molstar 4.2.0 → 4.4.0

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

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createIndex = exports.getFingerprint = exports.computeRings = void 0;
+exports.computeRings = computeRings;
+exports.getFingerprint = getFingerprint;
+exports.createIndex = createIndex;
 const int_1 = require("../../../../../mol-data/int");
 const graph_1 = require("../../../../../mol-math/graph");
 const types_1 = require("../../../model/types");
@@ -21,7 +23,6 @@ function computeRings(unit) {
     }
     return state.rings;
 }
-exports.computeRings = computeRings;
 function State(unit, capacity) {
     return {
         startVertex: 0,
@@ -261,7 +262,6 @@ function getFingerprint(elements) {
         return buildFinderprint(elements, rotNormal);
     return buildFinderprint(reversed, rotReversed);
 }
-exports.getFingerprint = getFingerprint;
 function getMinimalRotation(elements) {
     // adapted from http://en.wikipedia.org/wiki/Lexicographically_minimal_string_rotation
     const len = elements.length;
@@ -360,4 +360,3 @@ function createIndex(rings, aromaticRings) {
     }
     return { elementRingIndices, elementAromaticRingIndices, ringComponentIndex, ringComponents };
 }
-exports.createIndex = createIndex;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeStructureBoundary = void 0;
+exports.computeStructureBoundary = computeStructureBoundary;
 const geometry_1 = require("../../../../mol-math/geometry");
 const boundary_helper_1 = require("../../../../mol-math/geometry/boundary-helper");
 const tmpSphere = (0, geometry_1.Sphere3D)();
@@ -46,4 +46,3 @@ function computeStructureBoundary(s) {
     }
     return { box: boundaryHelper.getBox(), sphere: boundaryHelper.getSphere() };
 }
-exports.computeStructureBoundary = computeStructureBoundary;

package/lib/commonjs/mol-model/structure/structure/util/lookup3d.js

@@ -7,7 +7,8 @@
  * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureLookup3D = exports.StructureLookup3DResultContext = exports.StructureResult = void 0;
+exports.StructureLookup3D = exports.StructureResult = void 0;
+exports.StructureLookup3DResultContext = StructureLookup3DResultContext;
 const geometry_1 = require("../../../../mol-math/geometry");
 const linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 const int_1 = require("../../../../mol-data/int");
@@ -40,7 +41,6 @@ var StructureResult;
 function StructureLookup3DResultContext() {
     return { result: StructureResult.create(), closeUnitsResult: geometry_1.Result.create(), unitGroupResult: geometry_1.Result.create() };
 }
-exports.StructureLookup3DResultContext = StructureLookup3DResultContext;
 class StructureLookup3D {
     findUnitIndices(x, y, z, radius) {
         return this.unitLookup.find(x, y, z, radius);

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

@@ -5,7 +5,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getProteinElements = exports.getNucleotideElements = exports.getCoarseGapElements = exports.getAtomicGapElements = exports.getCoarsePolymerElements = exports.getAtomicPolymerElements = void 0;
+exports.getAtomicPolymerElements = getAtomicPolymerElements;
+exports.getCoarsePolymerElements = getCoarsePolymerElements;
+exports.getAtomicGapElements = getAtomicGapElements;
+exports.getCoarseGapElements = getCoarseGapElements;
+exports.getNucleotideElements = getNucleotideElements;
+exports.getProteinElements = getProteinElements;
 const structure_1 = require("../../../../mol-model/structure");
 const int_1 = require("../../../../mol-data/int");
 const sorted_ranges_1 = require("../../../../mol-data/int/sorted-ranges");
@@ -31,7 +36,6 @@ function getAtomicPolymerElements(unit) {
     }
     return int_1.SortedArray.ofSortedArray(indices);
 }
-exports.getAtomicPolymerElements = getAtomicPolymerElements;
 function getCoarsePolymerElements(unit) {
     const indices = [];
     const { elements, model } = unit;
@@ -46,7 +50,6 @@ function getCoarsePolymerElements(unit) {
     }
     return int_1.SortedArray.ofSortedArray(indices);
 }
-exports.getCoarsePolymerElements = getCoarsePolymerElements;
 //
 function getAtomicGapElements(unit) {
     const indices = [];
@@ -65,7 +68,6 @@ function getAtomicGapElements(unit) {
     }
     return int_1.SortedArray.ofSortedArray(indices);
 }
-exports.getAtomicGapElements = getAtomicGapElements;
 function getCoarseGapElements(unit) {
     const indices = [];
     const { elements, model } = unit;
@@ -78,7 +80,6 @@ function getCoarseGapElements(unit) {
     }
     return int_1.SortedArray.ofSortedArray(indices);
 }
-exports.getCoarseGapElements = getCoarseGapElements;
 //
 function getNucleotideElements(unit) {
     const indices = [];
@@ -99,7 +100,6 @@ function getNucleotideElements(unit) {
     }
     return int_1.SortedArray.ofSortedArray(indices);
 }
-exports.getNucleotideElements = getNucleotideElements;
 function getProteinElements(unit) {
     const indices = [];
     const { elements, model } = unit;
@@ -119,4 +119,3 @@ function getProteinElements(unit) {
     }
     return int_1.SortedArray.ofSortedArray(indices);
 }
-exports.getProteinElements = getProteinElements;

package/lib/commonjs/mol-model/structure/structure/util/principal-axes.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPrincipalAxes = exports.toPositionsArray = void 0;
+exports.toPositionsArray = toPositionsArray;
+exports.getPrincipalAxes = getPrincipalAxes;
 const principal_axes_1 = require("../../../../mol-math/linear-algebra/matrix/principal-axes");
 const linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 const tempPos = (0, linear_algebra_1.Vec3)();
@@ -18,9 +19,7 @@ function toPositionsArray(unit) {
     }
     return positions;
 }
-exports.toPositionsArray = toPositionsArray;
 function getPrincipalAxes(unit) {
     const positions = toPositionsArray(unit);
     return principal_axes_1.PrincipalAxes.ofPositions(positions);
 }
-exports.getPrincipalAxes = getPrincipalAxes;

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

@@ -6,7 +6,7 @@
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.alignAndSuperposeWithSIFTSMapping = void 0;
+exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
 const int_1 = require("../../../../mol-data/int");
 const minimize_rmsd_1 = require("../../../../mol-math/linear-algebra/3d/minimize-rmsd");
 const sifts_mapping_1 = require("../../../../mol-model-props/sequence/sifts-mapping");
@@ -40,7 +40,6 @@ function alignAndSuperposeWithSIFTSMapping(structures, options) {
     }
     return { entries, zeroOverlapPairs, failedPairs };
 }
-exports.alignAndSuperposeWithSIFTSMapping = alignAndSuperposeWithSIFTSMapping;
 function getPositionTables(index, pivot, other, N) {
     const xs = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);
     const ys = minimize_rmsd_1.MinimizeRmsd.Positions.empty(N);

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

@@ -6,7 +6,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPositionTable = exports.alignAndSuperpose = exports.superpose = void 0;
+exports.superpose = superpose;
+exports.alignAndSuperpose = alignAndSuperpose;
+exports.getPositionTable = getPositionTable;
 const minimize_rmsd_1 = require("../../../../mol-math/linear-algebra/3d/minimize-rmsd");
 const element_1 = require("../element");
 const int_1 = require("../../../../mol-data/int");
@@ -29,7 +31,6 @@ function superpose(xs) {
     }
     return ret;
 }
-exports.superpose = superpose;
 const reProtein = /(polypeptide|cyclic-pseudo-peptide)/i;
 function alignAndSuperpose(xs) {
     const ret = [];
@@ -56,7 +57,6 @@ function alignAndSuperpose(xs) {
     }
     return ret;
 }
-exports.alignAndSuperpose = alignAndSuperpose;
 function getPositionTable(xs, n) {
     const ret = minimize_rmsd_1.MinimizeRmsd.Positions.empty(n);
     let o = 0;
@@ -77,7 +77,6 @@ function getPositionTable(xs, n) {
     }
     return ret;
 }
-exports.getPositionTable = getPositionTable;
 function getMinSize(xs) {
     if (xs.length === 0)
         return 0;

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

@@ -5,7 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPositions = exports.getAtomIdForAtomRole = exports.getAtomicMoleculeType = exports.getElementMoleculeType = exports.getCoarseBegCompId = void 0;
+exports.getCoarseBegCompId = getCoarseBegCompId;
+exports.getElementMoleculeType = getElementMoleculeType;
+exports.getAtomicMoleculeType = getAtomicMoleculeType;
+exports.getAtomIdForAtomRole = getAtomIdForAtomRole;
+exports.getPositions = getPositions;
 const types_1 = require("./model/types");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 function getCoarseBegCompId(unit, element) {
@@ -14,7 +18,6 @@ function getCoarseBegCompId(unit, element) {
     const seq_id_begin = unit.coarseElements.seq_id_begin.value(element);
     return seq.compId.value(seq_id_begin - 1); // 1-indexed
 }
-exports.getCoarseBegCompId = getCoarseBegCompId;
 function getElementMoleculeType(unit, element) {
     switch (unit.kind) {
         case 0 /* Unit.Kind.Atomic */:
@@ -29,11 +32,9 @@ function getElementMoleculeType(unit, element) {
     }
     return 0 /* MoleculeType.Unknown */;
 }
-exports.getElementMoleculeType = getElementMoleculeType;
 function getAtomicMoleculeType(model, rI) {
     return model.atomicHierarchy.derived.residue.moleculeType[rI];
 }
-exports.getAtomicMoleculeType = getAtomicMoleculeType;
 const EmptyAtomIds = new Set();
 function getAtomIdForAtomRole(polymerType, atomRole) {
     const p = types_1.PolymerTypeAtomRoleId[polymerType];
@@ -44,7 +45,6 @@ function getAtomIdForAtomRole(polymerType, atomRole) {
     }
     return EmptyAtomIds;
 }
-exports.getAtomIdForAtomRole = getAtomIdForAtomRole;
 const tmpPositionsVec = linear_algebra_1.Vec3.zero();
 function getPositions(unit, indices) {
     const c = unit.conformation;
@@ -56,4 +56,3 @@ function getPositions(unit, indices) {
     }
     return positions;
 }
-exports.getPositions = getPositions;

package/lib/commonjs/mol-model/volume/volume.d.ts

@@ -78,24 +78,24 @@ export declare namespace Volume {
         }>, number>;
     }>;
     const IsoValueParam: PD.Conditioned<Readonly<{
-        kind: 'absolute';
+        kind: "absolute";
         absoluteValue: number;
     }> | Readonly<{
-        kind: 'relative';
+        kind: "relative";
         relativeValue: number;
     }>, PD.Base<Readonly<{
-        kind: 'absolute';
+        kind: "absolute";
         absoluteValue: number;
     }> | Readonly<{
-        kind: 'relative';
+        kind: "relative";
         relativeValue: number;
     }>>, {
         absolute: PD.Converted<Readonly<{
-            kind: 'absolute';
+            kind: "absolute";
             absoluteValue: number;
         }>, number>;
         relative: PD.Converted<Readonly<{
-            kind: 'relative';
+            kind: "relative";
             relativeValue: number;
         }>, number>;
     }>;

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

@@ -36,6 +36,7 @@ export declare const PlyShapeParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -87,6 +88,7 @@ export declare function shapeFromPly(source: PlyFile, params?: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

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

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.shapeFromPly = exports.PlyShapeParams = void 0;
+exports.PlyShapeParams = void 0;
+exports.shapeFromPly = shapeFromPly;
 const mol_task_1 = require("../../mol-task");
 const color_1 = require("../../mol-util/color");
 const mesh_builder_1 = require("../../mol-geo/geometry/mesh/mesh-builder");
@@ -262,4 +263,3 @@ function shapeFromPly(source, params) {
         };
     });
 }
-exports.shapeFromPly = shapeFromPly;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getAtomicHierarchyAndConformation = void 0;
+exports.getAtomicHierarchyAndConformation = getAtomicHierarchyAndConformation;
 const db_1 = require("../../../mol-data/db");
 const int_1 = require("../../../mol-data/int");
 const schema_1 = require("../../../mol-io/reader/cif/schema");
@@ -156,4 +156,3 @@ function getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, che
     const conformation = getConformation(atom_site);
     return { sameAsPrevious, hierarchy, conformation, chainOperatorMapping };
 }
-exports.getAtomicHierarchyAndConformation = getAtomicHierarchyAndConformation;

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

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getCoarse = exports.EmptyCoarse = void 0;
+exports.EmptyCoarse = void 0;
+exports.getCoarse = getCoarse;
 const coarse_1 = require("../../../mol-model/structure/model/properties/coarse");
 const coarse_keys_1 = require("../../../mol-model/structure/model/properties/utils/coarse-keys");
 const mol_util_1 = require("../../../mol-util");
@@ -40,7 +41,6 @@ function getCoarse(data, chemicalComponentMap) {
         }
     };
 }
-exports.getCoarse = getCoarse;
 function getSphereConformation(data) {
     return {
         x: data.Cartn_x.toArray({ array: Float32Array }),

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

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getEntitiesWithPRD = exports.getEntityData = void 0;
+exports.getEntityData = getEntityData;
+exports.getEntitiesWithPRD = getEntitiesWithPRD;
 const db_1 = require("../../../mol-data/db");
 const common_1 = require("../../../mol-model/structure/model/properties/common");
 const types_1 = require("../../../mol-model/structure/model/types");
@@ -113,7 +114,6 @@ function getEntityData(data) {
         getEntityIndex
     };
 }
-exports.getEntityData = getEntityData;
 function getEntitiesWithPRD(data, entities, structAsymMap) {
     var _a;
     if (!data.pdbx_molecule || !data.pdbx_molecule.prd_id.isDefined) {
@@ -135,4 +135,3 @@ function getEntitiesWithPRD(data, entities, structAsymMap) {
         prd_id: prdIdColumn
     };
 }
-exports.getEntitiesWithPRD = getEntitiesWithPRD;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createModels = void 0;
+exports.createModels = createModels;
 const db_1 = require("../../../mol-data/db");
 const uuid_1 = require("../../../mol-util/uuid");
 const model_1 = require("../../../mol-model/structure/model/model");
@@ -30,7 +30,6 @@ async function createModels(data, format, ctx) {
     }
     return new trajectory_1.ArrayTrajectory(models);
 }
-exports.createModels = createModels;
 function getCommonProperties(data, format) {
     return {
         missingResidues: (0, properties_1.getMissingResidues)(data),

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

@@ -6,7 +6,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getStructAsymMap = exports.getSaccharideComponentMap = exports.getChemicalComponentMap = exports.getMissingResidues = void 0;
+exports.getMissingResidues = getMissingResidues;
+exports.getChemicalComponentMap = getChemicalComponentMap;
+exports.getSaccharideComponentMap = getSaccharideComponentMap;
+exports.getStructAsymMap = getStructAsymMap;
 const db_1 = require("../../../mol-data/db");
 const types_1 = require("../../../mol-model/structure/model/types");
 const constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
@@ -31,7 +34,6 @@ function getMissingResidues(data) {
         size: map.size
     };
 }
-exports.getMissingResidues = getMissingResidues;
 function getChemicalComponentMap(data) {
     const map = new Map();
     if (data.chem_comp._rowCount > 0) {
@@ -48,7 +50,6 @@ function getChemicalComponentMap(data) {
     }
     return map;
 }
-exports.getChemicalComponentMap = getChemicalComponentMap;
 function getSaccharideComponentMap(data) {
     const map = new Map();
     if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -95,7 +96,6 @@ function getSaccharideComponentMap(data) {
     }
     return map;
 }
-exports.getSaccharideComponentMap = getSaccharideComponentMap;
 const getUniqueComponentNames = (0, memoize_1.memoize1)((data) => {
     const uniqueNames = new Set();
     const { label_comp_id, auth_comp_id } = data.atom_site;
@@ -128,4 +128,3 @@ function getStructAsymMap(atomic, data) {
     }
     return map;
 }
-exports.getStructAsymMap = getStructAsymMap;

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

@@ -63,6 +63,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db").Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: import("../../../mol-data/db").Column.Schema.List<string>;
         pdbx_number_of_molecules: import("../../../mol-data/db").Column.Schema.Int;
+        pdbx_parent_entity_id: import("../../../mol-data/db").Column.Schema.Str;
         pdbx_mutation: import("../../../mol-data/db").Column.Schema.Str;
         pdbx_fragment: import("../../../mol-data/db").Column.Schema.Str;
         pdbx_ec: import("../../../mol-data/db").Column.Schema.List<string>;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createBasic = exports.BasicSchema = void 0;
+exports.BasicSchema = void 0;
+exports.createBasic = createBasic;
 const mmcif_1 = require("../../../mol-io/reader/cif/schema/mmcif");
 const db_1 = require("../../../mol-data/db");
 const mmcif_extras_1 = require("../../../mol-io/reader/cif/schema/mmcif-extras");
@@ -44,4 +45,3 @@ function createBasic(data, normalize = false) {
     }
     return basic;
 }
-exports.createBasic = createBasic;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSequence = void 0;
+exports.getSequence = getSequence;
 const sequence_1 = require("../../../mol-model/structure/model/properties/sequence");
 const db_1 = require("../../../mol-data/db");
 const sequence_2 = require("../../../mol-model/sequence");
@@ -36,4 +36,3 @@ function getSequence(data, entities, atomicHierarchy, coarseHierarchy) {
     }
     return { byEntityKey, sequences };
 }
-exports.getSequence = getSequence;

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

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.sortAtomSite = void 0;
+exports.sortAtomSite = sortAtomSite;
 const util_1 = require("../../../mol-data/util");
 const db_1 = require("../../../mol-data/db");
 const array_1 = require("../../../mol-util/array");
@@ -37,4 +37,3 @@ async function sortAtomSite(ctx, atom_site, start, end) {
         sourceIndex: db_1.Column.ofIntArray(indices)
     };
 }
-exports.sortAtomSite = sortAtomSite;

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

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNormalizedAtomSite = exports.getModelGroupName = void 0;
+exports.getModelGroupName = getModelGroupName;
+exports.getNormalizedAtomSite = getNormalizedAtomSite;
 const db_1 = require("../../../mol-data/db");
 function getModelGroupName(model_id, data) {
     const { ihm_model_group, ihm_model_group_link } = data;
@@ -18,7 +19,6 @@ function getModelGroupName(model_id, data) {
     }
     return '';
 }
-exports.getModelGroupName = getModelGroupName;
 //
 function hasPresentValues(column) {
     for (let i = 0, il = column.rowCount; i < il; i++) {
@@ -42,4 +42,3 @@ function getNormalizedAtomSite(atom_site) {
     substUndefinedColumn(normalized, 'label_asym_id', 'auth_asym_id');
     return normalized;
 }
-exports.getNormalizedAtomSite = getNormalizedAtomSite;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromCifCore = exports.CifCoreFormat = void 0;
+exports.CifCoreFormat = void 0;
+exports.trajectoryFromCifCore = trajectoryFromCifCore;
 const db_1 = require("../../mol-data/db");
 const mol_task_1 = require("../../mol-task");
 const parser_1 = require("./basic/parser");
@@ -244,4 +245,3 @@ function trajectoryFromCifCore(frame) {
     const format = CifCoreFormat.fromFrame(frame);
     return mol_task_1.Task.create('Parse CIF Core', ctx => getModels(format.data.db, format, ctx));
 }
-exports.trajectoryFromCifCore = trajectoryFromCifCore;

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

@@ -31,6 +31,7 @@ export declare class EntityBuilder {
         type: Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: Column.Schema.List<string>;
         pdbx_number_of_molecules: Column.Schema.Int;
+        pdbx_parent_entity_id: Column.Schema.Str;
         pdbx_mutation: Column.Schema.Str;
         pdbx_fragment: Column.Schema.Str;
         pdbx_ec: Column.Schema.List<string>;

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

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromCube = void 0;
+exports.trajectoryFromCube = trajectoryFromCube;
 const db_1 = require("../../mol-data/db");
 const types_1 = require("../../mol-model/structure/model/types");
 const mol_task_1 = require("../../mol-task");
@@ -64,4 +64,3 @@ var MolFormat;
 function trajectoryFromCube(cube) {
     return mol_task_1.Task.create('Parse Cube', ctx => getModels(cube, ctx));
 }
-exports.trajectoryFromCube = trajectoryFromCube;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.coordinatesFromDcd = void 0;
+exports.coordinatesFromDcd = coordinatesFromDcd;
 const mol_task_1 = require("../../mol-task");
 const coordinates_1 = require("../../mol-model/structure/coordinates");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
@@ -55,4 +55,3 @@ function coordinatesFromDcd(dcdFile) {
         return coordinates_1.Coordinates.create(frames, deltaTime, offsetTime);
     });
 }
-exports.coordinatesFromDcd = coordinatesFromDcd;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromGRO = exports.GroFormat = void 0;
+exports.GroFormat = void 0;
+exports.trajectoryFromGRO = trajectoryFromGRO;
 const mol_task_1 = require("../../mol-task");
 const db_1 = require("../../mol-data/db");
 const util_1 = require("./util");
@@ -107,4 +108,3 @@ function trajectoryFromGRO(gro) {
         return new trajectory_1.ArrayTrajectory(models);
     });
 }
-exports.trajectoryFromGRO = trajectoryFromGRO;

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

@@ -7,7 +7,9 @@
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromCCD = exports.CCDFormat = exports.trajectoryFromMmCIF = exports.MmcifFormat = void 0;
+exports.CCDFormat = exports.MmcifFormat = void 0;
+exports.trajectoryFromMmCIF = trajectoryFromMmCIF;
+exports.trajectoryFromCCD = trajectoryFromCCD;
 const model_1 = require("../../mol-model/structure/model/model");
 const mol_task_1 = require("../../mol-task");
 const cif_1 = require("../../mol-io/reader/cif");
@@ -95,7 +97,6 @@ function trajectoryFromMmCIF(frame, file) {
     const basic = (0, schema_1.createBasic)(format.data.db, true);
     return mol_task_1.Task.create('Create mmCIF Model', ctx => (0, parser_1.createModels)(basic, format, ctx));
 }
-exports.trajectoryFromMmCIF = trajectoryFromMmCIF;
 var CCDFormat;
 (function (CCDFormat) {
     const CoordinateTypeProp = '__CcdCoordinateType__';
@@ -122,7 +123,6 @@ function trajectoryFromCCD(frame) {
     const format = CCDFormat.fromFrame(frame);
     return mol_task_1.Task.create('Create CCD Models', ctx => createCcdModels(format.data.db, CCDFormat.fromFrame(frame), ctx));
 }
-exports.trajectoryFromCCD = trajectoryFromCCD;
 async function createCcdModels(data, format, ctx) {
     const ideal = await createCcdModel(data, format, { coordinateType: 'ideal', cartn_x: 'pdbx_model_Cartn_x_ideal', cartn_y: 'pdbx_model_Cartn_y_ideal', cartn_z: 'pdbx_model_Cartn_z_ideal' }, ctx);
     const model = await createCcdModel(data, format, { coordinateType: 'model', cartn_x: 'model_Cartn_x', cartn_y: 'model_Cartn_y', cartn_z: 'model_Cartn_z' }, ctx);

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

@@ -7,7 +7,9 @@
  * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromMol = exports.MolFormat = exports.getMolModels = void 0;
+exports.MolFormat = void 0;
+exports.getMolModels = getMolModels;
+exports.trajectoryFromMol = trajectoryFromMol;
 const db_1 = require("../../mol-data/db");
 const parser_1 = require("../../mol-io/reader/mol/parser");
 const mol_task_1 = require("../../mol-task");
@@ -73,7 +75,6 @@ async function getMolModels(mol, format, ctx) {
     }
     return models;
 }
-exports.getMolModels = getMolModels;
 var MolFormat;
 (function (MolFormat) {
     function is(x) {
@@ -88,4 +89,3 @@ var MolFormat;
 function trajectoryFromMol(mol) {
     return mol_task_1.Task.create('Parse MOL', ctx => getMolModels(mol, void 0, ctx));
 }
-exports.trajectoryFromMol = trajectoryFromMol;

package/lib/commonjs/mol-model-formats/structure/mol2.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromMol2 = exports.Mol2Format = void 0;
+exports.Mol2Format = void 0;
+exports.trajectoryFromMol2 = trajectoryFromMol2;
 const db_1 = require("../../mol-data/db");
 const mol_task_1 = require("../../mol-task");
 const parser_1 = require("./basic/parser");
@@ -141,4 +142,3 @@ var Mol2Format;
 function trajectoryFromMol2(mol2) {
     return mol_task_1.Task.create('Parse MOL2', ctx => getModels(mol2, ctx));
 }
-exports.trajectoryFromMol2 = trajectoryFromMol2;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.coordinatesFromNctraj = void 0;
+exports.coordinatesFromNctraj = coordinatesFromNctraj;
 const mol_task_1 = require("../../mol-task");
 const coordinates_1 = require("../../mol-model/structure/coordinates");
 const cell_1 = require("../../mol-math/geometry/spacegroup/cell");
@@ -46,4 +46,3 @@ function coordinatesFromNctraj(file) {
         return coordinates_1.Coordinates.create(frames, deltaTime, offsetTime);
     });
 }
-exports.coordinatesFromNctraj = coordinatesFromNctraj;