molstar 2.3.9 → 3.0.0-dev.10

package/lib/mol-io/reader/_spec/mol2.spec.js

@@ -1,161 +0,0 @@
-import { __awaiter, __generator } from "tslib";
-import { parseMol2 } from '../mol2/parser';
-var Mol2String = "@<TRIPOS>MOLECULE\n5816\n 26 26 0 0 0\nSMALL\nGASTEIGER\n\n@<TRIPOS>ATOM\n      1 O           1.7394   -2.1169   -1.0894 O.3     1  LIG1       -0.3859\n      2 O          -2.2941    1.0781   -1.7979 O.3     1  LIG1       -0.5033\n      3 O          -3.6584    0.5842    0.5722 O.3     1  LIG1       -0.5033\n      4 N           2.6359    1.0243    0.7030 N.3     1  LIG1       -0.3162\n      5 C           1.6787   -1.1447   -0.0373 C.3     1  LIG1        0.0927\n      6 C           0.2684   -0.6866    0.1208 C.ar    1  LIG1       -0.0143\n      7 C           2.6376    0.0193   -0.3576 C.3     1  LIG1        0.0258\n      8 C          -0.3658   -0.0099   -0.9212 C.ar    1  LIG1       -0.0109\n      9 C          -0.4164   -0.9343    1.3105 C.ar    1  LIG1       -0.0524\n     10 C          -1.6849    0.4191   -0.7732 C.ar    1  LIG1        0.1586\n     11 C          -1.7353   -0.5053    1.4585 C.ar    1  LIG1       -0.0162\n     12 C          -2.3696    0.1713    0.4166 C.ar    1  LIG1        0.1582\n     13 C           3.5645    2.1013    0.3950 C.3     1  LIG1       -0.0157\n     14 H           2.0210   -1.6511    0.8741 H       1  LIG1        0.0656\n     15 H           2.3808    0.4742   -1.3225 H       1  LIG1        0.0453\n     16 H           3.6478   -0.3931   -0.4831 H       1  LIG1        0.0453\n     17 H           0.1501    0.1801   -1.8589 H       1  LIG1        0.0659\n     18 H           0.0640   -1.4598    2.1315 H       1  LIG1        0.0622\n     19 H           2.9013    0.5888    1.5858 H       1  LIG1        0.1217\n     20 H          -2.2571   -0.7050    2.3907 H       1  LIG1        0.0655\n     21 H           2.6646   -2.4067   -1.1652 H       1  LIG1        0.2103\n     22 H           3.2862    2.6124   -0.5325 H       1  LIG1        0.0388\n     23 H           4.5925    1.7346    0.3078 H       1  LIG1        0.0388\n     24 H           3.5401    2.8441    1.1985 H       1  LIG1        0.0388\n     25 H          -3.2008    1.2997   -1.5231 H       1  LIG1        0.2923\n     26 H          -3.9690    0.3259    1.4570 H       1  LIG1        0.2923\n@<TRIPOS>BOND\n     1     1     5    1\n     2     1    21    1\n     3     2    10    1\n     4     2    25    1\n     5     3    12    1\n     6     3    26    1\n     7     4     7    1\n     8     4    13    1\n     9     4    19    1\n    10     5     6    1\n    11     5     7    1\n    12     5    14    1\n    13     6     8   ar\n    14     6     9   ar\n    15     7    15    1\n    16     7    16    1\n    17     8    10   ar\n    18     8    17    1\n    19     9    11   ar\n    20     9    18    1\n    21    10    12   ar\n    22    11    12   ar\n    23    11    20    1\n    24    13    22    1\n    25    13    23    1\n    26    13    24    1";
-var Mol2StringMultiBlocks = "@<TRIPOS>MOLECULE\n5816\n 26 26 0 0 0\nSMALL\nGASTEIGER\n\n@<TRIPOS>ATOM\n      1 O           1.7394   -2.1169   -1.0894 O.3     1  LIG1       -0.3859\n      2 O          -2.2941    1.0781   -1.7979 O.3     1  LIG1       -0.5033\n      3 O          -3.6584    0.5842    0.5722 O.3     1  LIG1       -0.5033\n      4 N           2.6359    1.0243    0.7030 N.3     1  LIG1       -0.3162\n      5 C           1.6787   -1.1447   -0.0373 C.3     1  LIG1        0.0927\n      6 C           0.2684   -0.6866    0.1208 C.ar    1  LIG1       -0.0143\n      7 C           2.6376    0.0193   -0.3576 C.3     1  LIG1        0.0258\n      8 C          -0.3658   -0.0099   -0.9212 C.ar    1  LIG1       -0.0109\n      9 C          -0.4164   -0.9343    1.3105 C.ar    1  LIG1       -0.0524\n     10 C          -1.6849    0.4191   -0.7732 C.ar    1  LIG1        0.1586\n     11 C          -1.7353   -0.5053    1.4585 C.ar    1  LIG1       -0.0162\n     12 C          -2.3696    0.1713    0.4166 C.ar    1  LIG1        0.1582\n     13 C           3.5645    2.1013    0.3950 C.3     1  LIG1       -0.0157\n     14 H           2.0210   -1.6511    0.8741 H       1  LIG1        0.0656\n     15 H           2.3808    0.4742   -1.3225 H       1  LIG1        0.0453\n     16 H           3.6478   -0.3931   -0.4831 H       1  LIG1        0.0453\n     17 H           0.1501    0.1801   -1.8589 H       1  LIG1        0.0659\n     18 H           0.0640   -1.4598    2.1315 H       1  LIG1        0.0622\n     19 H           2.9013    0.5888    1.5858 H       1  LIG1        0.1217\n     20 H          -2.2571   -0.7050    2.3907 H       1  LIG1        0.0655\n     21 H           2.6646   -2.4067   -1.1652 H       1  LIG1        0.2103\n     22 H           3.2862    2.6124   -0.5325 H       1  LIG1        0.0388\n     23 H           4.5925    1.7346    0.3078 H       1  LIG1        0.0388\n     24 H           3.5401    2.8441    1.1985 H       1  LIG1        0.0388\n     25 H          -3.2008    1.2997   -1.5231 H       1  LIG1        0.2923\n     26 H          -3.9690    0.3259    1.4570 H       1  LIG1        0.2923\n@<TRIPOS>BOND\n     1     1     5    1\n     2     1    21    1\n     3     2    10    1\n     4     2    25    1\n     5     3    12    1\n     6     3    26    1\n     7     4     7    1\n     8     4    13    1\n     9     4    19    1\n    10     5     6    1\n    11     5     7    1\n    12     5    14    1\n    13     6     8   ar\n    14     6     9   ar\n    15     7    15    1\n    16     7    16    1\n    17     8    10   ar\n    18     8    17    1\n    19     9    11   ar\n    20     9    18    1\n    21    10    12   ar\n    22    11    12   ar\n    23    11    20    1\n    24    13    22    1\n    25    13    23    1\n    26    13    24    1\n@<TRIPOS>MOLECULE\n5816\n 26 26 0 0 0\nSMALL\nGASTEIGER\n\n@<TRIPOS>ATOM\n      1 O           1.7394   -2.1169   -1.0894 O.3     1  LIG1       -0.3859\n      2 O          -2.2941    1.0781   -1.7979 O.3     1  LIG1       -0.5033\n      3 O          -3.6584    0.5842    0.5722 O.3     1  LIG1       -0.5033\n      4 N           2.6359    1.0243    0.7030 N.3     1  LIG1       -0.3162\n      5 C           1.6787   -1.1447   -0.0373 C.3     1  LIG1        0.0927\n      6 C           0.2684   -0.6866    0.1208 C.ar    1  LIG1       -0.0143\n      7 C           2.6376    0.0193   -0.3576 C.3     1  LIG1        0.0258\n      8 C          -0.3658   -0.0099   -0.9212 C.ar    1  LIG1       -0.0109\n      9 C          -0.4164   -0.9343    1.3105 C.ar    1  LIG1       -0.0524\n     10 C          -1.6849    0.4191   -0.7732 C.ar    1  LIG1        0.1586\n     11 C          -1.7353   -0.5053    1.4585 C.ar    1  LIG1       -0.0162\n     12 C          -2.3696    0.1713    0.4166 C.ar    1  LIG1        0.1582\n     13 C           3.5645    2.1013    0.3950 C.3     1  LIG1       -0.0157\n     14 H           2.0210   -1.6511    0.8741 H       1  LIG1        0.0656\n     15 H           2.3808    0.4742   -1.3225 H       1  LIG1        0.0453\n     16 H           3.6478   -0.3931   -0.4831 H       1  LIG1        0.0453\n     17 H           0.1501    0.1801   -1.8589 H       1  LIG1        0.0659\n     18 H           0.0640   -1.4598    2.1315 H       1  LIG1        0.0622\n     19 H           2.9013    0.5888    1.5858 H       1  LIG1        0.1217\n     20 H          -2.2571   -0.7050    2.3907 H       1  LIG1        0.0655\n     21 H           2.6646   -2.4067   -1.1652 H       1  LIG1        0.2103\n     22 H           3.2862    2.6124   -0.5325 H       1  LIG1        0.0388\n     23 H           4.5925    1.7346    0.3078 H       1  LIG1        0.0388\n     24 H           3.5401    2.8441    1.1985 H       1  LIG1        0.0388\n     25 H          -3.2008    1.2997   -1.5231 H       1  LIG1        0.2923\n     26 H          -3.9690    0.3259    1.4570 H       1  LIG1        0.2923\n@<TRIPOS>BOND\n     1     1     5    1\n     2     1    21    1\n     3     2    10    1\n     4     2    25    1\n     5     3    12    1\n     6     3    26    1\n     7     4     7    1\n     8     4    13    1\n     9     4    19    1\n    10     5     6    1\n    11     5     7    1\n    12     5    14    1\n    13     6     8   ar\n    14     6     9   ar\n    15     7    15    1\n    16     7    16    1\n    17     8    10   ar\n    18     8    17    1\n    19     9    11   ar\n    20     9    18    1\n    21    10    12   ar\n    22    11    12   ar\n    23    11    20    1\n    24    13    22    1\n    25    13    23    1\n    26    13    24    1";
-var Mol2StringMinimal = "@<TRIPOS>MOLECULE\n5816\n 26 26 0 0 0\nSMALL\nGASTEIGER\n\n@<TRIPOS>ATOM\n      1 O           1.7394   -2.1169   -1.0894 O.3\n      2 O          -2.2941    1.0781   -1.7979 O.3\n      3 O          -3.6584    0.5842    0.5722 O.3\n      4 N           2.6359    1.0243    0.7030 N.3\n      5 C           1.6787   -1.1447   -0.0373 C.3\n      6 C           0.2684   -0.6866    0.1208 C.ar\n      7 C           2.6376    0.0193   -0.3576 C.3\n      8 C          -0.3658   -0.0099   -0.9212 C.ar\n      9 C          -0.4164   -0.9343    1.3105 C.ar\n     10 C          -1.6849    0.4191   -0.7732 C.ar\n     11 C          -1.7353   -0.5053    1.4585 C.ar\n     12 C          -2.3696    0.1713    0.4166 C.ar\n     13 C           3.5645    2.1013    0.3950 C.3\n     14 H           2.0210   -1.6511    0.8741 H\n     15 H           2.3808    0.4742   -1.3225 H\n     16 H           3.6478   -0.3931   -0.4831 H\n     17 H           0.1501    0.1801   -1.8589 H\n     18 H           0.0640   -1.4598    2.1315 H\n     19 H           2.9013    0.5888    1.5858 H\n     20 H          -2.2571   -0.7050    2.3907 H\n     21 H           2.6646   -2.4067   -1.1652 H\n     22 H           3.2862    2.6124   -0.5325 H\n     23 H           4.5925    1.7346    0.3078 H\n     24 H           3.5401    2.8441    1.1985 H\n     25 H          -3.2008    1.2997   -1.5231 H\n     26 H          -3.9690    0.3259    1.4570 H\n@<TRIPOS>BOND\n     1     1     5    1\n     2     1    21    1\n     3     2    10    1\n     4     2    25    1\n     5     3    12    1\n     6     3    26    1\n     7     4     7    1\n     8     4    13    1\n     9     4    19    1\n    10     5     6    1\n    11     5     7    1\n    12     5    14    1\n    13     6     8   ar\n    14     6     9   ar\n    15     7    15    1\n    16     7    16    1\n    17     8    10   ar\n    18     8    17    1\n    19     9    11   ar\n    20     9    18    1\n    21    10    12   ar\n    22    11    12   ar\n    23    11    20    1\n    24    13    22    1\n    25    13    23    1\n    26    13    24    1";
-describe('mol2 reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, mol2File, data, molecule, atoms, bonds;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseMol2(Mol2String, '').run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.message);
-                    }
-                    mol2File = parsed.result;
-                    // number of structures
-                    expect(mol2File.structures.length).toBe(1);
-                    data = mol2File.structures[0];
-                    molecule = data.molecule, atoms = data.atoms, bonds = data.bonds;
-                    // molecule fields
-                    expect(molecule.mol_name).toBe('5816');
-                    expect(molecule.num_atoms).toBe(26);
-                    expect(molecule.num_bonds).toBe(26);
-                    expect(molecule.num_subst).toBe(0);
-                    expect(molecule.num_feat).toBe(0);
-                    expect(molecule.num_sets).toBe(0);
-                    expect(molecule.mol_type).toBe('SMALL');
-                    expect(molecule.charge_type).toBe('GASTEIGER');
-                    expect(molecule.status_bits).toBe('');
-                    expect(molecule.mol_comment).toBe('');
-                    // required atom fields
-                    expect(atoms.count).toBe(26);
-                    expect(atoms.atom_id.value(0)).toBe(1);
-                    expect(atoms.atom_name.value(0)).toBe('O');
-                    expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
-                    expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
-                    expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
-                    expect(atoms.atom_type.value(0)).toBe('O.3');
-                    // optional atom fields
-                    expect(atoms.subst_id.value(0)).toBe(1);
-                    expect(atoms.subst_name.value(0)).toBe('LIG1');
-                    expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
-                    expect(atoms.status_bit.value(0)).toBe('');
-                    // required bond fields
-                    expect(bonds.count).toBe(26);
-                    expect(bonds.bond_id.value(0)).toBe(1);
-                    expect(bonds.origin_atom_id.value(0)).toBe(1);
-                    expect(bonds.target_atom_id.value(0)).toBe(5);
-                    expect(bonds.bond_type.value(0)).toBe('1');
-                    // optional bond fields
-                    expect(bonds.status_bits.value(0)).toBe('');
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('multiblocks', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, mol2File, data, molecule, atoms, bonds;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseMol2(Mol2StringMultiBlocks, '').run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.message);
-                    }
-                    mol2File = parsed.result;
-                    // number of structures
-                    expect(mol2File.structures.length).toBe(2);
-                    data = mol2File.structures[1];
-                    molecule = data.molecule, atoms = data.atoms, bonds = data.bonds;
-                    // molecule fields
-                    expect(molecule.mol_name).toBe('5816');
-                    expect(molecule.num_atoms).toBe(26);
-                    expect(molecule.num_bonds).toBe(26);
-                    expect(molecule.num_subst).toBe(0);
-                    expect(molecule.num_feat).toBe(0);
-                    expect(molecule.num_sets).toBe(0);
-                    expect(molecule.mol_type).toBe('SMALL');
-                    expect(molecule.charge_type).toBe('GASTEIGER');
-                    expect(molecule.status_bits).toBe('');
-                    expect(molecule.mol_comment).toBe('');
-                    // required atom fields
-                    expect(atoms.count).toBe(26);
-                    expect(atoms.atom_id.value(0)).toBe(1);
-                    expect(atoms.atom_name.value(0)).toBe('O');
-                    expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
-                    expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
-                    expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
-                    expect(atoms.atom_type.value(0)).toBe('O.3');
-                    // optional atom fields
-                    expect(atoms.subst_id.value(0)).toBe(1);
-                    expect(atoms.subst_name.value(0)).toBe('LIG1');
-                    expect(atoms.charge.value(0)).toBeCloseTo(-0.3859);
-                    expect(atoms.status_bit.value(0)).toBe('');
-                    // required bond fields
-                    expect(bonds.count).toBe(26);
-                    expect(bonds.bond_id.value(0)).toBe(1);
-                    expect(bonds.origin_atom_id.value(0)).toBe(1);
-                    expect(bonds.target_atom_id.value(0)).toBe(5);
-                    expect(bonds.bond_type.value(0)).toBe('1');
-                    // optional bond fields
-                    expect(bonds.status_bits.value(0)).toBe('');
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('minimal', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, mol2File, data, molecule, atoms, bonds;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parseMol2(Mol2StringMinimal, '').run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.message);
-                    }
-                    mol2File = parsed.result;
-                    // number of structures
-                    expect(mol2File.structures.length).toBe(1);
-                    data = mol2File.structures[0];
-                    molecule = data.molecule, atoms = data.atoms, bonds = data.bonds;
-                    // molecule fields
-                    expect(molecule.mol_name).toBe('5816');
-                    expect(molecule.num_atoms).toBe(26);
-                    expect(molecule.num_bonds).toBe(26);
-                    expect(molecule.num_subst).toBe(0);
-                    expect(molecule.num_feat).toBe(0);
-                    expect(molecule.num_sets).toBe(0);
-                    expect(molecule.mol_type).toBe('SMALL');
-                    expect(molecule.charge_type).toBe('GASTEIGER');
-                    expect(molecule.status_bits).toBe('');
-                    expect(molecule.mol_comment).toBe('');
-                    // required atom fields
-                    expect(atoms.count).toBe(26);
-                    expect(atoms.atom_id.value(0)).toBe(1);
-                    expect(atoms.atom_name.value(0)).toBe('O');
-                    expect(atoms.x.value(0)).toBeCloseTo(1.7394, 0.001);
-                    expect(atoms.y.value(0)).toBeCloseTo(-2.1169, 0.0001);
-                    expect(atoms.z.value(0)).toBeCloseTo(-1.0893, 0.0001);
-                    expect(atoms.atom_type.value(0)).toBe('O.3');
-                    // optional atom fields
-                    expect(atoms.subst_id.value(0)).toBe(0);
-                    expect(atoms.subst_name.value(0)).toBe('');
-                    expect(atoms.charge.value(0)).toBeCloseTo(0);
-                    expect(atoms.status_bit.value(0)).toBe('');
-                    // required bond fields
-                    expect(bonds.count).toBe(26);
-                    expect(bonds.bond_id.value(0)).toBe(1);
-                    expect(bonds.origin_atom_id.value(0)).toBe(1);
-                    expect(bonds.target_atom_id.value(0)).toBe(5);
-                    expect(bonds.bond_type.value(0)).toBe('1');
-                    // optional bond fields
-                    expect(bonds.status_bits.value(0)).toBe('');
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=mol2.spec.js.map

package/lib/mol-io/reader/_spec/mol2.spec.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"mol2.spec.js","sourceRoot":"","sources":["../../../../src/mol-io/reader/_spec/mol2.spec.ts"],"names":[],"mappings":";AACA,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAE3C,IAAM,UAAU,GAAG,+sFA2DK,CAAC;AAEzB,IAAM,qBAAqB,GAAG,85KAuHN,CAAC;AAEzB,IAAM,iBAAiB,GAAG,uhEA2DF,CAAC;AAEzB,QAAQ,CAAC,aAAa,EAAE;IACpB,EAAE,CAAC,OAAO,EAAE;;;;wBACO,qBAAM,SAAS,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAA9C,MAAM,GAAG,SAAqC;oBACpD,IAAI,MAAM,CAAC,OAAO,EAAE;wBAChB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;qBACnC;oBACK,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC;oBAE/B,uBAAuB;oBACvB,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAErC,IAAI,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;oBAC5B,QAAQ,GAAmB,IAAI,SAAvB,EAAE,KAAK,GAAY,IAAI,MAAhB,EAAE,KAAK,GAAK,IAAI,MAAT,CAAU;oBAExC,kBAAkB;oBAClB,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;oBACvC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACnC,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAClC,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAClC,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;oBACxC,MAAM,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;oBAC/C,MAAM,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACtC,MAAM,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAEtC,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC7B,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACvC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAC3C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;oBACpD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;oBACtD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;oBACtD,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;oBAE7C,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;oBAC/C,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC,CAAC;oBACnD,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAE3C,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC7B,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACvC,MAAM,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC9C,MAAM,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC9C,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAE3C,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;;;;SAC/C,CAAC,CAAC;IAEH,EAAE,CAAC,aAAa,EAAE;;;;wBACC,qBAAM,SAAS,CAAC,qBAAqB,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAAzD,MAAM,GAAG,SAAgD;oBAC/D,IAAI,MAAM,CAAC,OAAO,EAAE;wBAChB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;qBACnC;oBACK,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC;oBAE/B,uBAAuB;oBACvB,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAErC,IAAI,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;oBAC5B,QAAQ,GAAmB,IAAI,SAAvB,EAAE,KAAK,GAAY,IAAI,MAAhB,EAAE,KAAK,GAAK,IAAI,MAAT,CAAU;oBAExC,kBAAkB;oBAClB,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;oBACvC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACnC,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAClC,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAClC,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;oBACxC,MAAM,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;oBAC/C,MAAM,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACtC,MAAM,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAEtC,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC7B,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACvC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAC3C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;oBACpD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;oBACtD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;oBACtD,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;oBAE7C,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,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package/lib/mol-io/reader/_spec/ply.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/ply.spec.js

@@ -1,66 +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 { parsePly } from '../ply/parser';
-var plyString = "ply\nformat ascii 1.0\ncomment file created by MegaMol\nelement vertex 6\nproperty float x\nproperty float y\nproperty float z\nproperty uchar red\nproperty uchar green\nproperty uchar blue\nproperty uchar alpha\nproperty float nx\nproperty float ny\nproperty float nz\nproperty int atomid\nproperty uchar contactcount_r\nproperty uchar contactcount_g\nproperty uchar contactcount_b\nproperty uchar contactsteps_r\nproperty uchar contactsteps_g\nproperty uchar contactsteps_b\nproperty uchar hbonds_r\nproperty uchar hbonds_g\nproperty uchar hbonds_b\nproperty uchar hbondsteps_r\nproperty uchar hbondsteps_g\nproperty uchar hbondsteps_b\nproperty uchar molcount_r\nproperty uchar molcount_g\nproperty uchar molcount_b\nproperty uchar spots_r\nproperty uchar spots_g\nproperty uchar spots_b\nproperty uchar rmsf_r\nproperty uchar rmsf_g\nproperty uchar rmsf_b\nelement face 2\nproperty list uchar int vertex_index\nend_header\n130.901 160.016 163.033 90 159 210 255 -0.382 -0.895 -0.231 181 21 100 150 24 102 151 20 100 150 20 100 150 30 106 154 20 100 150 171 196 212\n131.372 159.778 162.83 90 159 210 255 -0.618 -0.776 -0.129 178 21 100 150 24 102 151 20 100 150 20 100 150 30 106 154 20 100 150 141 177 199\n131.682 159.385 163.089 90 159 210 255 -0.773 -0.579 -0.259 180 21 100 150 24 102 151 20 100 150 20 100 150 30 106 154 20 100 150 172 196 212\n131.233 160.386 162.11 90 159 210 255 -0.708 -0.383 -0.594 178 21 100 150 24 102 151 20 100 150 20 100 150 30 106 154 20 100 150 141 177 199\n130.782 160.539 162.415 90 159 210 255 -0.482 -0.459 -0.746 181 21 100 150 24 102 151 20 100 150 20 100 150 30 106 154 20 100 150 171 196 212\n131.482 160.483 161.621 90 159 210 255 -0.832 -0.431 -0.349 179 21 100 150 24 102 151 20 100 150 20 100 150 30 106 154 20 100 150 171 196 212\n3 0 2 1\n3 3 5 4\n";
-var plyCubeString = "ply\nformat ascii 1.0\ncomment test cube\nelement vertex 24\nproperty float32 x\nproperty float32 y\nproperty float32 z\nproperty uint32 material_index\nelement face 6\nproperty list uint8 int32 vertex_indices\nelement material 6\nproperty uint8 red\nproperty uint8 green\nproperty uint8 blue\nend_header\n-1 -1 -1 0\n1 -1 -1 0\n1 1 -1 0\n-1 1 -1 0\n1 -1 1 1\n-1 -1 1 1\n-1 1 1 1\n1 1 1 1\n1 1 1 2\n1 1 -1 2\n1 -1 -1 2\n1 -1 1 2\n-1 1 -1 3\n-1 1 1 3\n-1 -1 1 3\n-1 -1 -1 3\n-1 1 1 4\n-1 1 -1 4\n1 1 -1 4\n1 1 1 4\n1 -1 1 5\n1 -1 -1 5\n-1 -1 -1 5\n-1 -1 1 5\n4 0 1 2 3\n4 4 5 6 7\n4 8 9 10 11\n4 12 13 14 15\n4 16 17 18 19\n4 20 21 22 23\n255 0 0\n0 255 0\n0 0 255\n255 255 0\n0 255 255\n255 0 255\n";
-describe('ply reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, plyFile, vertex, x, face;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parsePly(plyString).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    plyFile = parsed.result;
-                    vertex = plyFile.getElement('vertex');
-                    if (!vertex)
-                        return [2 /*return*/];
-                    x = vertex.getProperty('x');
-                    if (!x)
-                        return [2 /*return*/];
-                    expect(x.value(0)).toEqual(130.901);
-                    face = plyFile.getElement('face');
-                    if (!face)
-                        return [2 /*return*/];
-                    expect(face.value(0)).toEqual({ count: 3, entries: [0, 2, 1] });
-                    expect(face.value(1)).toEqual({ count: 3, entries: [3, 5, 4] });
-                    expect.assertions(3);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-    it('material', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, plyFile, vertex, face, material;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parsePly(plyCubeString).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        return [2 /*return*/];
-                    plyFile = parsed.result;
-                    vertex = plyFile.getElement('vertex');
-                    if (!vertex)
-                        return [2 /*return*/];
-                    expect(vertex.rowCount).toBe(24);
-                    face = plyFile.getElement('face');
-                    if (!face)
-                        return [2 /*return*/];
-                    expect(face.rowCount).toBe(6);
-                    material = plyFile.getElement('face');
-                    if (!material)
-                        return [2 /*return*/];
-                    expect(face.rowCount).toBe(6);
-                    expect.assertions(3);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=ply.spec.js.map

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

@@ -1 +0,0 @@
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package/lib/mol-io/reader/_spec/psf.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/psf.spec.js

@@ -1,50 +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 { parsePsf } from '../psf/parser';
-var psfString = "PSF CMAP CHEQ\n\n       2 !NTITLE\n* BETA HARPIN IN IMPLICIT SOLVENT\n*  DATE:    11/22/10     16:54: 9      CREATED BY USER: aokur\n\n      42 !NATOM\n       1 ALA3 1    ALA  CAY    24  -0.270000       12.0110           0   0.00000     -0.301140E-02\n       2 ALA3 1    ALA  HY1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n       3 ALA3 1    ALA  HY2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n       4 ALA3 1    ALA  HY3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n       5 ALA3 1    ALA  CY     20   0.510000       12.0110           0   0.00000     -0.301140E-02\n       6 ALA3 1    ALA  OY     70  -0.510000       15.9990           0   0.00000     -0.301140E-02\n       7 ALA3 1    ALA  N      54  -0.470000       14.0070           0   0.00000     -0.301140E-02\n       8 ALA3 1    ALA  HN      1   0.310000       1.00800           0   0.00000     -0.301140E-02\n       9 ALA3 1    ALA  CA     22   0.700000E-01   12.0110           0   0.00000     -0.301140E-02\n      10 ALA3 1    ALA  HA      6   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      11 ALA3 1    ALA  CB     24  -0.270000       12.0110           0   0.00000     -0.301140E-02\n      12 ALA3 1    ALA  HB1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      13 ALA3 1    ALA  HB2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      14 ALA3 1    ALA  HB3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      15 ALA3 1    ALA  C      20   0.510000       12.0110           0   0.00000     -0.301140E-02\n      16 ALA3 1    ALA  O      70  -0.510000       15.9990           0   0.00000     -0.301140E-02\n      17 ALA3 2    ALA  N      54  -0.470000       14.0070           0   0.00000     -0.301140E-02\n      18 ALA3 2    ALA  HN      1   0.310000       1.00800           0   0.00000     -0.301140E-02\n      19 ALA3 2    ALA  CA     22   0.700000E-01   12.0110           0   0.00000     -0.301140E-02\n      20 ALA3 2    ALA  HA      6   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      21 ALA3 2    ALA  CB     24  -0.270000       12.0110           0   0.00000     -0.301140E-02\n      22 ALA3 2    ALA  HB1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      23 ALA3 2    ALA  HB2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      24 ALA3 2    ALA  HB3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      25 ALA3 2    ALA  C      20   0.510000       12.0110           0   0.00000     -0.301140E-02\n      26 ALA3 2    ALA  O      70  -0.510000       15.9990           0   0.00000     -0.301140E-02\n      27 ALA3 3    ALA  N      54  -0.470000       14.0070           0   0.00000     -0.301140E-02\n      28 ALA3 3    ALA  HN      1   0.310000       1.00800           0   0.00000     -0.301140E-02\n      29 ALA3 3    ALA  CA     22   0.700000E-01   12.0110           0   0.00000     -0.301140E-02\n      30 ALA3 3    ALA  HA      6   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      31 ALA3 3    ALA  CB     24  -0.270000       12.0110           0   0.00000     -0.301140E-02\n      32 ALA3 3    ALA  HB1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      33 ALA3 3    ALA  HB2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      34 ALA3 3    ALA  HB3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      35 ALA3 3    ALA  C      20   0.510000       12.0110           0   0.00000     -0.301140E-02\n      36 ALA3 3    ALA  O      70  -0.510000       15.9990           0   0.00000     -0.301140E-02\n      37 ALA3 3    ALA  NT     54  -0.470000       14.0070           0   0.00000     -0.301140E-02\n      38 ALA3 3    ALA  HNT     1   0.310000       1.00800           0   0.00000     -0.301140E-02\n      39 ALA3 3    ALA  CAT    24  -0.110000       12.0110           0   0.00000     -0.301140E-02\n      40 ALA3 3    ALA  HT1     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      41 ALA3 3    ALA  HT2     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n      42 ALA3 3    ALA  HT3     3   0.900000E-01   1.00800           0   0.00000     -0.301140E-02\n\n      41 !NBOND: bonds\n       5       1       5       7       1       2       1       3\n       1       4       6       5      11       9       7       8\n       7       9      15       9      15      17       9      10\n      11      12      11      13      11      14      16      15\n      21      19      17      18      17      19      25      19\n      25      27      19      20      21      22      21      23\n      21      24      26      25      31      29      27      28\n      27      29      35      29      29      30      31      32\n      31      33      31      34      36      35      35      37\n      37      38      37      39      39      40      39      41\n      39      42\n";
-describe('psf reader', function () {
-    it('basic', function () { return __awaiter(void 0, void 0, void 0, function () {
-        var parsed, psfFile, id, title, atoms, bonds;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, parsePsf(psfString).run()];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError) {
-                        throw new Error(parsed.message);
-                    }
-                    psfFile = parsed.result;
-                    id = psfFile.id, title = psfFile.title, atoms = psfFile.atoms, bonds = psfFile.bonds;
-                    expect(id).toBe('PSF CMAP CHEQ');
-                    expect(title).toEqual([
-                        'BETA HARPIN IN IMPLICIT SOLVENT',
-                        'DATE:    11/22/10     16:54: 9      CREATED BY USER: aokur'
-                    ]);
-                    expect(atoms.atomId.value(0)).toBe(1);
-                    expect(atoms.atomId.value(41)).toBe(42);
-                    expect(atoms.segmentName.value(0)).toBe('ALA3');
-                    expect(atoms.residueId.value(0)).toBe(1);
-                    expect(atoms.residueId.value(41)).toBe(3);
-                    expect(atoms.residueName.value(0)).toBe('ALA');
-                    expect(atoms.atomName.value(0)).toBe('CAY');
-                    expect(atoms.atomName.value(41)).toBe('HT3');
-                    expect(atoms.atomType.value(0)).toBe('24');
-                    expect(atoms.atomType.value(41)).toBe('3');
-                    expect(atoms.charge.value(0)).toBeCloseTo(-0.270000, 0.00001);
-                    expect(atoms.charge.value(41)).toBeCloseTo(0.090000, 0.00001);
-                    expect(atoms.mass.value(0)).toBeCloseTo(12.0110, 0.00001);
-                    expect(atoms.mass.value(41)).toBeCloseTo(1.00800, 0.00001);
-                    expect(bonds.atomIdA.value(0)).toBe(5);
-                    expect(bonds.atomIdB.value(0)).toBe(1);
-                    expect(bonds.atomIdA.value(40)).toBe(39);
-                    expect(bonds.atomIdB.value(40)).toBe(42);
-                    return [2 /*return*/];
-            }
-        });
-    }); });
-});
-//# sourceMappingURL=psf.spec.js.map

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

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

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

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

@@ -1,52 +0,0 @@
-import { __awaiter, __generator } from "tslib";
-import { parseSdf } from '../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 __awaiter(void 0, void 0, void 0, function () {
-        var parsed, compound1, compound2, compound3, molFile, dataItems, atoms, bonds;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, 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

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

@@ -1 +0,0 @@
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package/lib/mol-io/reader/ccp4/parser.js.map

@@ -1 +0,0 @@
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package/lib/mol-io/reader/ccp4/schema.js.map

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package/lib/mol-io/reader/cif/binary/field.js.map

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package/lib/mol-io/reader/cif/binary/parser.js.map

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package/lib/mol-io/reader/cif/data-model.js.map

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package/lib/mol-io/reader/cif/schema/bird.js.map

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package/lib/mol-io/reader/cif/schema/ccd-extras.js.map

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