molstar 2.3.9 → 3.0.0-dev.10

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

@@ -1,284 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { Tensor as T } from '../tensor';
-import { Mat4 } from '../3d/mat4';
-describe('tensor', function () {
-    it('vector', function () {
-        var V = T.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 = T.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 = T.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 = T.ColumnMajorMatrix(4, 4);
-        var data = M.create();
-        var m = 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.setValue(m, i, j, v);
-            }
-        }
-        for (var i = 0; i < 16; i++)
-            expect(data[i]).toEqual(m[i]);
-    });
-    it('2d ij', function () {
-        var M = T.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 = T.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 = T.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 = T.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 = T.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 = T.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 = T.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 = T.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 = T.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 = T.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 = T.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/mol-math/linear-algebra/_spec/tensor.spec.js.map

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

@@ -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/mol-math/linear-algebra/_spec/vec3.spec.js

@@ -1,18 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
- */
-import { Vec3 } from '../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.angle(vec1, vec1) * 360 / (2 * Math.PI)).toBe(0.0);
-        expect(Vec3.angle(orthVec1, orthVec2) * 360 / (2 * Math.PI)).toBe(90.0);
-        expect(Vec3.angle(vec1, vec2)).toBeCloseTo(0.666946);
-    });
-});
-//# sourceMappingURL=vec3.spec.js.map

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

@@ -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,OAAO,EAAE,IAAI,EAAE,MAAM,YAAY,CAAC;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,IAAI,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,IAAI,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,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC;IACzD,CAAC,CAAC,CAAC;AACP,CAAC,CAAC,CAAC"}

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

@@ -1 +0,0 @@
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package/lib/mol-math/linear-algebra/matrix/matrix.js.map

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package/lib/mol-math/linear-algebra/matrix/svd.js.map

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package/lib/mol-math/linear-algebra/tensor.js.map

@@ -1 +0,0 @@
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package/lib/mol-math/linear-algebra.js.map

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package/lib/mol-math/misc.js.map

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package/lib/mol-model/location.js.map

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package/lib/mol-model/loci.js.map

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

@@ -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/mol-model/sequence/alignment/_spec/alignment.spec.js

@@ -1,23 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { align } from '../alignment';
-describe('Alignment', function () {
-    it('basic', function () {
-        // 3PQR: Rhodopsin
-        var seqA = 'MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA';
-        // 3SN6: Endolysin,Beta-2 adrenergic
-        var seqB = 'DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSG';
-        var _a = 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/mol-model/sequence/alignment/_spec/alignment.spec.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"alignment.spec.js","sourceRoot":"","sources":["../../../../../src/mol-model/sequence/alignment/_spec/alignment.spec.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,KAAK,EAAE,MAAM,cAAc,CAAC;AAErC,QAAQ,CAAC,WAAW,EAAE;IAClB,EAAE,CAAC,OAAO,EAAE;QACR,kBAAkB;QAClB,IAAM,IAAI,GAAG,8VAA8V,CAAC;QAC5W,oCAAoC;QACpC,IAAM,IAAI,GAAG,ogBAAogB,CAAC;QAE5gB,IAAA,KAAwB,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE;YAC5C,UAAU,EAAE,CAAC,EAAE;YACf,mBAAmB,EAAE,CAAC,CAAC;YACvB,WAAW,EAAE,UAAU;SAC1B,CAAC,EAJM,IAAI,UAAA,EAAE,IAAI,UAAA,EAAE,KAAK,WAIvB,CAAC;QAEH,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,uhBAAuhB,CAAC,CAAC;QAC9iB,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,uhBAAuhB,CAAC,CAAC;QAC9iB,MAAM,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IAC/B,CAAC,CAAC,CAAC;AACP,CAAC,CAAC,CAAC"}

package/lib/mol-model/sequence/alignment/alignment.js.map

@@ -1 +0,0 @@
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package/lib/mol-model/sequence/alignment/sequence.js.map

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