molstar
Version:
A comprehensive macromolecular library.
54 lines • 9.75 kB
JavaScript
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
var tslib_1 = require("tslib");
var parser_1 = require("../sdf/parser");
var SdfString = "\n Mrv1718007121815122D\n\n 5 4 0 0 0 0 999 V2000\n 0.0000 0.8250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n -0.8250 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -0.8250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8250 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n 4 1 1 0 0 0 0\n 4 2 2 0 0 0 0\n 4 3 1 0 0 0 0\n 4 5 1 0 0 0 0\nM CHG 3 1 -1 3 -1 5 -1\nM END\n> <DATABASE_ID>\n0\n\n> <DATABASE_NAME>\ndrugbank\n\n> 5225 <TEST_FIELD>\nwhatever\n\n> <INCHI_IDENTIFIER>\nInChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3\n\n> <INCHI_KEY>\nNBIIXXVUZAFLBC-UHFFFAOYSA-K\n\n> <FORMULA>\nO4P\n\n> <MOLECULAR_WEIGHT>\n94.9714\n\n> <EXACT_MASS>\n94.95342\n\n> <JCHEM_ACCEPTOR_COUNT>\n4\n\n> <JCHEM_ATOM_COUNT>\n5\n\n> <JCHEM_AVERAGE_POLARIZABILITY>\n4.932162910070488\n\n> <JCHEM_BIOAVAILABILITY>\n1\n\n> <JCHEM_DONOR_COUNT>\n0\n\n> <JCHEM_FORMAL_CHARGE>\n-3\n\n> <JCHEM_GHOSE_FILTER>\n0\n\n> <JCHEM_IUPAC>\nphosphate\n\n> <JCHEM_LOGP>\n-1.0201038226666665\n\n> <JCHEM_MDDR_LIKE_RULE>\n0\n\n> <JCHEM_NUMBER_OF_RINGS>\n0\n\n> <JCHEM_PHYSIOLOGICAL_CHARGE>\n-2\n\n> <JCHEM_PKA>\n6.951626889535468\n\n> <JCHEM_PKA_STRONGEST_ACIDIC>\n1.7961261340181292\n\n> <JCHEM_POLAR_SURFACE_AREA>\n86.25\n\n> <JCHEM_REFRACTIVITY>\n11.2868\n\n> <JCHEM_ROTATABLE_BOND_COUNT>\n0\n\n> <JCHEM_RULE_OF_FIVE>\n1\n\n> <JCHEM_TRADITIONAL_IUPAC>\nphosphate\n\n> <JCHEM_VEBER_RULE>\n0\n\n> <DRUGBANK_ID>\nDB14523\n\n> <DRUG_GROUPS>\nexperimental\n\n> <GENERIC_NAME>\nPhosphate ion\n\n> <SYNONYMS>\nOrthophosphate; Phosphate\n\n$$$$\n\nComp 2\n\n5 4 0 0 0 0 999 V2000\n 0.0000 0.8250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n -0.8250 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 -0.8250 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0\n 0.8250 0.0000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0\n4 1 1 0 0 0 0\n4 2 2 0 0 0 0\n4 3 1 0 0 0 0\n4 5 1 0 0 0 0\nM CHG 3 1 -1 3 -1 5 -1\nM END\n> <DATABASE_ID>\n1\n\n$$$$\n\n2244\n -OEChem-04122119123D\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\n> <PUBCHEM_COMPOUND_CID>\n2244\n\n> <PUBCHEM_CONFORMER_RMSD>\n0.6\n\n> <PUBCHEM_CONFORMER_DIVERSEORDER>\n1\n11\n10\n3\n15\n17\n13\n5\n16\n7\n14\n9\n8\n4\n18\n6\n12\n2\n\n> <PUBCHEM_MMFF94_PARTIAL_CHARGES>\n18\n1 -0.23\n10 -0.15\n11 0.63\n12 0.66\n13 0.06\n14 0.15\n15 0.15\n16 0.15\n17 0.15\n2 -0.65\n21 0.5\n3 -0.57\n4 -0.57\n5 0.08\n6 0.09\n7 -0.15\n8 -0.15\n9 -0.15\n\n> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>\n3\n\n> <PUBCHEM_PHARMACOPHORE_FEATURES>\n5\n1 2 acceptor\n1 3 acceptor\n1 4 acceptor\n3 2 3 11 anion\n6 5 6 7 8 9 10 rings\n\n> <PUBCHEM_HEAVY_ATOM_COUNT>\n13\n\n> <PUBCHEM_ATOM_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_DEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_BOND_UDEF_STEREO_COUNT>\n0\n\n> <PUBCHEM_ISOTOPIC_ATOM_COUNT>\n0\n\n> <PUBCHEM_COMPONENT_COUNT>\n1\n\n> <PUBCHEM_CACTVS_TAUTO_COUNT>\n1\n\n> <PUBCHEM_CONFORMER_ID>\n000008C400000001\n\n> <PUBCHEM_MMFF94_ENERGY>\n39.5952\n\n> <PUBCHEM_FEATURE_SELFOVERLAP>\n25.432\n\n> <PUBCHEM_SHAPE_FINGERPRINT>\n1 1 18265615372930943622\n100427 49 16967750034970055351\n12138202 97 18271247217817981012\n12423570 1 16692715976000295083\n12524768 44 16753525617747228747\n12716758 59 18341332292274886536\n13024252 1 17968377969333732145\n14181834 199 17830728755827362645\n14614273 12 18262232214645093005\n15207287 21 17703787037639964108\n15775835 57 18340488876329928641\n16945 1 18271533103414939405\n193761 8 17907860604865584321\n20645476 183 17677348215414174190\n20871998 184 18198632231250704846\n21040471 1 18411412921197846465\n21501502 16 18123463883164380929\n23402539 116 18271795865171824860\n23419403 2 13539898140662769886\n23552423 10 18048876295495619569\n23559900 14 18272369794190581304\n241688 4 16179044415907240795\n257057 1 17478316999871287486\n2748010 2 18339085878070479087\n305870 269 18263645056784260212\n528862 383 18117272558388284091\n53812653 8 18410289211719108569\n7364860 26 17910392788380644719\n81228 2 18050568744116491203\n\n> <PUBCHEM_SHAPE_MULTIPOLES>\n244.06\n3.86\n2.45\n0.89\n1.95\n1.58\n0.15\n-1.85\n0.38\n-0.61\n-0.02\n0.29\n0.01\n-0.33\n\n> <PUBCHEM_SHAPE_SELFOVERLAP>\n513.037\n\n> <PUBCHEM_SHAPE_VOLUME>\n136\n\n> <PUBCHEM_COORDINATE_TYPE>\n2\n5\n10\n\n$$$$\n";
describe('sdf reader', function () {
it('basic', function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
var parsed, compound1, compound2, compound3, molFile, dataItems, atoms, bonds;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, (0, parser_1.parseSdf)(SdfString).run()];
case 1:
parsed = _a.sent();
if (parsed.isError) {
throw new Error(parsed.message);
}
compound1 = parsed.result.compounds[0];
compound2 = parsed.result.compounds[1];
compound3 = parsed.result.compounds[2];
molFile = compound1.molFile, dataItems = compound1.dataItems;
atoms = molFile.atoms, bonds = molFile.bonds;
expect(parsed.result.compounds.length).toBe(3);
// number of structures
expect(atoms.count).toBe(5);
expect(bonds.count).toBe(4);
expect(compound2.molFile.atoms.count).toBe(5);
expect(compound2.molFile.bonds.count).toBe(4);
expect(atoms.x.value(0)).toBeCloseTo(0, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(0.8250, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(0, 0.0001);
expect(atoms.type_symbol.value(0)).toBe('O');
expect(bonds.atomIdxA.value(3)).toBe(4);
expect(bonds.atomIdxB.value(3)).toBe(5);
expect(bonds.order.value(3)).toBe(1);
expect(dataItems.dataHeader.value(0)).toBe('<DATABASE_ID>');
expect(dataItems.data.value(0)).toBe('0');
expect(dataItems.dataHeader.value(1)).toBe('<DATABASE_NAME>');
expect(dataItems.data.value(1)).toBe('drugbank');
expect(dataItems.dataHeader.value(2)).toBe('5225 <TEST_FIELD>');
expect(dataItems.data.value(2)).toBe('whatever');
expect(dataItems.dataHeader.value(31)).toBe('<SYNONYMS>');
expect(dataItems.data.value(31)).toBe('Orthophosphate; Phosphate');
expect(compound1.dataItems.data.value(0)).toBe('0');
expect(compound2.dataItems.data.value(0)).toBe('1');
expect(compound3.dataItems.dataHeader.value(2)).toBe('<PUBCHEM_CONFORMER_DIVERSEORDER>');
expect(compound3.dataItems.data.value(2)).toBe('1\n11\n10\n3\n15\n17\n13\n5\n16\n7\n14\n9\n8\n4\n18\n6\n12\n2');
expect(compound3.dataItems.dataHeader.value(21)).toBe('<PUBCHEM_COORDINATE_TYPE>');
expect(compound3.dataItems.data.value(21)).toBe('2\n5\n10');
return [2 /*return*/];
}
});
}); });
});
//# sourceMappingURL=sdf.spec.js.map