molstar 2.4.1 → 3.0.0-dev.4

package/lib/commonjs/mol-model-formats/structure/_spec/cif-core.spec.js

@@ -1,51 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2021 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 tslib_1 = require("tslib");
-var cif_1 = require("../../../mol-io/reader/cif");
-var cifCoreString = "data_n1379\n_audit_block_doi                 10.5517/ccy42jn\n_database_code_depnum_ccdc_archive 'CCDC 867861'\nloop_\n_citation_id\n_citation_doi\n_citation_year\n1 10.1002/chem.201202070 2012\n_audit_update_record\n;\n2012-02-20 deposited with the CCDC.\n2016-10-08 downloaded from the CCDC.\n;\n\nloop_\n_atom_type_symbol\n_atom_type_description\n_atom_type_scat_dispersion_real\n_atom_type_scat_dispersion_imag\n_atom_type_scat_source\nC C 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'\nH H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'\nN N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'\nO O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'\nF F 0.0727 0.0534 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'\n\n_symmetry_cell_setting           Triclinic\n_symmetry_space_group_name_H-M   P-1\n\n_cell_length_a                   11.0829(8)\n_cell_length_b                   14.6829(10)\n_cell_length_c                   16.8532(17)\n_cell_angle_alpha                105.728(6)\n_cell_angle_beta                 100.310(6)\n_cell_angle_gamma                110.620(4)\n_cell_volume                     2353.3(3)\n_cell_formula_units_Z            1\n_cell_measurement_temperature    100(2)\n_cell_measurement_reflns_used    5934\n_cell_measurement_theta_min      2.86\n_cell_measurement_theta_max      64.30\n\nloop_\n_atom_site_aniso_label\n_atom_site_aniso_U_11\n_atom_site_aniso_U_22\n_atom_site_aniso_U_33\n_atom_site_aniso_U_23\n_atom_site_aniso_U_13\n_atom_site_aniso_U_12\nPt1 0.0425(2) 0.0423(2) 0.0375(2) 0.00066(13) 0.01515(13) 0.00089(12)\nK1 0.0605(15) 0.0687(17) 0.0559(17) 0.000 0.0203(13) 0.000\nCl2 0.0511(11) 0.0554(11) 0.0533(13) 0.0078(10) 0.0225(9) 0.0027(9)\nCl3 0.0708(13) 0.0484(11) 0.0605(13) -0.0053(10) 0.0276(10) 0.0026(10)\nCl1 0.0950(16) 0.0442(11) 0.0942(18) -0.0051(12) 0.0526(14) 0.0035(12)\nN9 0.045(3) 0.047(4) 0.035(4) 0.004(3) 0.014(3) -0.003(3)\nN7 0.040(3) 0.048(4) 0.036(3) 0.008(3) 0.004(3) -0.004(3)\nO2 0.052(3) 0.098(4) 0.046(4) -0.012(4) 0.006(3) -0.016(3)\nN3 0.041(3) 0.044(3) 0.044(4) 0.001(3) 0.008(3) -0.002(3)\nO6 0.053(3) 0.093(4) 0.052(3) 0.008(3) 0.021(3) -0.019(3)\nC4 0.044(4) 0.032(4) 0.050(5) 0.004(4) 0.011(4) 0.003(3)\nN1 0.049(4) 0.049(4) 0.040(4) 0.004(3) 0.014(3) -0.005(3)\nC8 0.050(4) 0.045(4) 0.033(4) -0.007(4) 0.000(3) -0.004(4)\nC5 0.036(4) 0.039(4) 0.045(5) 0.003(4) 0.013(3) -0.001(3)\nC2 0.047(4) 0.045(4) 0.039(5) -0.007(4) 0.011(4) -0.004(4)\nC7 0.041(4) 0.072(5) 0.055(5) 0.013(5) 0.006(4) -0.015(4)\nC1 0.061(5) 0.067(5) 0.043(5) -0.002(4) 0.017(4) -0.005(4)\nC3 0.038(4) 0.090(6) 0.054(5) 0.003(5) 0.013(4) -0.018(4)\nC6 0.045(4) 0.043(4) 0.038(4) 0.004(4) 0.008(3) -0.002(4)\n";
-describe('cif-core read', function () {
-    it('frame', function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        var parsed, cifFile, block;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, cif_1.CIF.parseText(cifCoreString).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    cifFile = parsed.result;
-                    block = cifFile.blocks[0];
-                    expect(block.getField('cell_length_a').float(0)).toBe(11.0829);
-                    expect(block.getField('symmetry_space_group_name_H-M').str(0)).toBe('P-1');
-                    expect.assertions(2);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('schema', function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        var parsed, cifFile, block, cifCore;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, cif_1.CIF.parseText(cifCoreString).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    cifFile = parsed.result;
-                    block = cifFile.blocks[0];
-                    cifCore = cif_1.CIF.schema.cifCore(block);
-                    expect(cifCore.cell.length_a.value(0)).toBe(11.0829);
-                    expect(cifCore.space_group['name_h-m_full'].value(0)).toBe('P-1');
-                    expect(cifCore.atom_site_aniso.u.value(0)).toEqual(new Float64Array([0.0425, 0, 0, 0.00089, 0.0423, 0, 0.01515, 0.00066, 0.0375]));
-                    expect.assertions(3);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=cif-core.spec.js.map

package/lib/commonjs/mol-model-formats/structure/_spec/cif-core.spec.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/mol-model-formats/structure/_spec/pdb.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/commonjs/mol-model-formats/structure/_spec/pdb.spec.js

@@ -1,26 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019 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 tokenizer_1 = require("../../../mol-io/reader/common/text/tokenizer");
-var util_1 = require("../util");
-var records = [
-    ['ATOM     19 HD23 LEU A   1     151.940 143.340 155.670  0.00  0.00', 'H'],
-    ['ATOM     38  CA  SER A   3     146.430 138.150 162.270  0.00  0.00', 'C'],
-    ['ATOM     38 NA   SER A   3     146.430 138.150 162.270  0.00  0.00', 'NA'],
-    ['ATOM     38  NAA SER A   3     146.430 138.150 162.270  0.00  0.00', 'N'],
-];
-describe('PDB to-cif', function () {
-    it('guess-element-symbol', function () {
-        for (var i = 0, il = records.length; i < il; ++i) {
-            var _a = records[i], data = _a[0], element = _a[1];
-            var tokens = tokenizer_1.TokenBuilder.create(data, 2);
-            (0, util_1.guessElementSymbolTokens)(tokens, data, 12, 16);
-            expect(data.substring(tokens.indices[0], tokens.indices[1])).toBe(element);
-        }
-    });
-});
-//# sourceMappingURL=pdb.spec.js.map

package/lib/commonjs/mol-model-formats/structure/_spec/pdb.spec.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/mol-model-formats/structure/basic/atomic.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/mol-model-formats/structure/basic/coarse.js.map

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package/lib/commonjs/mol-model-formats/structure/basic/entities.js.map

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package/lib/commonjs/mol-model-formats/structure/basic/parser.js.map

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package/lib/commonjs/mol-model-formats/structure/basic/properties.js.map

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package/lib/commonjs/mol-model-formats/structure/common/component.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/mol-model-formats/structure/common/entity.js.map

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package/lib/commonjs/mol-model-formats/structure/cube.js.map

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package/lib/commonjs/mol-model-formats/structure/dcd.js.map

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package/lib/commonjs/mol-model-formats/structure/mmcif.js.map

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package/lib/commonjs/mol-model-formats/structure/mol.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb/anisotropic.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb/conect.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb/entity.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb/secondary-structure.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb/to-cif.js.map

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package/lib/commonjs/mol-model-formats/structure/pdb.js.map

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package/lib/commonjs/mol-model-formats/structure/property/anisotropic.js.map

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package/lib/commonjs/mol-model-formats/structure/property/atoms/chem_comp.js.map

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package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js.map

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package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js.map

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package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js.map

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package/lib/commonjs/mol-model-formats/structure/property/partial-charge.js.map

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