molstar 3.3.1 → 3.6.0

package/lib/commonjs/mol-model/structure/structure/unit.js

@@ -152,7 +152,7 @@ var Unit;
         Atomic.prototype.remapModel = function (model, dynamicBonds, props) {
             var _a, _b;
             if (!props) {
-                props = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.props), { bonds: dynamicBonds && !((_b = (_a = this.props.bonds) === null || _a === void 0 ? void 0 : _a.props) === null || _b === void 0 ? void 0 : _b.canRemap)
+                props = tslib_1.__assign(tslib_1.__assign({}, this.props), { bonds: dynamicBonds && !((_b = (_a = this.props.bonds) === null || _a === void 0 ? void 0 : _a.props) === null || _b === void 0 ? void 0 : _b.canRemap)
                         ? undefined
                         : tryRemapBonds(this, this.props.bonds, model, dynamicBonds) });
                 if (!Unit.isSameConformation(this, model)) {
@@ -336,7 +336,7 @@ var Unit;
             var coarseConformation = this.getCoarseConformation();
             var modelCoarseConformation = getCoarseConformation(this.kind, model);
             if (!props) {
-                props = (0, tslib_1.__assign)({}, this.props);
+                props = tslib_1.__assign({}, this.props);
                 if (!Unit.isSameConformation(this, model)) { // TODO get rid of casting
                     props.boundary = undefined;
                     props.lookup3d = undefined;
@@ -414,7 +414,7 @@ var Unit;
         return BaseProperties();
     }
     var Spheres = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(Spheres, _super);
+        tslib_1.__extends(Spheres, _super);
         function Spheres() {
             return _super !== null && _super.apply(this, arguments) || this;
         }
@@ -422,7 +422,7 @@ var Unit;
     }(Coarse));
     Unit.Spheres = Spheres;
     var Gaussians = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(Gaussians, _super);
+        tslib_1.__extends(Gaussians, _super);
         function Gaussians() {
             return _super !== null && _super.apply(this, arguments) || this;
         }

package/lib/commonjs/mol-model/structure/structure/util/superposition.js

@@ -47,7 +47,7 @@ function alignAndSuperpose(xs) {
         var lociA = element_1.StructureElement.Loci(xs[0].structure, [a]);
         var lociB = element_1.StructureElement.Loci(xs[i].structure, [b]);
         var n = int_1.OrderedSet.size(a.indices);
-        ret.push((0, tslib_1.__assign)((0, tslib_1.__assign)({}, minimize_rmsd_1.MinimizeRmsd.compute({
+        ret.push(tslib_1.__assign(tslib_1.__assign({}, minimize_rmsd_1.MinimizeRmsd.compute({
             a: getPositionTable(lociA, n),
             b: getPositionTable(lociB, n)
         })), { alignmentScore: score }));

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

@@ -19,5 +19,5 @@ var bonds_1 = require("./structure/unit/bonds");
 Object.defineProperty(exports, "Bond", { enumerable: true, get: function () { return bonds_1.Bond; } });
 var properties_1 = require("./structure/properties");
 Object.defineProperty(exports, "StructureProperties", { enumerable: true, get: function () { return properties_1.StructureProperties; } });
-(0, tslib_1.__exportStar)(require("./structure/unit/rings"), exports);
-(0, tslib_1.__exportStar)(require("./export/mmcif"), exports);
+tslib_1.__exportStar(require("./structure/unit/rings"), exports);
+tslib_1.__exportStar(require("./export/mmcif"), exports);

package/lib/commonjs/mol-model/structure/topology.js

@@ -6,4 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./topology/topology"), exports);
+tslib_1.__exportStar(require("./topology/topology"), exports);

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

@@ -7,9 +7,9 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./structure/coordinates"), exports);
-(0, tslib_1.__exportStar)(require("./structure/topology"), exports);
-(0, tslib_1.__exportStar)(require("./structure/model"), exports);
-(0, tslib_1.__exportStar)(require("./structure/structure"), exports);
-(0, tslib_1.__exportStar)(require("./structure/query"), exports);
-(0, tslib_1.__exportStar)(require("./structure/trajectory"), exports);
+tslib_1.__exportStar(require("./structure/coordinates"), exports);
+tslib_1.__exportStar(require("./structure/topology"), exports);
+tslib_1.__exportStar(require("./structure/model"), exports);
+tslib_1.__exportStar(require("./structure/structure"), exports);
+tslib_1.__exportStar(require("./structure/query"), exports);
+tslib_1.__exportStar(require("./structure/trajectory"), exports);

package/lib/commonjs/mol-model/volume.js

@@ -7,5 +7,5 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./volume/volume"), exports);
-(0, tslib_1.__exportStar)(require("./volume/grid"), exports);
+tslib_1.__exportStar(require("./volume/volume"), exports);
+tslib_1.__exportStar(require("./volume/grid"), exports);

package/lib/commonjs/mol-model-formats/shape/ply.d.ts

@@ -30,6 +30,7 @@ export declare const PlyShapeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-model-formats/shape/ply.js

@@ -69,7 +69,7 @@ function createPlyShapeParams(plyFile) {
     }
     var defaultColoring = defaultValues.vRed && defaultValues.vGreen && defaultValues.vBlue ? 'vertex' :
         defaultValues.mRed && defaultValues.mGreen && defaultValues.mBlue ? 'material' : 'uniform';
-    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), { coloring: param_definition_1.ParamDefinition.MappedStatic(defaultColoring, {
+    return tslib_1.__assign(tslib_1.__assign({}, mesh_1.Mesh.Params), { coloring: param_definition_1.ParamDefinition.MappedStatic(defaultColoring, {
             vertex: param_definition_1.ParamDefinition.Group({
                 red: param_definition_1.ParamDefinition.Select(defaultValues.vRed, colorOptions, { label: 'Red Property' }),
                 green: param_definition_1.ParamDefinition.Select(defaultValues.vGreen, colorOptions, { label: 'Green Property' }),
@@ -125,9 +125,9 @@ function addFacesRange(begI, endI, state, face) {
     }
 }
 function getMesh(ctx, vertex, face, groupIds, mesh) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var builderState, x, y, z, nx, ny, nz, hasNormals, updateChunk, i, il, i, il, m;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     builderState = mesh_builder_1.MeshBuilder.createState(vertex.rowCount, vertex.rowCount / 4, mesh);
@@ -231,9 +231,9 @@ function makeShapeGetter() {
     var _mesh;
     var _coloring;
     var _grouping;
-    var getShape = function (ctx, plyFile, props, shape) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    var getShape = function (ctx, plyFile, props, shape) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var vertex, face, material, newMesh, newColor;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     vertex = plyFile.getElement('vertex');
@@ -279,8 +279,8 @@ function makeShapeGetter() {
 }
 function shapeFromPly(source, params) {
     var _this = this;
-    return mol_task_1.Task.create('Shape Provider', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Shape Provider', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, {
                     label: 'Mesh',
                     data: source,

package/lib/commonjs/mol-model-formats/structure/basic/atomic.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -40,14 +40,6 @@ function findHierarchyOffsets(atom_site) {
     }
     return { residues: residues, chains: chains };
 }
-function substUndefinedColumn(table, a, b) {
-    if (!table[a].isDefined) {
-        table[a] = table[b];
-    }
-    if (!table[b].isDefined) {
-        table[b] = table[a];
-    }
-}
 function createHierarchyData(atom_site, sourceIndex, offsets) {
     var atoms = db_1.Table.ofColumns(atomic_1.AtomsSchema, {
         type_symbol: db_1.Column.ofArray({ array: db_1.Column.mapToArray(atom_site.type_symbol, types_1.ElementSymbol), schema: db_1.Column.Schema.Aliased(db_1.Column.Schema.str) }),
@@ -77,11 +69,6 @@ function createHierarchyData(atom_site, sourceIndex, offsets) {
     // Optimize the numeric columns
     db_1.Table.columnToArray(residues, 'label_seq_id', Int32Array);
     db_1.Table.columnToArray(residues, 'auth_seq_id', Int32Array);
-    // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
-    substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
-    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
     return { atoms: atoms, residues: residues, chains: chains, atomSourceIndex: sourceIndex };
 }
 function getConformation(atom_site) {
@@ -162,7 +149,7 @@ function getAtomicHierarchy(atom_site, sourceIndex, entities, chemicalComponentM
     };
     var index = (0, atomic_index_1.getAtomicIndex)(hierarchyData, entities, hierarchySegments);
     var derived = (0, atomic_derived_1.getAtomicDerivedData)(hierarchyData, hierarchySegments, index, chemicalComponentMap);
-    var hierarchy = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, hierarchyData), hierarchySegments), { index: index, derived: derived });
+    var hierarchy = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, hierarchyData), hierarchySegments), { index: index, derived: derived });
     return { sameAsPrevious: false, hierarchy: hierarchy, chainOperatorMapping: chainOperatorMapping };
 }
 function getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, chemicalComponentMap, format, previous) {

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

@@ -31,8 +31,8 @@ function getCoarse(data, chemicalComponentMap) {
     return {
         hierarchy: {
             isDefined: true,
-            spheres: (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, sphereData), sphereKeys), sphereRanges),
-            gaussians: (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussianData), gaussianKeys), gaussianRanges),
+            spheres: tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, sphereData), sphereKeys), sphereRanges),
+            gaussians: tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussianData), gaussianKeys), gaussianRanges),
         },
         conformation: {
             id: mol_util_1.UUID.create22(),
@@ -79,5 +79,5 @@ function getSegments(asym_id, seq_id_begin, seq_id_end) {
 }
 function getData(data) {
     var entity_id = data.entity_id, seq_id_begin = data.seq_id_begin, seq_id_end = data.seq_id_end, asym_id = data.asym_id;
-    return (0, tslib_1.__assign)({ count: entity_id.rowCount, entity_id: entity_id, asym_id: asym_id, seq_id_begin: seq_id_begin, seq_id_end: seq_id_end }, getSegments(asym_id, seq_id_begin, seq_id_end));
+    return tslib_1.__assign({ count: entity_id.rowCount, entity_id: entity_id, asym_id: asym_id, seq_id_begin: seq_id_begin, seq_id_end: seq_id_end }, getSegments(asym_id, seq_id_begin, seq_id_end));
 }

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

@@ -99,7 +99,7 @@ function getEntityData(data) {
                 var entityId = label_entity_id.value(i);
                 if (!entityIds.has(entityId)) {
                     var compId = label_comp_id.value(i);
-                    var compType = chemCompType.get(compId) || '';
+                    var compType = chemCompType.get(compId) || 'other';
                     subtypes[getEntityIndex(entityId)] = (0, types_1.getEntitySubtype)(compId, compType);
                     entityIds.add(entityId);
                 }
@@ -131,6 +131,6 @@ function getEntitiesWithPRD(data, entities, structAsymMap) {
         }
     }
     var prdIdColumn = db_1.Column.ofArray({ array: prdIds, schema: db_1.Column.Schema.str });
-    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, entities), { prd_id: prdIdColumn });
+    return tslib_1.__assign(tslib_1.__assign({}, entities), { prd_id: prdIdColumn });
 }
 exports.getEntitiesWithPRD = getEntitiesWithPRD;

package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -22,9 +22,9 @@ var entities_1 = require("./entities");
 var util_1 = require("./util");
 var trajectory_1 = require("../../../mol-model/structure/trajectory");
 function createModels(data, format, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var properties, models, _a, i;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     properties = getCommonProperties(data, format);
@@ -60,7 +60,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var atomic = (0, atomic_1.getAtomicHierarchyAndConformation)(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
     var modelNum = atom_site.pdbx_PDB_model_num.value(0);
     if (previous && atomic.sameAsPrevious) {
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, previous), { id: uuid_1.UUID.create22(), modelNum: modelNum, atomicConformation: atomic.conformation, _dynamicPropertyData: Object.create(null) });
+        return tslib_1.__assign(tslib_1.__assign({}, previous), { id: uuid_1.UUID.create22(), modelNum: modelNum, atomicConformation: atomic.conformation, _dynamicPropertyData: Object.create(null) });
     }
     var coarse = coarse_1.EmptyCoarse;
     var sequence = (0, sequence_1.getSequence)(data, entities, atomic.hierarchy, coarse.hierarchy);
@@ -89,7 +89,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
+        properties: tslib_1.__assign(tslib_1.__assign({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -129,7 +129,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
+        properties: tslib_1.__assign(tslib_1.__assign({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -145,9 +145,9 @@ function findModelEnd(num, startIndex) {
     return endIndex;
 }
 function readStandard(ctx, data, properties, format) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var models, atomCount, entities, modelStart, modelEnd, _a, atom_site, sourceIndex, model;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     models = [];
@@ -188,9 +188,9 @@ function splitTable(table, col) {
     return ret;
 }
 function readIntegrative(ctx, data, properties, format) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var entities, atom_sites_modelColumn, atom_sites, sphere_sites, gauss_sites, models, _a, model_id, model_name, i, id, atom_site, atom_site_sourceIndex, e, _b, sorted, sourceIndex, ihm, model;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     entities = (0, entities_1.getEntityData)(data);

package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -88,7 +88,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db/column").Column.Schema.Aliased<"oligosaccharide">;
     };
     chem_comp: {
-        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: import("../../../mol-data/db/column").Column.Schema.Str;
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -160,7 +160,7 @@ export declare const BasicSchema: {
     };
     pdbx_unobs_or_zero_occ_residues: {
         id: import("../../../mol-data/db/column").Column.Schema.Int;
-        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         occupancy_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"1" | "0">;
         PDB_model_num: import("../../../mol-data/db/column").Column.Schema.Int;
         auth_asym_id: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -196,4 +196,4 @@ export interface BasicData {
     pdbx_unobs_or_zero_occ_residues: UnobsOrZeroOccResidues;
     pdbx_molecule: Molecule;
 }
-export declare function createBasic(data: Partial<BasicData>): BasicData;
+export declare function createBasic(data: Partial<BasicData>, normalize?: boolean): BasicData;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,6 +9,7 @@ exports.createBasic = exports.BasicSchema = void 0;
 var mmcif_1 = require("../../../mol-io/reader/cif/schema/mmcif");
 var db_1 = require("../../../mol-data/db");
 var mmcif_extras_1 = require("../../../mol-io/reader/cif/schema/mmcif-extras");
+var util_1 = require("./util");
 exports.BasicSchema = {
     entry: mmcif_1.mmCIF_Schema.entry,
     struct: mmcif_1.mmCIF_Schema.struct,
@@ -28,7 +29,8 @@ exports.BasicSchema = {
     pdbx_unobs_or_zero_occ_residues: mmcif_1.mmCIF_Schema.pdbx_unobs_or_zero_occ_residues,
     pdbx_molecule: mmcif_1.mmCIF_Schema.pdbx_molecule,
 };
-function createBasic(data) {
+function createBasic(data, normalize) {
+    if (normalize === void 0) { normalize = false; }
     var basic = Object.create(null);
     for (var _i = 0, _a = Object.keys(exports.BasicSchema); _i < _a.length; _i++) {
         var name_1 = _a[_i];
@@ -39,6 +41,9 @@ function createBasic(data) {
             basic[name_1] = db_1.Table.ofUndefinedColumns(exports.BasicSchema[name_1], 0);
         }
     }
+    if (normalize) {
+        basic.atom_site = (0, util_1.getNormalizedAtomSite)(basic.atom_site);
+    }
     return basic;
 }
 exports.createBasic = createBasic;

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

@@ -11,9 +11,9 @@ var util_1 = require("../../../mol-data/util");
 var db_1 = require("../../../mol-data/db");
 var array_1 = require("../../../mol-util/array");
 function sortAtomSite(ctx, atom_site, start, end) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var indices, label_entity_id, label_asym_id, label_seq_id, entityBuckets, ei, _eI, chainBuckets, cI, _cI, aI;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     indices = (0, util_1.createRangeArray)(start, end - 1);

package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts

@@ -1,8 +1,39 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { BasicData } from './schema';
+import { AtomSite, BasicData } from './schema';
+import { Column, Table } from '../../../mol-data/db';
 export declare function getModelGroupName(model_id: number, data: BasicData): string;
+/** Fix possibly missing auth_/label_ columns */
+export declare function getNormalizedAtomSite(atom_site: AtomSite): Table<{
+    auth_asym_id: Column.Schema.Str;
+    auth_atom_id: Column.Schema.Str;
+    auth_comp_id: Column.Schema.Str;
+    auth_seq_id: Column.Schema.Int;
+    B_iso_or_equiv: Column.Schema.Float;
+    Cartn_x: Column.Schema.Coordinate;
+    Cartn_y: Column.Schema.Coordinate;
+    Cartn_z: Column.Schema.Coordinate;
+    group_PDB: Column.Schema.Aliased<"ATOM" | "HETATM">;
+    id: Column.Schema.Int;
+    label_alt_id: Column.Schema.Str;
+    label_asym_id: Column.Schema.Str;
+    label_atom_id: Column.Schema.Str;
+    label_comp_id: Column.Schema.Str;
+    label_entity_id: Column.Schema.Str;
+    label_seq_id: Column.Schema.Int;
+    occupancy: Column.Schema.Float;
+    type_symbol: Column.Schema.Str;
+    pdbx_PDB_ins_code: Column.Schema.Str;
+    pdbx_PDB_model_num: Column.Schema.Int;
+    pdbx_formal_charge: Column.Schema.Int;
+    pdbx_label_index: Column.Schema.Int;
+    pdbx_sifts_xref_db_name: Column.Schema.Str;
+    pdbx_sifts_xref_db_acc: Column.Schema.Str;
+    pdbx_sifts_xref_db_num: Column.Schema.Str;
+    pdbx_sifts_xref_db_res: Column.Schema.Str;
+    ihm_model_id: Column.Schema.Int;
+}>;

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

@@ -1,12 +1,12 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModelGroupName = void 0;
+exports.getNormalizedAtomSite = exports.getModelGroupName = void 0;
 var db_1 = require("../../../mol-data/db");
 function getModelGroupName(model_id, data) {
     var ihm_model_group = data.ihm_model_group, ihm_model_group_link = data.ihm_model_group_link;
@@ -19,3 +19,27 @@ function getModelGroupName(model_id, data) {
     return '';
 }
 exports.getModelGroupName = getModelGroupName;
+//
+function hasPresentValues(column) {
+    for (var i = 0, il = column.rowCount; i < il; i++) {
+        if (column.valueKind(i) === 0 /* Present */)
+            return true;
+    }
+    return false;
+}
+function substUndefinedColumn(table, a, b) {
+    if (!table[a].isDefined || !hasPresentValues(table[a]))
+        table[a] = table[b];
+    if (!table[b].isDefined || !hasPresentValues(table[b]))
+        table[b] = table[a];
+}
+/** Fix possibly missing auth_/label_ columns */
+function getNormalizedAtomSite(atom_site) {
+    var normalized = db_1.Table.ofColumns(atom_site._schema, atom_site);
+    substUndefinedColumn(normalized, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(normalized, 'label_comp_id', 'auth_comp_id');
+    substUndefinedColumn(normalized, 'label_seq_id', 'auth_seq_id');
+    substUndefinedColumn(normalized, 'label_asym_id', 'auth_asym_id');
+    return normalized;
+}
+exports.getNormalizedAtomSite = getNormalizedAtomSite;

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

@@ -43,9 +43,9 @@ function getSymmetry(db) {
 }
 function getModels(db, format, ctx) {
     var _a;
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atomCount, MOL, A, seq_id, symmetry, m, _b, fract_x, fract_y, fract_z, x, y, z, v, i, _c, type_symbol, label, typeSymbol, formalCharge, element_symbol, formal_charge, i, ts, n, element_symbol, i, atom_site, name, entityBuilder, componentBuilder, basics, models, first, bondCount, labelIndexMap, label_1, i, il, bond_type, indexA, indexB, order, dist, flag, included, j, _d, atom_site_label_1, atom_site_label_2, valence, distance, i, iA, iB, id, t;
-        return (0, tslib_1.__generator)(this, function (_e) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var atomCount, MOL, A, seq_id, symmetry, m, _b, fract_x, fract_y, fract_z, x, y, z, v, i, _c, type_symbol, label, typeSymbol, formalCharge, element_symbol, formal_charge, i, ts, n, element_symbol, i, atom_site, name, entityBuilder, componentBuilder, basic, models, first, bondCount, labelIndexMap, label_1, i, il, bond_type, indexA, indexB, order, dist, flag, included, j, _d, atom_site_label_1, atom_site_label_2, valence, distance, i, iA, iB, id, t;
+        return tslib_1.__generator(this, function (_e) {
             switch (_e.label) {
                 case 0:
                     atomCount = db.atom_site._rowCount;
@@ -99,7 +99,7 @@ function getModels(db, format, ctx) {
                         element_symbol = new Array(atomCount);
                         for (i = 0; i < atomCount; ++i) {
                             // TODO can take as is if type_symbol not given?
-                            element_symbol[i] = (0, util_1.guessElementSymbolString)(label.value(i));
+                            element_symbol[i] = (0, util_1.guessElementSymbolString)(label.value(i), '');
                         }
                         typeSymbol = db_1.Column.ofStringArray(element_symbol);
                         formalCharge = db_1.Column.Undefined(atomCount, db_1.Column.Schema.int);
@@ -135,12 +135,12 @@ function getModels(db, format, ctx) {
                     componentBuilder = new component_1.ComponentBuilder(seq_id, db.atom_site.type_symbol);
                     componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, format, ctx)];
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, format, ctx)];
                 case 1:
                     models = _e.sent();
                     if (models.frameCount > 0) {

package/lib/commonjs/mol-model-formats/structure/common/component.d.ts

@@ -19,7 +19,7 @@ export declare class ComponentBuilder {
     private getType;
     has(compId: string): boolean;
     get(compId: string): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
@@ -28,7 +28,7 @@ export declare class ComponentBuilder {
         pdbx_synonyms: Column.Schema.List<string>;
     }, "name" | "id" | "type">> | undefined;
     add(compId: string, index: number): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
@@ -37,7 +37,7 @@ export declare class ComponentBuilder {
         pdbx_synonyms: Column.Schema.List<string>;
     }, "name" | "id" | "type">>;
     getChemCompTable(): Table<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;