molstar 4.3.0 → 4.4.0

package/lib/commonjs/mol-model/structure/query/queries/internal.js

@@ -5,7 +5,13 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.bundleGenerator = exports.bundleElementImpl = exports.spheres = exports.atomicHet = exports.water = exports.atomicSequence = exports.defaultBondTest = void 0;
+exports.defaultBondTest = defaultBondTest;
+exports.atomicSequence = atomicSequence;
+exports.water = water;
+exports.atomicHet = atomicHet;
+exports.spheres = spheres;
+exports.bundleElementImpl = bundleElementImpl;
+exports.bundleGenerator = bundleGenerator;
 const int_1 = require("../../../../mol-data/int");
 const element_1 = require("../../../../mol-model/structure/structure/element");
 const structure_1 = require("../../structure");
@@ -16,7 +22,6 @@ const bundle_1 = require("../../structure/element/bundle");
 function defaultBondTest(ctx) {
     return types_1.BondType.isCovalent(ctx.atomicBond.type);
 }
-exports.defaultBondTest = defaultBondTest;
 function atomicSequence() {
     return function query_atomicSequence(ctx) {
         const { inputStructure } = ctx;
@@ -43,7 +48,6 @@ function atomicSequence() {
         return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
     };
 }
-exports.atomicSequence = atomicSequence;
 function water() {
     return function query_water(ctx) {
         const { inputStructure } = ctx;
@@ -62,7 +66,6 @@ function water() {
         return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
     };
 }
-exports.water = water;
 function atomicHet() {
     return function query_atomicHet(ctx) {
         const { inputStructure } = ctx;
@@ -91,7 +94,6 @@ function atomicHet() {
         return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
     };
 }
-exports.atomicHet = atomicHet;
 function spheres() {
     return function query_spheres(ctx) {
         const { inputStructure } = ctx;
@@ -104,7 +106,6 @@ function spheres() {
         return selection_1.StructureSelection.Singletons(inputStructure, structure_2.Structure.create(units, { parent: inputStructure }));
     };
 }
-exports.spheres = spheres;
 function bundleElementImpl(groupedUnits, ranges, set) {
     return {
         groupedUnits: groupedUnits,
@@ -112,7 +113,6 @@ function bundleElementImpl(groupedUnits, ranges, set) {
         set: set
     };
 }
-exports.bundleElementImpl = bundleElementImpl;
 function bundleGenerator(elements) {
     return function query_bundleGenerator(ctx) {
         const bundle = {
@@ -122,4 +122,3 @@ function bundleGenerator(elements) {
         return selection_1.StructureSelection.Sequence(ctx.inputStructure, [bundle_1.Bundle.toStructure(bundle, ctx.inputStructure)]);
     };
 }
-exports.bundleGenerator = bundleGenerator;

package/lib/commonjs/mol-model/structure/query/queries/modifiers.js

@@ -6,7 +6,15 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.surroundingLigands = exports.includeConnected = exports.expandProperty = exports.union = exports.exceptBy = exports.intersectBy = exports.querySelection = exports.includeSurroundings = exports.wholeResidues = void 0;
+exports.wholeResidues = wholeResidues;
+exports.includeSurroundings = includeSurroundings;
+exports.querySelection = querySelection;
+exports.intersectBy = intersectBy;
+exports.exceptBy = exceptBy;
+exports.union = union;
+exports.expandProperty = expandProperty;
+exports.includeConnected = includeConnected;
+exports.surroundingLigands = surroundingLigands;
 const int_1 = require("../../../../mol-data/int");
 const selection_1 = require("../selection");
 const builders_1 = require("../utils/builders");
@@ -58,7 +66,6 @@ function wholeResidues(query) {
         }
     };
 }
-exports.wholeResidues = wholeResidues;
 function getIncludeSurroundings(ctx, source, structure, params) {
     const builder = new unique_subset_builder_1.StructureUniqueSubsetBuilder(source);
     const lookup = source.lookup3d;
@@ -157,7 +164,6 @@ function includeSurroundings(query, params) {
         }
     };
 }
-exports.includeSurroundings = includeSurroundings;
 function querySelection(selection, query) {
     return function query_querySelection(ctx) {
         const targetSel = selection(ctx);
@@ -175,7 +181,6 @@ function querySelection(selection, query) {
         return ret.getSelection();
     };
 }
-exports.querySelection = querySelection;
 function intersectBy(query, by) {
     return function query_intersectBy(ctx) {
         const selection = query(ctx);
@@ -196,7 +201,6 @@ function intersectBy(query, by) {
         return ret.getSelection();
     };
 }
-exports.intersectBy = intersectBy;
 function exceptBy(query, by) {
     return function query_exceptBy(ctx) {
         const selection = query(ctx);
@@ -217,7 +221,6 @@ function exceptBy(query, by) {
         return ret.getSelection();
     };
 }
-exports.exceptBy = exceptBy;
 function union(query) {
     return function query_union(ctx) {
         const ret = selection_1.StructureSelection.LinearBuilder(ctx.inputStructure);
@@ -225,7 +228,6 @@ function union(query) {
         return ret.getSelection();
     };
 }
-exports.union = union;
 function expandProperty(query, property) {
     return function query_expandProperty(ctx) {
         const src = query(ctx);
@@ -276,7 +278,6 @@ function expandProperty(query, property) {
         return ret.getSelection();
     };
 }
-exports.expandProperty = expandProperty;
 function includeConnected({ query, layerCount, wholeResidues, bondTest, fixedPoint }) {
     const lc = Math.max(layerCount, 0);
     return function query_includeConnected(ctx) {
@@ -307,7 +308,6 @@ function includeConnected({ query, layerCount, wholeResidues, bondTest, fixedPoi
         return builder.getSelection();
     };
 }
-exports.includeConnected = includeConnected;
 function includeConnectedStep(ctx, wholeResidues, structure) {
     const expanded = expandConnected(ctx, structure);
     if (wholeResidues)
@@ -493,7 +493,6 @@ function surroundingLigands({ query, radius, includeWater }) {
         }
     };
 }
-exports.surroundingLigands = surroundingLigands;
 const _entity_type = properties_1.StructureProperties.entity.type;
 function testIsWater(l) {
     return _entity_type(l) === 'water';

package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.checkStructureMaxRadiusDistance = exports.checkStructureMinMaxDistance = void 0;
+exports.checkStructureMinMaxDistance = checkStructureMinMaxDistance;
+exports.checkStructureMaxRadiusDistance = checkStructureMaxRadiusDistance;
 const linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 function checkStructureMinMaxDistance(ctx, a, b, minDist, maxDist, elementRadius) {
     if (a.elementCount === 0 || b.elementCount === 0)
@@ -14,7 +15,6 @@ function checkStructureMinMaxDistance(ctx, a, b, minDist, maxDist, elementRadius
         return MinMaxDist.check(ctx, a, b, minDist, maxDist, elementRadius);
     return MinMaxDist.check(ctx, b, a, minDist, maxDist, elementRadius);
 }
-exports.checkStructureMinMaxDistance = checkStructureMinMaxDistance;
 function checkStructureMaxRadiusDistance(ctx, a, b, maxDist, elementRadius) {
     if (a.elementCount === 0 || b.elementCount === 0)
         return true;
@@ -22,7 +22,6 @@ function checkStructureMaxRadiusDistance(ctx, a, b, maxDist, elementRadius) {
         return MaxRadiusDist.check(ctx, a, b, maxDist, elementRadius);
     return MaxRadiusDist.check(ctx, b, a, maxDist, elementRadius);
 }
-exports.checkStructureMaxRadiusDistance = checkStructureMaxRadiusDistance;
 var MinMaxDist;
 (function (MinMaxDist) {
     const distVec = (0, linear_algebra_1.Vec3)();

package/lib/commonjs/mol-model/structure/query/utils/structure-set.js

@@ -5,7 +5,11 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.structureSubtract = exports.structureIntersect = exports.structureAreIntersecting = exports.structureAreEqual = exports.structureUnion = void 0;
+exports.structureUnion = structureUnion;
+exports.structureAreEqual = structureAreEqual;
+exports.structureAreIntersecting = structureAreIntersecting;
+exports.structureIntersect = structureIntersect;
+exports.structureSubtract = structureSubtract;
 const structure_1 = require("../../structure");
 const int_1 = require("../../../../mol-data/int");
 function structureUnion(source, structures) {
@@ -38,7 +42,6 @@ function structureUnion(source, structures) {
     unitMap.forEach(buildUnion, builder);
     return builder.getStructure();
 }
-exports.structureUnion = structureUnion;
 function buildUnion(elements, id) {
     this.setUnit(id, elements);
 }
@@ -58,7 +61,6 @@ function structureAreEqual(sA, sB) {
     }
     return true;
 }
-exports.structureAreEqual = structureAreEqual;
 function structureAreIntersecting(sA, sB) {
     if (sA === sB)
         return true;
@@ -82,7 +84,6 @@ function structureAreIntersecting(sA, sB) {
     }
     return false;
 }
-exports.structureAreIntersecting = structureAreIntersecting;
 function structureIntersect(sA, sB) {
     if (sA === sB)
         return sA;
@@ -111,7 +112,6 @@ function structureIntersect(sA, sB) {
     }
     return structure_1.Structure.create(units, { parent: sA.parent || sB.parent });
 }
-exports.structureIntersect = structureIntersect;
 function structureSubtract(a, b) {
     if (a === b)
         return structure_1.Structure.Empty;
@@ -133,4 +133,3 @@ function structureSubtract(a, b) {
     }
     return structure_1.Structure.create(units, { parent: a.parent || b.parent });
 }
-exports.structureSubtract = structureSubtract;

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

@@ -6,7 +6,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeCarbohydrates = void 0;
+exports.computeCarbohydrates = computeCarbohydrates;
 const int_1 = require("../../../../mol-data/int");
 const combination_1 = require("../../../../mol-data/util/combination");
 const graph_1 = require("../../../../mol-math/graph");
@@ -302,7 +302,6 @@ function computeCarbohydrates(structure) {
     }
     return { links, terminalLinks, elements, partialElements, ...buildLookups(elements, links, terminalLinks) };
 }
-exports.computeCarbohydrates = computeCarbohydrates;
 function buildLookups(elements, links, terminalLinks) {
     function key(unit, element) {
         return (0, util_2.cantorPairing)(unit.id, element);

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

@@ -6,7 +6,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SaccharideCompIdMap = exports.setSaccharideCompIdMapType = exports.MonosaccharidesColorTable = exports.SaccharidesSnfgMap = exports.UnknownSaccharideComponent = exports.getSaccharideShape = exports.getSaccharideName = exports.SaccharideType = exports.SaccharideColors = exports.SaccharideShape = void 0;
+exports.SaccharideCompIdMap = exports.MonosaccharidesColorTable = exports.SaccharidesSnfgMap = exports.UnknownSaccharideComponent = exports.SaccharideType = exports.SaccharideColors = exports.SaccharideShape = void 0;
+exports.getSaccharideName = getSaccharideName;
+exports.getSaccharideShape = getSaccharideShape;
+exports.setSaccharideCompIdMapType = setSaccharideCompIdMapType;
 const color_1 = require("../../../../mol-util/color");
 const saccharides_1 = require("../../model/types/saccharides");
 // follows community standard from https://www.ncbi.nlm.nih.gov/glycans/snfg.html
@@ -75,7 +78,6 @@ const SaccharideTypeNameMap = {
 function getSaccharideName(type) {
     return SaccharideTypeNameMap[type];
 }
-exports.getSaccharideName = getSaccharideName;
 const SaccharideTypeShapeMap = {
     [SaccharideType.Hexose]: SaccharideShape.FilledSphere,
     [SaccharideType.HexNAc]: SaccharideShape.FilledCube,
@@ -107,7 +109,6 @@ function getSaccharideShape(type, ringMemberCount) {
         return SaccharideTypeShapeMap[type];
     }
 }
-exports.getSaccharideShape = getSaccharideShape;
 exports.UnknownSaccharideComponent = {
     abbr: 'Unk',
     name: 'Unknown',
@@ -425,5 +426,4 @@ const GlycamSaccharideCompIdMap = (function () {
 function setSaccharideCompIdMapType(type) {
     exports.SaccharideCompIdMap = type === 'default' ? DefaultSaccharideCompIdMap : GlycamSaccharideCompIdMap;
 }
-exports.setSaccharideCompIdMapType = setSaccharideCompIdMapType;
 exports.SaccharideCompIdMap = DefaultSaccharideCompIdMap;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Loci = void 0;
+exports.Loci = Loci;
 const generic_1 = require("../../../../mol-data/generic");
 const int_1 = require("../../../../mol-data/int");
 const linear_algebra_1 = require("../../../../mol-math/linear-algebra");
@@ -24,7 +24,6 @@ const itDiff = tuple_1.IntTuple.diff;
 function Loci(structure, elements) {
     return { kind: 'element-loci', structure, elements: elements };
 }
-exports.Loci = Loci;
 (function (Loci) {
     function is(x) {
         return !!x && x.kind === 'element-loci';

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

@@ -6,20 +6,22 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.entityIndex = exports.chainIndex = exports.residueIndex = exports.coarseProperty = exports.atomicProperty = exports.property = void 0;
+exports.property = property;
+exports.atomicProperty = atomicProperty;
+exports.coarseProperty = coarseProperty;
+exports.residueIndex = residueIndex;
+exports.chainIndex = chainIndex;
+exports.entityIndex = entityIndex;
 const unit_1 = require("../unit");
 const properties_1 = require("../properties");
 function property(p) { return p; }
-exports.property = property;
 function _wrongUnitKind(kind) { throw new Error(`Property only available for ${kind} models.`); }
 function atomicProperty(p) {
     return property(l => unit_1.Unit.isAtomic(l.unit) ? p(l) : _wrongUnitKind('atomic'));
 }
-exports.atomicProperty = atomicProperty;
 function coarseProperty(p) {
     return property(l => unit_1.Unit.isCoarse(l.unit) ? p(l) : _wrongUnitKind('coarse'));
 }
-exports.coarseProperty = coarseProperty;
 function residueIndex(e) {
     if (unit_1.Unit.isAtomic(e.unit)) {
         return e.unit.residueIndex[e.element];
@@ -29,7 +31,6 @@ function residueIndex(e) {
         return -1;
     }
 }
-exports.residueIndex = residueIndex;
 function chainIndex(e) {
     if (unit_1.Unit.isAtomic(e.unit)) {
         return e.unit.chainIndex[e.element];
@@ -39,8 +40,6 @@ function chainIndex(e) {
         return -1;
     }
 }
-exports.chainIndex = chainIndex;
 function entityIndex(l) {
     return properties_1.StructureProperties.entity.key(l);
 }
-exports.entityIndex = entityIndex;

package/lib/commonjs/mol-model/structure/structure/properties.d.ts

@@ -61,6 +61,7 @@ declare const StructureProperties: {
         pdbx_mutation: StructureElement.Property<string>;
         pdbx_fragment: StructureElement.Property<string>;
         pdbx_ec: StructureElement.Property<string[]>;
+        pdbx_parent_entity_id: StructureElement.Property<string>;
         subtype: StructureElement.Property<import("../model/properties/common").EntitySubtype>;
         prd_id: StructureElement.Property<string>;
     };

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

@@ -144,6 +144,7 @@ const entity = {
     pdbx_mutation: p(l => l.unit.model.entities.data.pdbx_mutation.value(eK(l))),
     pdbx_fragment: p(l => l.unit.model.entities.data.pdbx_fragment.value(eK(l))),
     pdbx_ec: p(l => l.unit.model.entities.data.pdbx_ec.value(eK(l))),
+    pdbx_parent_entity_id: p(l => l.unit.model.entities.data.pdbx_parent_entity_id.value(eK(l))),
     subtype: p(l => l.unit.model.entities.subtype.value(eK(l))),
     prd_id: p(l => { var _a, _b; return (_b = (_a = l.unit.model.entities.prd_id) === null || _a === void 0 ? void 0 : _a.value(eK(l))) !== null && _b !== void 0 ? _b : ''; }),
 };

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

@@ -6,7 +6,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isHydrogen = exports.getPairingThreshold = exports.getElementThreshold = exports.getElementPairThreshold = exports.getElementIdx = exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
+exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
+exports.getElementIdx = getElementIdx;
+exports.getElementPairThreshold = getElementPairThreshold;
+exports.getElementThreshold = getElementThreshold;
+exports.getPairingThreshold = getPairingThreshold;
+exports.isHydrogen = isHydrogen;
 /** Default for atomic bonds */
 exports.DefaultBondMaxRadius = 4;
 exports.DefaultBondComputationProps = {
@@ -85,7 +90,6 @@ function getElementIdx(e) {
         return -1;
     return i;
 }
-exports.getElementIdx = getElementIdx;
 function getElementPairThreshold(i, j) {
     if (i < 0 || j < 0)
         return -1;
@@ -94,7 +98,6 @@ function getElementPairThreshold(i, j) {
         return -1;
     return r;
 }
-exports.getElementPairThreshold = getElementPairThreshold;
 function getElementThreshold(i) {
     if (i < 0)
         return __DefaultBondingRadius;
@@ -103,7 +106,6 @@ function getElementThreshold(i) {
         return __DefaultBondingRadius;
     return r;
 }
-exports.getElementThreshold = getElementThreshold;
 function getPairingThreshold(elementIndexA, elementIndexB, thresholdA, thresholdB) {
     const thresholdAB = getElementPairThreshold(elementIndexA, elementIndexB);
     return thresholdAB > 0
@@ -112,9 +114,7 @@ function getPairingThreshold(elementIndexA, elementIndexB, thresholdA, threshold
             ? thresholdA
             : (thresholdA + thresholdB) / 1.95; // not sure if avg or min but max is too big
 }
-exports.getPairingThreshold = getPairingThreshold;
 const H_ID = __ElementIndex['H'];
 function isHydrogen(i) {
     return i === H_ID;
 }
-exports.isHydrogen = isHydrogen;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeInterUnitBonds = void 0;
+exports.computeInterUnitBonds = computeInterUnitBonds;
 const structure_1 = require("../../structure");
 const unit_1 = require("../../unit");
 const common_1 = require("./common");
@@ -226,7 +226,6 @@ function computeInterUnitBonds(structure, props) {
         }),
     });
 }
-exports.computeInterUnitBonds = computeInterUnitBonds;
 function hasCommonStructConnRecord(unitA, unitB) {
     if (unitA.model !== unitB.model || !unit_1.Unit.isAtomic(unitA) || !unit_1.Unit.isAtomic(unitB))
         return false;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeIntraUnitBonds = void 0;
+exports.computeIntraUnitBonds = computeIntraUnitBonds;
 const data_1 = require("./data");
 const graph_1 = require("../../../../../mol-math/graph");
 const common_1 = require("./common");
@@ -251,4 +251,3 @@ function computeIntraUnitBonds(unit, props) {
         return findBonds(unit, p);
     }
 }
-exports.computeIntraUnitBonds = computeIntraUnitBonds;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getResonance = void 0;
+exports.getResonance = getResonance;
 const sorted_array_1 = require("../../../../mol-data/int/sorted-array");
 const util_1 = require("../../../../mol-data/util");
 const types_1 = require("../../model/types");
@@ -14,7 +14,6 @@ function getResonance(unit) {
         delocalizedTriplets: getDelocalizedTriplets(unit)
     };
 }
-exports.getResonance = getResonance;
 function getDelocalizedTriplets(unit) {
     const bonds = unit.bonds;
     const { b, edgeProps, offset } = bonds;

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;