol');
-                    if (strCol)
-                        expect(strCol.toStringArray()).toEqual(['string1', ' stri\nng2']);
-                    intCol = csvFile.table.getColumn('Int Col');
-                    if (intCol)
-                        expect(intCol.toIntArray()).toEqual([-1, 42]);
-                    floatCol = csvFile.table.getColumn('FloatCol');
-                    if (floatCol)
-                        expect(floatCol.toFloatArray()).toEqual([-340.0, 2.44]);
-                    expect.assertions(3);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('tabs', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, csvFile, strCol, intCol, floatCol;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseCsv(tabString, { delimiter: '\t' }).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    csvFile = parsed.result;
-                    strCol = csvFile.table.getColumn('StrCol');
-                    if (strCol)
-                        expect(strCol.toStringArray()).toEqual(['string1', 'string2']);
-                    intCol = csvFile.table.getColumn('IntCol');
-                    if (intCol)
-                        expect(intCol.toIntArray()).toEqual([-1, 42]);
-                    floatCol = csvFile.table.getColumn('FloatCol');
-                    if (floatCol)
-                        expect(floatCol.toFloatArray()).toEqual([-340.0, 2.44]);
-                    expect.assertions(3);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=csv.spec.js.map

package/lib/mol-io/reader/_spec/csv.spec.js.map

@@ -1 +0,0 @@
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package/lib/mol-io/reader/_spec/dcd.spec.d.ts

@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export {};

package/lib/mol-io/reader/_spec/dcd.spec.js

@@ -1,69 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { __awaiter, __generator } from "tslib";
-import { parseDcd } from '../dcd/parser';
-function createDcdData() {
-    var data = new Uint8Array(4 * 128);
-    var dv = new DataView(data.buffer);
-    // set little endian
-    dv.setInt32(0, 84);
-    // set format string
-    dv.setUint8(4, 'D'.charCodeAt(0));
-    dv.setUint8(5, 'R'.charCodeAt(0));
-    dv.setUint8(6, 'O'.charCodeAt(0));
-    dv.setUint8(7, 'C'.charCodeAt(0));
-    dv.setInt32(8, 1); // NSET
-    // header end
-    dv.setInt32(22 * 4, 84);
-    // title
-    var titleEnd = 164;
-    var titleStart = 23 * 4 + 1;
-    dv.setInt32(23 * 4, titleEnd);
-    dv.setInt32(titleStart + titleEnd + 4 - 1, titleEnd);
-    // atoms
-    var atomStart = 23 * 4 + titleEnd + 8;
-    dv.setInt32(atomStart, 4);
-    dv.setInt32(atomStart + 4, 1); // one atom
-    dv.setInt32(atomStart + 8, 4);
-    // coords
-    var coordsStart = atomStart + 12;
-    dv.setInt32(coordsStart, 4);
-    dv.setFloat32(coordsStart + 4, 0.1);
-    dv.setInt32(coordsStart + 8, 4);
-    dv.setInt32(coordsStart + 12, 4);
-    dv.setFloat32(coordsStart + 16, 0.2);
-    dv.setInt32(coordsStart + 20, 4);
-    dv.setInt32(coordsStart + 24, 4);
-    dv.setFloat32(coordsStart + 28, 0.3);
-    dv.setInt32(coordsStart + 32, 4);
-    return data;
-}
-describe('dcd reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var data, parsed, dcdFile, header, frames;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    data = createDcdData();
-                    return [4 /*yield*/, parseDcd(data).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.message);
-                    }
-                    dcdFile = parsed.result;
-                    header = dcdFile.header, frames = dcdFile.frames;
-                    expect(header.NSET).toBe(1);
-                    expect(header.NATOM).toBe(1);
-                    expect(frames[0].x[0]).toBeCloseTo(0.1, 0.0001);
-                    expect(frames[0].y[0]).toBeCloseTo(0.2, 0.0001);
-                    expect(frames[0].z[0]).toBeCloseTo(0.3, 0.0001);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=dcd.spec.js.map

package/lib/mol-io/reader/_spec/dcd.spec.js.map

@@ -1 +0,0 @@
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package/lib/mol-io/reader/_spec/gro.spec.d.ts

@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-export {};

package/lib/mol-io/reader/_spec/gro.spec.js

@@ -1,79 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { __awaiter, __generator } from "tslib";
-import { parseGRO } from '../gro/parser';
-var groString = "MD of 2 waters, t= 4.2\n    6\n    1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434\n    1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791\n    1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180\n    2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734\n    2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257\n    2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244\n   1.82060   2.82060   3.82060";
-var groStringHighPrecision = "Generated by trjconv : 2168 system t=  15.00000\n    3\n    1ETH     C1    1   2.735383   2.672010   1.450194  0.2345 -0.1622 0.2097\n    1ETH    H11    2   0.015804   2.716597   1.460588  0.8528 -0.7984 0.6605\n    1ETH    H12    3   2.744822   2.565544   1.409227 -2.3812  2.8618 1.8101\n   1.82060   2.82060   3.82060";
-describe('gro reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, groFile, data, header, atoms;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseGRO(groString).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        console.log(parsed);
-                        return [2 /*return*/];
-                    }
-                    groFile = parsed.result;
-                    data = groFile.structures[0];
-                    header = data.header, atoms = data.atoms;
-                    expect(header.title).toBe('MD of 2 waters');
-                    expect(header.timeInPs).toBeCloseTo(4.2);
-                    expect(header.hasVelocities).toBe(true);
-                    expect(header.precision.position).toBe(3);
-                    expect(header.precision.velocity).toBe(4);
-                    expect(header.box[0]).toBeCloseTo(1.82060, 0.00001);
-                    expect(header.box[1]).toBeCloseTo(2.82060, 0.00001);
-                    expect(header.box[2]).toBeCloseTo(3.82060, 0.00001);
-                    expect(atoms.count).toBe(6);
-                    expect(atoms.x.value(0)).toBeCloseTo(0.126, 0.001);
-                    expect(atoms.y.value(0)).toBeCloseTo(1.624, 0.001);
-                    expect(atoms.z.value(0)).toBeCloseTo(1.679, 0.001);
-                    expect(atoms.vx.value(5)).toBeCloseTo(1.9427, 0.0001);
-                    expect(atoms.vy.value(5)).toBeCloseTo(-0.8216, 0.0001);
-                    expect(atoms.vz.value(5)).toBeCloseTo(-0.0244, 0.0001);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('high precision', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, groFile, data, header, atoms;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseGRO(groStringHighPrecision).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        console.log(parsed);
-                        return [2 /*return*/];
-                    }
-                    groFile = parsed.result;
-                    data = groFile.structures[0];
-                    header = data.header, atoms = data.atoms;
-                    expect(header.title).toBe('Generated by trjconv : 2168 system');
-                    expect(header.timeInPs).toBeCloseTo(15);
-                    expect(header.hasVelocities).toBe(true);
-                    expect(header.precision.position).toBe(6);
-                    expect(header.precision.velocity).toBe(4);
-                    expect(header.box[0]).toBeCloseTo(1.82060, 0.00001);
-                    expect(header.box[1]).toBeCloseTo(2.82060, 0.00001);
-                    expect(header.box[2]).toBeCloseTo(3.82060, 0.00001);
-                    expect(atoms.count).toBe(3);
-                    expect(atoms.x.value(1)).toBeCloseTo(0.015804, 0.000001);
-                    expect(atoms.y.value(1)).toBeCloseTo(2.716597, 0.000001);
-                    expect(atoms.z.value(1)).toBeCloseTo(1.460588, 0.000001);
-                    expect(atoms.vx.value(0)).toBeCloseTo(0.2345, 0.0001);
-                    expect(atoms.vy.value(0)).toBeCloseTo(-0.1622, 0.0001);
-                    expect(atoms.vz.value(0)).toBeCloseTo(0.2097, 0.0001);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=gro.spec.js.map

package/lib/mol-io/reader/_spec/gro.spec.js.map

@@ -1 +0,0 @@
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package/lib/mol-io/reader/_spec/mol.spec.d.ts

@@ -1 +0,0 @@
-export {};

package/lib/mol-io/reader/_spec/mol.spec.js

@@ -1,31 +0,0 @@
-import { __awaiter, __generator } from "tslib";
-import { parseMol } from '../mol/parser';
-var MolString = "2244\n  -OEChem-04072009073D\n\n 21 21  0     0  0  0  0  0  0999 V2000\n    1.2333    0.5540    0.7792 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.6952   -2.7148   -0.7502 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7958   -2.1843    0.8685 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.7813    0.8105   -1.4821 O   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.0857    0.6088    0.4403 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7927   -0.5515    0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7288    1.8464    0.4133 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.1426   -0.4741   -0.2184 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.0787    1.9238    0.0706 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7855    0.7636   -0.2453 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1409   -1.8536    0.1477 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.1094    0.6715   -0.3113 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.5305    0.5996    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.1851    2.7545    0.6593 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.7247   -1.3605   -0.4564 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -2.5797    2.8872    0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -3.8374    0.8238   -0.5090 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7290    1.4184    0.8593 H   0  0  0  0  0  0  0  0  0  0  0  0\n    4.2045    0.6969   -0.6924 H   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7105   -0.3659    0.6426 H   0  0  0  0  0  0  0  0  0  0  0  0\n   -0.2555   -3.5916   -0.7337 H   0  0  0  0  0  0  0  0  0  0  0  0\n  1  5  1  0  0  0  0\n  1 12  1  0  0  0  0\n  2 11  1  0  0  0  0\n  2 21  1  0  0  0  0\n  3 11  2  0  0  0  0\n  4 12  2  0  0  0  0\n  5  6  1  0  0  0  0\n  5  7  2  0  0  0  0\n  6  8  2  0  0  0  0\n  6 11  1  0  0  0  0\n  7  9  1  0  0  0  0\n  7 14  1  0  0  0  0\n  8 10  1  0  0  0  0\n  8 15  1  0  0  0  0\n  9 10  2  0  0  0  0\n  9 16  1  0  0  0  0\n 10 17  1  0  0  0  0\n 12 13  1  0  0  0  0\n 13 18  1  0  0  0  0\n 13 19  1  0  0  0  0\n 13 20  1  0  0  0  0\nM  END";
-describe('mol reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, _a, atoms, bonds;
-        return __generator(this, function (_b) {
-            switch (_b.label) {
-                case 0: return [4 /*yield*/, parseMol(MolString).run()];
-                case 1:
-                    parsed = _b.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.message);
-                    }
-                    _a = parsed.result, atoms = _a.atoms, bonds = _a.bonds;
-                    // number of structures
-                    expect(atoms.count).toBe(21);
-                    expect(bonds.count).toBe(21);
-                    expect(atoms.x.value(0)).toBeCloseTo(1.2333, 0.001);
-                    expect(atoms.y.value(0)).toBeCloseTo(0.5540, 0.0001);
-                    expect(atoms.z.value(0)).toBeCloseTo(0.7792, 0.0001);
-                    expect(atoms.type_symbol.value(0)).toBe('O');
-                    expect(bonds.atomIdxA.value(20)).toBe(13);
-                    expect(bonds.atomIdxB.value(20)).toBe(20);
-                    expect(bonds.order.value(20)).toBe(1);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=mol.spec.js.map

package/lib/mol-io/reader/_spec/mol.spec.js.map

@@ -1 +0,0 @@
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package/lib/mol-io/reader/_spec/mol2.spec.d.ts

@@ -1 +0,0 @@
-export {};