molstar 4.3.0 → 4.4.1

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;

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

@@ -5,7 +5,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.addAnisotropic = exports.getAnisotropic = exports.getAnisotropicTemplate = void 0;
+exports.getAnisotropicTemplate = getAnisotropicTemplate;
+exports.getAnisotropic = getAnisotropic;
+exports.addAnisotropic = addAnisotropic;
 const cif_1 = require("../../../mol-io/reader/cif");
 const tokenizer_1 = require("../../../mol-io/reader/common/text/tokenizer");
 const util_1 = require("../util");
@@ -37,7 +39,6 @@ function getAnisotropicTemplate(data, count) {
         pdbx_auth_atom_id: ts(),
     };
 }
-exports.getAnisotropicTemplate = getAnisotropicTemplate;
 function getAnisotropic(sites) {
     const pdbx_auth_seq_id = cif_1.CifField.ofTokens(sites.pdbx_auth_seq_id);
     const pdbx_auth_comp_id = cif_1.CifField.ofTokens(sites.pdbx_auth_comp_id);
@@ -65,7 +66,6 @@ function getAnisotropic(sites) {
     fields['U[2][3]'] = cif_1.CifField.ofNumbers(sites['U[2][3]']);
     return fields;
 }
-exports.getAnisotropic = getAnisotropic;
 function addAnisotropic(sites, model, data, s, e) {
     const { data: str } = data;
     const length = e - s;
@@ -126,4 +126,3 @@ function addAnisotropic(sites, model, data, s, e) {
     // TODO
     sites.index++;
 }
-exports.addAnisotropic = addAnisotropic;

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

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMtrix = exports.parseRemark350 = exports.parseCryst1 = void 0;
+exports.parseCryst1 = parseCryst1;
+exports.parseRemark350 = parseRemark350;
+exports.parseMtrix = parseMtrix;
 const cif_1 = require("../../../mol-io/reader/cif");
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 function parseCryst1(id, record) {
@@ -41,7 +43,6 @@ function parseCryst1(id, record) {
     };
     return [cif_1.CifCategory.ofFields('cell', cell), cif_1.CifCategory.ofFields('symmetry', symmetry)];
 }
-exports.parseCryst1 = parseCryst1;
 function PdbAssembly(id, details) {
     return { id, details, groups: [] };
 }
@@ -170,7 +171,6 @@ function parseRemark350(lines, lineStart, lineEnd) {
         cif_1.CifCategory.ofFields('pdbx_struct_oper_list', pdbx_struct_oper_list)
     ];
 }
-exports.parseRemark350 = parseRemark350;
 function parseMtrix(lines, lineStart, lineEnd) {
     const matrices = [];
     let matrix;
@@ -221,4 +221,3 @@ function parseMtrix(lines, lineStart, lineEnd) {
     }
     return [cif_1.CifCategory.ofFields('struct_ncs_oper', struct_ncs_oper)];
 }
-exports.parseMtrix = parseMtrix;

package/lib/commonjs/mol-model-formats/structure/pdb/atom-site.js

@@ -6,7 +6,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.addAtom = exports.getAtomSite = exports.getAtomSiteTemplate = void 0;
+exports.getAtomSiteTemplate = getAtomSiteTemplate;
+exports.getAtomSite = getAtomSite;
+exports.addAtom = addAtom;
 const cif_1 = require("../../../mol-io/reader/cif");
 const tokenizer_1 = require("../../../mol-io/reader/common/text/tokenizer");
 const util_1 = require("../util");
@@ -36,7 +38,6 @@ function getAtomSiteTemplate(data, count) {
         partial_charge: ts(),
     };
 }
-exports.getAtomSiteTemplate = getAtomSiteTemplate;
 function getAtomSite(sites, terIndices, options) {
     const pdbx_PDB_model_num = cif_1.CifField.ofStrings(sites.pdbx_PDB_model_num);
     const auth_asym_id = cif_1.CifField.ofTokens(sites.auth_asym_id);
@@ -164,7 +165,6 @@ function getAtomSite(sites, terIndices, options) {
         partial_charge: cif_1.CifField.ofTokens(sites.partial_charge)
     };
 }
-exports.getAtomSite = getAtomSite;
 function addAtom(sites, model, data, s, e, isPdbqt) {
     const { data: str } = data;
     const length = e - s;
@@ -240,4 +240,3 @@ function addAtom(sites, model, data, s, e, isPdbqt) {
     sites.pdbx_PDB_model_num[sites.index] = model;
     sites.index++;
 }
-exports.addAtom = addAtom;

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

@@ -6,7 +6,7 @@
  * @author Yakov Pechersky <ffxen158@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseConect = void 0;
+exports.parseConect = parseConect;
 const cif_1 = require("../../../mol-io/reader/cif");
 function parseConect(lines, lineStart, lineEnd, sites) {
     const idMap = {};
@@ -84,4 +84,3 @@ function parseConect(lines, lineStart, lineEnd, sites) {
     };
     return cif_1.CifCategory.ofFields('struct_conn', struct_conn);
 }
-exports.parseConect = parseConect;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseHetnam = exports.parseCmpnd = void 0;
+exports.parseCmpnd = parseCmpnd;
+exports.parseHetnam = parseHetnam;
 const Spec = {
     'MOL_ID': '',
     'MOLECULE': '',
@@ -84,7 +85,6 @@ function parseCmpnd(lines, lineStart, lineEnd) {
     }
     return singletons;
 }
-exports.parseCmpnd = parseCmpnd;
 function parseHetnam(lines, lineStart, lineEnd) {
     const getLine = (n) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
     const hetnams = new Map();
@@ -107,4 +107,3 @@ function parseHetnam(lines, lineStart, lineEnd) {
     }
     return hetnams;
 }
-exports.parseHetnam = parseHetnam;

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

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.addHeader = void 0;
+exports.addHeader = addHeader;
 function addHeader(data, s, e, header) {
     //     COLUMNS       DATA  TYPE     FIELD             DEFINITION
     // ------------------------------------------------------------------------------------
@@ -18,4 +18,3 @@ function addHeader(data, s, e, header) {
     header.dep_date = line.substring(50, 59).trim() || undefined;
     header.classification = line.substring(10, 50).trim() || undefined;
 }
-exports.addHeader = addHeader;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseSheet = exports.parseHelix = void 0;
+exports.parseHelix = parseHelix;
+exports.parseSheet = parseSheet;
 const cif_1 = require("../../../mol-io/reader/cif");
 const db_1 = require("../../../mol-data/db");
 const HelixTypes = {
@@ -106,7 +107,6 @@ function parseHelix(lines, lineStart, lineEnd) {
     };
     return cif_1.CifCategory.ofFields('struct_conf', struct_conf);
 }
-exports.parseHelix = parseHelix;
 function parseSheet(lines, lineStart, lineEnd) {
     const sheets = [];
     const getLine = (n) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
@@ -201,4 +201,3 @@ function parseSheet(lines, lineStart, lineEnd) {
     };
     return cif_1.CifCategory.ofFields('struct_sheet_range', struct_sheet_range);
 }
-exports.parseSheet = parseSheet;

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

@@ -7,7 +7,7 @@
  * @author Yana Rose <yana.v.rose@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.pdbToMmCif = void 0;
+exports.pdbToMmCif = pdbToMmCif;
 const string_1 = require("../../../mol-util/string");
 const cif_1 = require("../../../mol-io/reader/cif");
 const tokenizer_1 = require("../../../mol-io/reader/common/text/tokenizer");
@@ -254,4 +254,3 @@ async function pdbToMmCif(pdb) {
         categories
     };
 }
-exports.pdbToMmCif = pdbToMmCif;