molstar 2.3.6 → 2.4.0

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

@@ -3,6 +3,7 @@ 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$$$$\n";
+var V3000SdfString = "FYI-001\nFYICenter.com\n123456789012345678901234567890123456789012345678901234567890\n 0  0  0     0  0            999 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 13 14 0 0 0\nM  V30 BEGIN ATOM\nM  V30 1 N 0.84 -0.16 0 0\nM  V30 2 N 1.48 0.43 0 0\nM  V30 3 N 0.09 0.27 0 0\nM  V30 4 C 1.11 1.21 0 0\nM  V30 5 C 0.27 1.12 0 0\nM  V30 6 C 0.84 -1.03 0 0\nM  V30 7 C 1.53 1.99 0 0\nM  V30 8 Cl 1.07 2.74 0.01 0\nM  V30 9 C 1.59 -1.46 0 0\nM  V30 10 C 0.08 -1.46 0 0\nM  V30 11 C 1.59 -2.33 0 0\nM  V30 12 C 0.07 -2.32 0 0\nM  V30 13 C 0.84 -2.76 0 0\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 1 1 2 1\nM  V30 2 1 3 1\nM  V30 3 1 6 1\nM  V30 4 2 4 2\nM  V30 5 2 5 3\nM  V30 6 1 7 4\nM  V30 7 1 4 5\nM  V30 8 1 9 6\nM  V30 9 2 10 6\nM  V30 10 1 8 7\nM  V30 11 2 11 9\nM  V30 12 1 12 10\nM  V30 13 1 13 11\nM  V30 14 2 13 12\nM  V30 END BOND\nM  V30 END CTAB\nM  END\n> <Comment>\nThis is an SDF example.\nWith a multi-line comment.\n\n> <source>\nThis was retrieved from biotech.fyicenter.com\n\n$$$$\nL-Alanine\nGSMACCS-II07189510252D 1 0.00366 0.00000 0\nFigure 1, J. Chem. Inf. Comput. Sci., Vol 32, No. 3., 1992\n 0 0 0 0 0 999 V3000\nM V30 BEGIN CTAB\nM V30 COUNTS 6 5 0 0 1\nM V30 BEGIN ATOM\nM V30 1 C -0.6622 0.5342 0 0 CFG=2\nM V30 2 C 0.6622 -0.3 0 0\nM V30 3 C -0.7207 2.0817 0 0 MASS=13\nM V30 4 N -1.8622 -0.3695 0 0 CHG=1\nM V30 5 O 0.622 -1.8037 0 0\nM V30 6 O 1.9464 0.4244 0 0 CHG=-1\nM V30 END ATOM\nM V30 BEGIN BOND\nM V30 1 1 1 2\nM V30 2 1 1 3 CFG=1\nM V30 3 1 1 4\nM V30 4 2 2 5\nM V30 5 1 2 6\nM V30 END BOND\nM V30 END CTAB\nM END\n\n$$$$\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;
@@ -50,5 +51,55 @@ describe('sdf reader', function () {
             }
         });
     }); });
+    it('v3000', function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
+        var parsed, compound1, compound2;
+        return (0, tslib_1.__generator)(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, (0, parser_1.parseSdf)(V3000SdfString).run()];
+                case 1:
+                    parsed = _a.sent();
+                    if (parsed.isError) {
+                        throw new Error(parsed.message);
+                    }
+                    expect(parsed.result.compounds.length).toBe(2);
+                    compound1 = parsed.result.compounds[0];
+                    expect(compound1.molFile.atoms.count).toBe(13);
+                    expect(compound1.molFile.atoms.x.rowCount).toBe(13);
+                    expect(compound1.molFile.atoms.y.rowCount).toBe(13);
+                    expect(compound1.molFile.atoms.z.rowCount).toBe(13);
+                    expect(compound1.molFile.atoms.type_symbol.rowCount).toBe(13);
+                    expect(compound1.molFile.bonds.count).toBe(14);
+                    expect(compound1.molFile.bonds.atomIdxA.rowCount).toBe(14);
+                    expect(compound1.molFile.bonds.atomIdxB.rowCount).toBe(14);
+                    expect(compound1.molFile.bonds.order.rowCount).toBe(14);
+                    expect(compound1.molFile.atoms.x.value(7)).toBe(1.07);
+                    expect(compound1.molFile.atoms.y.value(7)).toBe(2.74);
+                    expect(compound1.molFile.atoms.z.value(7)).toBe(0.01);
+                    expect(compound1.molFile.atoms.type_symbol.value(7)).toBe('Cl');
+                    expect(compound1.molFile.bonds.atomIdxA.value(10)).toBe(11);
+                    expect(compound1.molFile.bonds.atomIdxB.value(10)).toBe(9);
+                    expect(compound1.molFile.bonds.order.value(10)).toBe(2);
+                    expect(compound1.dataItems.dataHeader.rowCount).toBe(2);
+                    expect(compound1.dataItems.data.rowCount).toBe(2);
+                    expect(compound1.dataItems.dataHeader.value(0)).toBe('<Comment>');
+                    expect(compound1.dataItems.data.value(0)).toBe("This is an SDF example.\nWith a multi-line comment.");
+                    expect(compound1.dataItems.dataHeader.value(1)).toBe('<source>');
+                    expect(compound1.dataItems.data.value(1)).toBe('This was retrieved from biotech.fyicenter.com');
+                    compound2 = parsed.result.compounds[1];
+                    expect(compound2.molFile.atoms.count).toBe(6);
+                    expect(compound2.molFile.bonds.count).toBe(5);
+                    expect(compound2.molFile.atoms.x.value(4)).toBe(0.622);
+                    expect(compound2.molFile.atoms.y.value(4)).toBe(-1.8037);
+                    expect(compound2.molFile.atoms.z.value(4)).toBe(0);
+                    expect(compound2.molFile.atoms.type_symbol.value(4)).toBe('O');
+                    expect(compound2.molFile.bonds.atomIdxA.value(1)).toBe(1);
+                    expect(compound2.molFile.bonds.atomIdxB.value(1)).toBe(3);
+                    expect(compound2.molFile.bonds.order.value(1)).toBe(1);
+                    expect(compound2.dataItems.dataHeader.rowCount).toBe(0);
+                    expect(compound2.dataItems.data.rowCount).toBe(0);
+                    return [2 /*return*/];
+            }
+        });
+    }); });
 });
 //# sourceMappingURL=sdf.spec.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"sdf.spec.js","sourceRoot":"","sources":["../../../../../src/mol-io/reader/_spec/sdf.spec.ts"],"names":[],"mappings":";;;AACA,wCAAyC;AAEzC,IAAM,SAAS,GAAG,+1MAyUjB,CAAC;AAEF,IAAM,cAAc,GAAG,shDAwEtB,CAAC;AAEF,QAAQ,CAAC,YAAY,EAAE;IACnB,EAAE,CAAC,OAAO,EAAE;;;;wBACO,qBAAM,IAAA,iBAAQ,EAAC,SAAS,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAAxC,MAAM,GAAG,SAA+B;oBAC9C,IAAI,MAAM,CAAC,OAAO,EAAE;wBAChB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;qBACnC;oBACK,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBACvC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBACvC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBACrC,OAAO,GAAgB,SAAS,QAAzB,EAAE,SAAS,GAAK,SAAS,UAAd,CAAe;oBACjC,KAAK,GAAY,OAAO,MAAnB,EAAE,KAAK,GAAK,OAAO,MAAZ,CAAa;oBAEjC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAE/C,uBAAuB;oBACvB,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC5B,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAE5B,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAC9C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAE9C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;oBAC/C,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;oBACrD,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC;oBAChD,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAE7C,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBACxC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAErC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC;oBAC5D,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAE1C,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;oBAC9D,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;oBAEjD,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC;oBAChE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;oBAEjD,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;oBAC1D,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;oBAEnE,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;oBAEpD,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,kCAAkC,CAAC,CAAC;oBACzF,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,+DAA+D,CAAC,CAAC;oBAEhH,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;oBACnF,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;;;;SAC/D,CAAC,CAAC;IAEH,EAAE,CAAC,OAAO,EAAE;;;;wBACO,qBAAM,IAAA,iBAAQ,EAAC,cAAc,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAA7C,MAAM,GAAG,SAAoC;oBACnD,IAAI,MAAM,CAAC,OAAO,EAAE;wBAChB,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;qBACnC;oBAED,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;oBAEzC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;oBAC7C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC/C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACpD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC9D,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC/C,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC3D,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC3D,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAExD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACtD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACtD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACtD,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;oBAEhE,MAAM,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBAC5D,MAAM,CAAC,SAAS,CA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package/lib/commonjs/mol-io/reader/ccp4/parser.js

@@ -127,7 +127,7 @@ function getCcp4DataType(mode) {
         case 6: typed_array_1.TypedArrayValueType.Uint16;
         case 16: throw new Error('mode 16 unsupported, unsigned char * 3 (for rgb data, non-standard)');
     }
-    throw new Error("unknown mode '" + mode + "'");
+    throw new Error("unknown mode '".concat(mode, "'"));
 }
 /** check if the file was converted by mapmode2to0, see https://github.com/uglymol/uglymol */
 function isMapmode2to0(header) {

package/lib/commonjs/mol-io/reader/ccp4/parser.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-io/reader/cif/binary/parser.js

@@ -50,7 +50,7 @@ function parseCifBinary(data) {
             try {
                 unpacked = (0, decode_1.decodeMsgPack)(data);
                 if (!checkVersions(minVersion, unpacked.version.match(/(\d)\.(\d)\.\d/).slice(1).map(function (v) { return +v; }))) {
-                    return [2 /*return*/, result_1.ReaderResult.error("Unsupported format version. Current " + unpacked.version + ", required " + minVersion.join('.') + ".")];
+                    return [2 /*return*/, result_1.ReaderResult.error("Unsupported format version. Current ".concat(unpacked.version, ", required ").concat(minVersion.join('.'), "."))];
                 }
                 file = Data.CifFile(unpacked.dataBlocks.map(function (block) {
                     var cats = Object.create(null);

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

@@ -1 +1 @@
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+{"version":3,"file":"parser.js","sourceRoot":"","sources":["../../../../../../src/mol-io/reader/cif/binary/parser.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;;AAEH,+DAAsC;AAEtC,iCAAgC;AAChC,uCAAsD;AACtD,yDAA+D;AAC/D,iDAA4C;AAE5C,SAAS,aAAa,CAAC,GAAa,EAAE,OAAiB;IACnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QACxB,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC;YAAE,OAAO,KAAK,CAAC;KACzC;IACD,OAAO,IAAI,CAAC;AAChB,CAAC;AAED,SAAS,QAAQ,CAAC,IAAqB;IACnC,IAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAChC,IAAM,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAClC,KAAkB,UAAY,EAAZ,KAAA,IAAI,CAAC,OAAO,EAAZ,cAAY,EAAZ,IAAY;QAAzB,IAAM,GAAG,SAAA;QAAkB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC;KAAA;IACpD,OAAO;QACH,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,IAAI,EAAE,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC;QACzB,UAAU,EAAE,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,IAAI,EAAN,CAAM,CAAC;QACzC,QAAQ,YAAC,IAAI;YACT,IAAM,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC;YACtB,IAAI,CAAC,GAAG;gBAAE,OAAO,KAAK,CAAC,CAAC;YACxB,IAAI,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC;gBAAE,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC;YACtC,KAAK,CAAC,IAAI,CAAC,GAAG,IAAA,aAAK,EAAC,GAAG,CAAC,CAAC;YACzB,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC;QACvB,CAAC;KACJ,CAAC;AACN,CAAC;AAED,SAAgB,cAAc,CAAC,IAAgB;IAA/C,iBAmBC;IAlBG,OAAO,eAAI,CAAC,MAAM,CAAuB,iBAAiB,EAAE,UAAM,GAAG;;;YAC3D,UAAU,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YAE1B,IAAI;gBACM,QAAQ,GAAG,IAAA,sBAAa,EAAC,IAAI,CAAgB,CAAC;gBACpD,IAAI,CAAC,aAAa,CAAC,UAAU,EAAE,QAAQ,CAAC,OAAO,CAAC,KAAK,CAAC,gBAAgB,CAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,EAAF,CAAE,CAAC,CAAC,EAAE;oBAC7F,sBAAO,qBAAM,CAAC,KAAK,CAAe,8CAAuC,QAAQ,CAAC,OAAO,wBAAc,UAAU,CAAC,IAAI,CAAC,GAAG,CAAC,MAAG,CAAC,EAAC;iBACnI;gBACK,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAC,GAAG,CAAC,UAAA,KAAK;oBACnD,IAAM,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;oBACjC,KAAkB,UAAgB,EAAhB,KAAA,KAAK,CAAC,UAAU,EAAhB,cAAgB,EAAhB,IAAgB;wBAA7B,IAAM,GAAG,SAAA;wBAAsB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;qBAAA;oBAC7E,OAAO,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAhB,CAAgB,CAAC,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;gBAC1F,CAAC,CAAC,CAAC,CAAC;gBACJ,sBAAO,qBAAM,CAAC,OAAO,CAAC,IAAI,CAAC,EAAC;aAC/B;YAAC,OAAO,CAAC,EAAE;gBACR,sBAAO,qBAAM,CAAC,KAAK,CAAe,EAAE,GAAG,CAAC,CAAC,EAAC;aAC7C;;;SACJ,CAAC,CAAC;AACP,CAAC;AAnBD,wCAmBC"}

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

@@ -200,7 +200,7 @@ var CifField;
                 float = function (row) { return NaN; };
                 break;
             default:
-                throw new Error("unsupported valueType '" + column.schema.valueType + "'");
+                throw new Error("unsupported valueType '".concat(column.schema.valueType, "'"));
         }
         return {
             __array: void 0,
@@ -228,16 +228,16 @@ function tensorFieldNameGetter(field, rank, zeroIndexed, namingVariant) {
     switch (rank) {
         case 1:
             return namingVariant === 'brackets'
-                ? function (i) { return field + "[" + (i + offset) + "]"; }
-                : function (i) { return field + "_" + (i + offset); };
+                ? function (i) { return "".concat(field, "[").concat(i + offset, "]"); }
+                : function (i) { return "".concat(field, "_").concat(i + offset); };
         case 2:
             return namingVariant === 'brackets'
-                ? function (i, j) { return field + "[" + (i + offset) + "][" + (j + offset) + "]"; }
-                : function (i, j) { return field + "_" + (i + offset) + (j + offset); };
+                ? function (i, j) { return "".concat(field, "[").concat(i + offset, "][").concat(j + offset, "]"); }
+                : function (i, j) { return "".concat(field, "_").concat(i + offset).concat(j + offset); };
         case 3:
             return namingVariant === 'brackets'
-                ? function (i, j, k) { return field + "[" + (i + offset) + "][" + (j + offset) + "][" + (k + offset) + "]"; }
-                : function (i, j, k) { return field + "_" + (i + offset) + (j + offset) + (k + offset); };
+                ? function (i, j, k) { return "".concat(field, "[").concat(i + offset, "][").concat(j + offset, "][").concat(k + offset, "]"); }
+                : function (i, j, k) { return "".concat(field, "_").concat(i + offset).concat(j + offset).concat(k + offset); };
         default:
             throw new Error('Tensors with rank > 3 or rank 0 are currently not supported.');
     }

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

@@ -1 +1 @@
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package/lib/commonjs/mol-io/reader/cif/schema/bird.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -479,7 +479,7 @@ export declare const BIRD_Schema: {
         /**
          * An identifier for the wwPDB site creating or modifying the molecule.
          */
-        processing_site: Schema.Aliased<"RCSB" | "BMRB" | "PDBJ" | "PDBC" | "PDBe">;
+        processing_site: Schema.Aliased<"RCSB" | "PDBE" | "BMRB" | "PDBJ" | "PDBC">;
         /**
          * The action associated with this audit record.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/cif/schema/ccd.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/cif/schema/cif-core.d.ts

@@ -106,7 +106,7 @@ export declare const CifCore_Schema: {
      * Abstracts. This ordering is used in _chemical_formula.moiety
      * and _chemical_formula.sum.
      *
-     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.IUPAC      '[Mo (C O)4 (C18 H33 P)2]'
      * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
      * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
      * _chemical_formula.sum         'C40 H66 Mo O4 P2'
@@ -138,7 +138,7 @@ export declare const CifCore_Schema: {
         sum: Schema.Str;
         /**
          * Mass corresponding to the formulae _chemical_formula.structural,
-         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
          * parameters yield the density given as _exptl_crystal.density_diffrn.
          */
         weight: Schema.Float;
@@ -470,7 +470,7 @@ export declare const CifCore_Schema: {
          * A concatenated series of single-letter codes which indicate the
          * refinement restraints or constraints applied to this site. This
          * item should not be used. It has been replaced by
-         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
          * retained in this dictionary only to provide compatibility with
          * legacy CIFs.
          */
@@ -497,9 +497,9 @@ export declare const CifCore_Schema: {
          * atomic  displacement parameter, U(equiv), in angstroms squared,
          * calculated from anisotropic atomic displacement  parameters.
          *
-         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
          *
-         * a  = the real-space cell lengths
+         * a  = the real-space cell vectors
          * a* = the reciprocal-space cell lengths
          * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
          */
@@ -659,8 +659,11 @@ export declare const CifCore_Aliases: {
     'geom_bond.atom_site_label_1': string[];
     'geom_bond.atom_site_label_2': string[];
     'geom_bond.distance': string[];
+    'audit.block_doi': string[];
     'database_code.cod': string[];
     'database_code.csd': string[];
+    'database_code.depnum_ccdc_archive': string[];
+    'database_code.depnum_ccdc_fiz': string[];
     'database_code.icsd': string[];
     'database_code.mdf': string[];
     'database_code.nbs': string[];

package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js

@@ -113,7 +113,7 @@ exports.CifCore_Schema = {
      * Abstracts. This ordering is used in _chemical_formula.moiety
      * and _chemical_formula.sum.
      *
-     * _chemical_formula.iupac      '[Mo (C O)4 (C18 H33 P)2]'
+     * _chemical_formula.IUPAC      '[Mo (C O)4 (C18 H33 P)2]'
      * _chemical_formula.moiety     'C40 H66 Mo O4 P2'
      * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
      * _chemical_formula.sum         'C40 H66 Mo O4 P2'
@@ -145,7 +145,7 @@ exports.CifCore_Schema = {
         sum: str,
         /**
          * Mass corresponding to the formulae _chemical_formula.structural,
-         * *_iupac, *_moiety or *_sum and, together with the Z value and cell
+         * *_IUPAC, *_moiety or *_sum and, together with the Z value and cell
          * parameters yield the density given as _exptl_crystal.density_diffrn.
          */
         weight: float,
@@ -477,7 +477,7 @@ exports.CifCore_Schema = {
          * A concatenated series of single-letter codes which indicate the
          * refinement restraints or constraints applied to this site. This
          * item should not be used. It has been replaced by
-         * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
+         * _atom_site.refinement_flags_posn, _ADP and _occupancy. It is
          * retained in this dictionary only to provide compatibility with
          * legacy CIFs.
          */
@@ -504,9 +504,9 @@ exports.CifCore_Schema = {
          * atomic  displacement parameter, U(equiv), in angstroms squared,
          * calculated from anisotropic atomic displacement  parameters.
          *
-         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
+         * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~.a~j~)]
          *
-         * a  = the real-space cell lengths
+         * a  = the real-space cell vectors
          * a* = the reciprocal-space cell lengths
          * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
          */
@@ -681,12 +681,21 @@ exports.CifCore_Aliases = {
     'geom_bond.distance': [
         'geom_bond_dist',
     ],
+    'audit.block_doi': [
+        'audit_block_DOI',
+    ],
     'database_code.cod': [
         'database_code_COD',
     ],
     'database_code.csd': [
         'database_code_CSD',
     ],
+    'database_code.depnum_ccdc_archive': [
+        'database_code_depnum_CCDC_archive',
+    ],
+    'database_code.depnum_ccdc_fiz': [
+        'database_code_depnum_CCDC_fiz',
+    ],
     'database_code.icsd': [
         'database_code_ICSD',
     ],
@@ -697,6 +706,7 @@ exports.CifCore_Aliases = {
         'database_code_NBS',
     ],
     'atom_site.adp_type': [
+        'atom_site_ADP_type',
         'atom_site_thermal_displace_type',
     ],
     'atom_site.label': [

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

@@ -1 +1 @@
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package/lib/commonjs/mol-io/reader/cif/schema/density-server.d.ts

@@ -10,11 +10,11 @@ export declare const DensityServer_Header_Schema: {
         server_version: Schema.Str;
         datetime_utc: Schema.Str;
         guid: Schema.Str;
-        is_empty: Schema.Aliased<"no" | "n" | "yes" | "y">;
-        has_error: Schema.Aliased<"no" | "n" | "yes" | "y">;
+        is_empty: Schema.Aliased<"y" | "no" | "n" | "yes">;
+        has_error: Schema.Aliased<"y" | "no" | "n" | "yes">;
         error: Schema.Str;
         query_source_id: Schema.Str;
-        query_type: Schema.Aliased<"cell" | "box">;
+        query_type: Schema.Aliased<"box" | "cell">;
         query_box_type: Schema.Aliased<"cartesian" | "fractional">;
         query_box_a: Schema.Tensor;
         query_box_b: Schema.Tensor;

package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */
@@ -1974,7 +1974,7 @@ export declare const mmCIF_Schema: {
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
          */
-        occupancy_flag: Schema.Aliased<"0" | "1">;
+        occupancy_flag: Schema.Aliased<"1" | "0">;
         /**
          * Part of the identifier for the unobserved or zero occupancy residue.
          *
@@ -3343,7 +3343,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of post modeling analysis being carried out.
          */
-        type: Schema.Aliased<"filter" | "other" | "cluster" | "rescore" | "validation" | "none">;
+        type: Schema.Aliased<"other" | "filter" | "cluster" | "rescore" | "validation" | "none">;
         /**
          * The parameter/feature used in the post modeling analysis.
          */
@@ -3566,7 +3566,7 @@ export declare const mmCIF_Schema: {
         /**
          * The application / utilization of the dataset group in modeling.
          */
-        application: Schema.Aliased<"filter" | "other" | "validation" | "restraint" | "representation" | "sampling">;
+        application: Schema.Aliased<"other" | "filter" | "validation" | "restraint" | "representation" | "sampling">;
         /**
          * Additional details regarding the dataset group.
          */

package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.350, IHM 1.17, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/cif/schema.js

@@ -24,7 +24,7 @@ var FieldPath;
     FieldPath.equal = equal;
     function create(category, field, asCanonical) {
         if (asCanonical === void 0) { asCanonical = false; }
-        var p = "" + category + (field ? "." + field : '');
+        var p = "".concat(category).concat(field ? ".".concat(field) : '');
         return asCanonical ? canonical(p) : p;
     }
     FieldPath.create = create;
@@ -86,13 +86,13 @@ function createListColumn(schema, category, key) {
 }
 function createTensorColumn(schema, category, key) {
     var space = schema.space;
-    var zeroOffset = (category.fieldNames.includes(key + "[0]") ||
-        category.fieldNames.includes(key + "[0][0]") ||
-        category.fieldNames.includes(key + "[0][0][0]"));
+    var zeroOffset = (category.fieldNames.includes("".concat(key, "[0]")) ||
+        category.fieldNames.includes("".concat(key, "[0][0]")) ||
+        category.fieldNames.includes("".concat(key, "[0][0][0]")));
     var fst = zeroOffset ? 0 : 1;
-    var namingVariant = (category.fieldNames.includes(key + "_1") ||
-        category.fieldNames.includes(key + "_11") ||
-        category.fieldNames.includes(key + "_111")) ? 'underscore' : 'brackets';
+    var namingVariant = (category.fieldNames.includes("".concat(key, "_1")) ||
+        category.fieldNames.includes("".concat(key, "_11")) ||
+        category.fieldNames.includes("".concat(key, "_111"))) ? 'underscore' : 'brackets';
     var getName = Data.tensorFieldNameGetter(key, space.rank, zeroOffset, namingVariant);
     var first = category.getField(getName(fst, fst, fst)) || db_1.Column.Undefined(category.rowCount, schema);
     var value = function (row) { return Data.getTensor(category, space, row, getName); };

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

@@ -1 +1 @@
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