npm - molstar - Versions diffs - 3.0.0-dev.0 → 3.0.0-dev.2 - Mend

molstar 3.0.0-dev.0 → 3.0.0-dev.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (2946) hide show

package/lib/commonjs/mol-math/linear-algebra/_spec/tensor.spec.js DELETED Viewed

@@ -1,286 +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 });
-var tensor_1 = require("../tensor");
-var mat4_1 = require("../3d/mat4");
-describe('tensor', function () {
-    it('vector', function () {
-        var V = tensor_1.Tensor.Vector(3);
-        var data = V.create();
-        V.set(data, 0, 1);
-        V.set(data, 1, 2);
-        V.set(data, 2, 3);
-        expect(data).toEqual(new Float64Array([1, 2, 3]));
-        expect(V.get(data, 0)).toEqual(1);
-        expect(V.get(data, 1)).toEqual(2);
-        expect(V.get(data, 2)).toEqual(3);
-    });
-    it('matrix cm', function () {
-        var M = tensor_1.Tensor.ColumnMajorMatrix(3, 2, Int32Array);
-        var data = M.create();
-        // rows: [ [0, 1], [1, 2], [2, 3]  ]
-        for (var i = 0; i < 3; i++) {
-            for (var j = 0; j < 2; j++) {
-                M.set(data, i, j, i + j);
-            }
-        }
-        expect(data).toEqual(new Int32Array([0, 1, 2, 1, 2, 3]));
-    });
-    it('matrix rm', function () {
-        var M = tensor_1.Tensor.RowMajorMatrix(3, 2, Int32Array);
-        var data = M.create();
-        // rows: [ [0, 1], [1, 2], [2, 3]  ]
-        for (var i = 0; i < 3; i++) {
-            for (var j = 0; j < 2; j++) {
-                M.set(data, i, j, i + j);
-            }
-        }
-        expect(data).toEqual(new Int32Array([0, 1, 1, 2, 2, 3]));
-    });
-    it('mat4 equiv', function () {
-        var M = tensor_1.Tensor.ColumnMajorMatrix(4, 4);
-        var data = M.create();
-        var m = (0, mat4_1.Mat4)();
-        for (var i = 0; i < 4; i++) {
-            for (var j = 0; j < 4; j++) {
-                var v = (i + 1) * (j + 2);
-                M.set(data, i, j, v);
-                mat4_1.Mat4.setValue(m, i, j, v);
-            }
-        }
-        for (var i = 0; i < 16; i++)
-            expect(data[i]).toEqual(m[i]);
-    });
-    it('2d ij', function () {
-        var M = tensor_1.Tensor.Space([3, 4], [0, 1]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 4);
-        var o = 0;
-        for (var i = 0; i < 3; i++) {
-            for (var j = 0; j < 4; j++) {
-                M.set(data, i, j, o);
-                expect(M.get(data, i, j)).toBe(o);
-                exp[o] = o;
-                o++;
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('2d ji', function () {
-        var M = tensor_1.Tensor.Space([3, 4], [1, 0]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 4);
-        var o = 0;
-        for (var j = 0; j < 4; j++) {
-            for (var i = 0; i < 3; i++) {
-                M.set(data, i, j, o);
-                expect(M.get(data, i, j)).toBe(o);
-                exp[o] = o;
-                o++;
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('3d ijk', function () {
-        var M = tensor_1.Tensor.Space([3, 4, 5], [0, 1, 2]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 4 * 5);
-        var o = 0;
-        for (var i = 0; i < 3; i++) {
-            for (var j = 0; j < 4; j++) {
-                for (var k = 0; k < 5; k++) {
-                    M.set(data, i, j, k, o);
-                    expect(M.get(data, i, j, k)).toBe(o);
-                    exp[o] = o;
-                    o++;
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('3d ikj', function () {
-        var M = tensor_1.Tensor.Space([3, 3, 3], [0, 2, 1]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 3 * 3);
-        var o = 0;
-        for (var i = 0; i < 3; i++) {
-            for (var k = 0; k < 3; k++) {
-                for (var j = 0; j < 3; j++) {
-                    M.set(data, i, j, k, o);
-                    expect(M.get(data, i, j, k)).toBe(o);
-                    exp[o] = o;
-                    o++;
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('3d jik', function () {
-        var M = tensor_1.Tensor.Space([3, 3, 3], [1, 0, 2]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 3 * 3);
-        var o = 0;
-        for (var j = 0; j < 3; j++) {
-            for (var i = 0; i < 3; i++) {
-                for (var k = 0; k < 3; k++) {
-                    M.set(data, i, j, k, o);
-                    expect(M.get(data, i, j, k)).toBe(o);
-                    exp[o] = o;
-                    o++;
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('3d jki', function () {
-        var M = tensor_1.Tensor.Space([3, 3, 3], [1, 2, 0]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 3 * 3);
-        var o = 0;
-        for (var j = 0; j < 3; j++) {
-            for (var k = 0; k < 3; k++) {
-                for (var i = 0; i < 3; i++) {
-                    M.set(data, i, j, k, o);
-                    expect(M.get(data, i, j, k)).toBe(o);
-                    exp[o] = o;
-                    o++;
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('3d kij', function () {
-        var M = tensor_1.Tensor.Space([3, 3, 3], [2, 0, 1]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 3 * 3);
-        var o = 0;
-        for (var k = 0; k < 3; k++) {
-            for (var i = 0; i < 3; i++) {
-                for (var j = 0; j < 3; j++) {
-                    M.set(data, i, j, k, o);
-                    expect(M.get(data, i, j, k)).toBe(o);
-                    exp[o] = o;
-                    o++;
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('3d kji', function () {
-        var M = tensor_1.Tensor.Space([3, 3, 3], [2, 1, 0]);
-        var data = M.create();
-        var exp = new Float64Array(3 * 3 * 3);
-        var o = 0;
-        for (var k = 0; k < 3; k++) {
-            for (var j = 0; j < 3; j++) {
-                for (var i = 0; i < 3; i++) {
-                    M.set(data, i, j, k, o);
-                    expect(M.get(data, i, j, k)).toBe(o);
-                    exp[o] = o;
-                    o++;
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('4d jikl', function () {
-        var M = tensor_1.Tensor.Space([2, 3, 4, 5], [1, 0, 2, 3]);
-        var data = M.create();
-        var exp = new Float64Array(2 * 3 * 4 * 5);
-        var o = 0;
-        for (var j = 0; j < 3; j++) {
-            for (var i = 0; i < 2; i++) {
-                for (var k = 0; k < 4; k++) {
-                    for (var l = 0; l < 5; l++) {
-                        M.set(data, i, j, k, l, o);
-                        expect(M.get(data, i, j, k, l)).toBe(o);
-                        exp[o] = o;
-                        o++;
-                    }
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('4d jilk', function () {
-        var M = tensor_1.Tensor.Space([2, 3, 4, 5], [1, 0, 3, 2]);
-        var data = M.create();
-        var exp = new Float64Array(2 * 3 * 4 * 5);
-        var o = 0;
-        for (var j = 0; j < 3; j++) {
-            for (var i = 0; i < 2; i++) {
-                for (var l = 0; l < 5; l++) {
-                    for (var k = 0; k < 4; k++) {
-                        M.set(data, i, j, k, l, o);
-                        expect(M.get(data, i, j, k, l)).toBe(o);
-                        exp[o] = o;
-                        o++;
-                    }
-                }
-            }
-        }
-        expect(data).toEqual(exp);
-    });
-    it('indexing', function () {
-        function permutations(inputArr) {
-            var result = [];
-            function permute(arr, m) {
-                if (m === void 0) { m = []; }
-                if (arr.length === 0) {
-                    result.push(m);
-                }
-                else {
-                    for (var i = 0; i < arr.length; i++) {
-                        var curr = arr.slice();
-                        var next = curr.splice(i, 1);
-                        permute(curr.slice(), m.concat(next));
-                    }
-                }
-            }
-            permute(inputArr);
-            return result;
-        }
-        var _loop_1 = function (dim) {
-            var axes = [], dims = [];
-            var u = [], v = [];
-            for (var i = 0; i < dim; i++) {
-                axes.push(i);
-                dims.push(3);
-                u.push(0);
-                v.push(0);
-            }
-            var forEachDim = function (space, d) {
-                if (d === dim) {
-                    var o = space.dataOffset.apply(space, u);
-                    space.getCoords(o, v);
-                    for (var e = 0; e < dims.length; e++) {
-                        expect(u[e]).toEqual(v[e]);
-                        return false;
-                    }
-                }
-                else {
-                    for (var i = 0; i < dims[d]; i++) {
-                        u[d] = i;
-                        if (!forEachDim(space, d + 1))
-                            return false;
-                    }
-                }
-                return true;
-            };
-            for (var _i = 0, _a = permutations(axes); _i < _a.length; _i++) {
-                var ao = _a[_i];
-                var space = tensor_1.Tensor.Space(dims, ao);
-                if (!forEachDim(space, 0))
-                    break;
-            }
-        };
-        for (var dim = 1; dim <= 5; dim++) {
-            _loop_1(dim);
-        }
-    });
-});
-//# sourceMappingURL=tensor.spec.js.map

package/lib/commonjs/mol-math/linear-algebra/_spec/tensor.spec.js.map DELETED Viewed

@@ -1 +0,0 @@

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package/lib/commonjs/mol-math/linear-algebra/_spec/vec3.spec.d.ts DELETED Viewed

@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-export {};

package/lib/commonjs/mol-math/linear-algebra/_spec/vec3.spec.js DELETED Viewed

@@ -1,20 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-var vec3_1 = require("../3d/vec3");
-describe('vec3', function () {
-    var vec1 = [1, 2, 3];
-    var vec2 = [2, 3, 1];
-    var orthVec1 = [0, 1, 0];
-    var orthVec2 = [1, 0, 0];
-    it('angle calculation', function () {
-        expect(vec3_1.Vec3.angle(vec1, vec1) * 360 / (2 * Math.PI)).toBe(0.0);
-        expect(vec3_1.Vec3.angle(orthVec1, orthVec2) * 360 / (2 * Math.PI)).toBe(90.0);
-        expect(vec3_1.Vec3.angle(vec1, vec2)).toBeCloseTo(0.666946);
-    });
-});
-//# sourceMappingURL=vec3.spec.js.map

package/lib/commonjs/mol-math/linear-algebra/_spec/vec3.spec.js.map DELETED Viewed

@@ -1 +0,0 @@

- {"version":3,"file":"vec3.spec.js","sourceRoot":"","sources":["../../../../../src/mol-math/linear-algebra/_spec/vec3.spec.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;AAEH,mCAAkC;AAElC,QAAQ,CAAC,MAAM,EAAE;IACb,IAAM,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAS,CAAC;IAC/B,IAAM,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAS,CAAC;IAC/B,IAAM,QAAQ,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAS,CAAC;IACnC,IAAM,QAAQ,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAS,CAAC;IAEnC,EAAE,CAAC,mBAAmB,EAAE;QACpB,MAAM,CAAC,WAAI,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC/D,MAAM,CAAC,WAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,GAAG,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACxE,MAAM,CAAC,WAAI,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC;IACzD,CAAC,CAAC,CAAC;AACP,CAAC,CAAC,CAAC"}

package/lib/commonjs/mol-math/linear-algebra/matrix/evd.js.map DELETED Viewed

@@ -1 +0,0 @@

- 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package/lib/commonjs/mol-model/loci.js.map DELETED Viewed

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package/lib/commonjs/mol-model/sequence/alignment/_spec/alignment.spec.d.ts DELETED Viewed

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

package/lib/commonjs/mol-model/sequence/alignment/_spec/alignment.spec.js DELETED Viewed

@@ -1,25 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-var alignment_1 = require("../alignment");
-describe('Alignment', function () {
-    it('basic', function () {
-        // 3PQR: Rhodopsin
-        var seqA = 'MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA';
-        // 3SN6: Endolysin,Beta-2 adrenergic
-        var seqB = 'DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSG';
-        var _a = (0, alignment_1.align)(seqA, seqB, {
-            gapPenalty: -11,
-            gapExtensionPenalty: -1,
-            substMatrix: 'blosum62'
-        }), aliA = _a.aliA, aliB = _a.aliB, score = _a.score;
-        expect(aliA).toEqual('------------------------------------------------------------------------------------------------------------------------------------------------MNGTEGPNFYVPFSNKTGVVRSPFEA---PQYYLAEPWQFSM--LAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH---GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMS-NFRFGENHAIMGVAFTWVMA-LACAAPPLVGWSRYI-PEGMQC----SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLV----------------FTVKEAAAQQQESATTQ----------KAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA');
-        expect(aliB).toEqual('DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS-RWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFG---NVLVITAIAKFERLQTVTNYFITSLACADLVM---GLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETC-CDFFT------NQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMG-TFTLCWLPFF-IVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIY-CRSPDFRIAFQELLCLRRSSL--KAYGNGYSSNGNTGEQSG');
-        expect(score).toEqual(118);
-    });
-});
-//# sourceMappingURL=alignment.spec.js.map

package/lib/commonjs/mol-model/sequence/alignment/_spec/alignment.spec.js.map DELETED Viewed

@@ -1 +0,0 @@

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package/lib/commonjs/mol-model/sequence/alignment/alignment.js.map DELETED Viewed

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