molstar 3.2.0 → 3.4.0

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

@@ -27,11 +27,13 @@ function State(unit, capacity) {
         startVertex: 0,
         endVertex: 0,
         count: 0,
-        visited: new Int32Array(capacity),
+        isRingAtom: new Int32Array(capacity),
+        marked: new Int32Array(capacity),
         queue: new Int32Array(capacity),
         pred: new Int32Array(capacity),
-        left: new Int32Array(4 /* MaxDepth */),
-        right: new Int32Array(4 /* MaxDepth */),
+        depth: new Int32Array(capacity),
+        left: new Int32Array(5 /* MaxDepth */),
+        right: new Int32Array(5 /* MaxDepth */),
         color: new Int32Array(capacity),
         currentColor: 0,
         currentAltLoc: '',
@@ -45,16 +47,24 @@ function State(unit, capacity) {
 }
 function resetState(state) {
     state.count = state.endVertex - state.startVertex;
-    var visited = state.visited, pred = state.pred, color = state.color;
+    var isRingAtom = state.isRingAtom, pred = state.pred, color = state.color, depth = state.depth, marked = state.marked;
     for (var i = 0; i < state.count; i++) {
-        visited[i] = -1;
+        isRingAtom[i] = 0;
         pred[i] = -1;
+        marked[i] = -1;
         color[i] = 0;
+        depth[i] = 0;
     }
     state.currentColor = 0;
     state.currentAltLoc = '';
     state.hasAltLoc = false;
 }
+function resetDepth(state) {
+    var depth = state.depth;
+    for (var i = 0; i < state.count; i++) {
+        depth[i] = state.count + 1;
+    }
+}
 function largestResidue(unit) {
     var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
     var size = 0;
@@ -64,8 +74,16 @@ function largestResidue(unit) {
     }
     return size;
 }
+function isStartIndex(state, i) {
+    var bondOffset = state.bonds.offset;
+    var a = state.startVertex + i;
+    var bStart = bondOffset[a], bEnd = bondOffset[a + 1];
+    var bondCount = bEnd - bStart;
+    if (bondCount <= 1 || (state.isRingAtom[i] && bondCount === 2))
+        return false;
+    return true;
+}
 function processResidue(state, start, end) {
-    var visited = state.visited;
     state.startVertex = start;
     state.endVertex = end;
     // no two atom rings
@@ -79,12 +97,14 @@ function processResidue(state, start, end) {
         (0, array_1.arraySetAdd)(altLocs, altLoc);
     }
     (0, array_1.arraySetRemove)(altLocs, '');
+    var mark = 1;
     if (altLocs.length === 0) {
         resetState(state);
         for (var i = 0; i < state.count; i++) {
-            if (visited[i] >= 0)
+            if (!isStartIndex(state, i))
                 continue;
-            findRings(state, i);
+            resetDepth(state);
+            mark = findRings(state, i, mark);
         }
     }
     else {
@@ -93,13 +113,14 @@ function processResidue(state, start, end) {
             state.hasAltLoc = true;
             state.currentAltLoc = altLocs[aI];
             for (var i = 0; i < state.count; i++) {
-                if (visited[i] >= 0)
+                if (!isStartIndex(state, i))
                     continue;
                 var altLoc = state.altLoc.value(elements[state.startVertex + i]);
                 if (altLoc && altLoc !== state.currentAltLoc) {
                     continue;
                 }
-                findRings(state, i);
+                resetDepth(state);
+                mark = findRings(state, i, mark);
             }
         }
     }
@@ -107,15 +128,15 @@ function processResidue(state, start, end) {
         state.rings.push(state.currentRings[i]);
     }
 }
-function addRing(state, a, b) {
+function addRing(state, a, b, isRingAtom) {
     // only "monotonous" rings
     if (b < a) {
-        return;
+        return false;
     }
     var pred = state.pred, color = state.color, left = state.left, right = state.right;
     var nc = ++state.currentColor;
     var current = a;
-    for (var t = 0; t < 4 /* MaxDepth */; t++) {
+    for (var t = 0; t < 5 /* MaxDepth */; t++) {
         color[current] = nc;
         current = pred[current];
         if (current < 0)
@@ -124,7 +145,7 @@ function addRing(state, a, b) {
     var leftOffset = 0, rightOffset = 0;
     var found = false, target = 0;
     current = b;
-    for (var t = 0; t < 4 /* MaxDepth */; t++) {
+    for (var t = 0; t < 5 /* MaxDepth */; t++) {
         if (color[current] === nc) {
             target = current;
             found = true;
@@ -136,10 +157,10 @@ function addRing(state, a, b) {
             break;
     }
     if (!found) {
-        return;
+        return false;
     }
     current = a;
-    for (var t = 0; t < 4 /* MaxDepth */; t++) {
+    for (var t = 0; t < 5 /* MaxDepth */; t++) {
         left[leftOffset++] = current;
         if (target === current)
             break;
@@ -150,46 +171,45 @@ function addRing(state, a, b) {
     var len = leftOffset + rightOffset;
     // rings must have at least three elements
     if (len < 3) {
-        return;
+        return false;
     }
     var ring = new Int32Array(len);
     var ringOffset = 0;
-    for (var t = 0; t < leftOffset; t++)
+    for (var t = 0; t < leftOffset; t++) {
         ring[ringOffset++] = state.startVertex + left[t];
-    for (var t = rightOffset - 1; t >= 0; t--)
+        isRingAtom[left[t]] = 1;
+    }
+    for (var t = rightOffset - 1; t >= 0; t--) {
         ring[ringOffset++] = state.startVertex + right[t];
+        isRingAtom[right[t]] = 1;
+    }
     (0, util_1.sortArray)(ring);
-    if (state.hasAltLoc) {
-        // we need to check if the ring was already added because alt locs are present.
-        for (var rI = 0, _rI = state.currentRings.length; rI < _rI; rI++) {
-            var r = state.currentRings[rI];
-            if (ring[0] !== r[0])
-                continue;
-            if (ring.length !== r.length)
-                continue;
-            var areSame = true;
-            for (var aI = 0, _aI = ring.length; aI < _aI; aI++) {
-                if (ring[aI] !== r[aI]) {
-                    areSame = false;
-                    break;
-                }
-            }
-            if (areSame) {
-                return;
-            }
+    // Check if the ring is unique and another one is not it's subset
+    for (var rI = 0, _rI = state.currentRings.length; rI < _rI; rI++) {
+        var r = state.currentRings[rI];
+        if (ring.length === r.length) {
+            if (int_1.SortedArray.areEqual(ring, r))
+                return false;
+        }
+        else if (ring.length > r.length) {
+            if (int_1.SortedArray.isSubset(ring, r))
+                return false;
         }
     }
     state.currentRings.push(int_1.SortedArray.ofSortedArray(ring));
+    return true;
 }
-function findRings(state, from) {
-    var bonds = state.bonds, startVertex = state.startVertex, endVertex = state.endVertex, visited = state.visited, queue = state.queue, pred = state.pred;
+function findRings(state, from, mark) {
+    var bonds = state.bonds, startVertex = state.startVertex, endVertex = state.endVertex, isRingAtom = state.isRingAtom, marked = state.marked, queue = state.queue, pred = state.pred, depth = state.depth;
     var elements = state.unit.elements;
     var neighbor = bonds.b, bondFlags = bonds.edgeProps.flags, offset = bonds.offset;
-    visited[from] = 1;
+    marked[from] = mark;
+    depth[from] = 0;
     queue[0] = from;
     var head = 0, size = 1;
     while (head < size) {
         var top_1 = queue[head++];
+        var d = depth[top_1];
         var a = startVertex + top_1;
         var start = offset[a], end = offset[a + 1];
         for (var i = start; i < end; i++) {
@@ -203,17 +223,24 @@ function findRings(state, from) {
                 }
             }
             var other = b - startVertex;
-            if (visited[other] > 0) {
+            if (marked[other] === mark) {
                 if (pred[other] !== top_1 && pred[top_1] !== other) {
-                    addRing(state, top_1, other);
+                    if (addRing(state, top_1, other, isRingAtom)) {
+                        return mark + 1;
+                    }
                 }
                 continue;
             }
-            visited[other] = 1;
+            var newDepth = Math.min(depth[other], d + 1);
+            if (newDepth > 5 /* MaxDepth */)
+                continue;
+            depth[other] = newDepth;
+            marked[other] = mark;
             queue[size++] = other;
             pred[other] = top_1;
         }
     }
+    return mark + 1;
 }
 function getFingerprint(elements) {
     var len = elements.length;
@@ -334,4 +361,3 @@ function createIndex(rings, aromaticRings) {
     return { elementRingIndices: elementRingIndices, elementAromaticRingIndices: elementAromaticRingIndices, ringComponentIndex: ringComponentIndex, ringComponents: ringComponents };
 }
 exports.createIndex = createIndex;
-//# sourceMappingURL=compute.js.map

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

@@ -215,4 +215,3 @@ function getAromaticRings(unit, rings) {
     }
     return aromaticRings;
 }
-//# sourceMappingURL=rings.js.map

package/lib/commonjs/mol-model/structure/structure/unit.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>
@@ -17,6 +17,7 @@ import { IntMap, SortedArray } from '../../../mol-data/int';
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { PrincipalAxes } from '../../../mol-math/linear-algebra/matrix/principal-axes';
 import { Boundary } from '../../../mol-math/geometry/boundary';
+import { UnitResonance } from './unit/resonance';
 /**
  * A building block of a structure that corresponds to an atomic or
  * a coarse grained representation 'conveniently grouped together'.
@@ -130,6 +131,7 @@ declare namespace Unit {
         get principalAxes(): PrincipalAxes;
         get bonds(): IntraUnitBonds;
         get rings(): UnitRings;
+        get resonance(): UnitResonance;
         get polymerElements(): SortedArray<ElementIndex>;
         get gapElements(): SortedArray<ElementIndex>;
         get nucleotideElements(): SortedArray<ElementIndex>;
@@ -141,6 +143,7 @@ declare namespace Unit {
     interface AtomicProperties extends BaseProperties {
         bonds?: IntraUnitBonds;
         rings?: UnitRings;
+        resonance?: UnitResonance;
         nucleotideElements?: SortedArray<ElementIndex>;
         proteinElements?: SortedArray<ElementIndex>;
         residueCount?: number;

package/lib/commonjs/mol-model/structure/structure/unit.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>
@@ -23,6 +23,7 @@ var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var index_pair_1 = require("../../../mol-model-formats/structure/property/bonds/index-pair");
 var element_set_intra_bond_cache_1 = require("./unit/bonds/element-set-intra-bond-cache");
 var symmetry_1 = require("../../../mol-model-formats/structure/property/symmetry");
+var resonance_1 = require("./unit/resonance");
 var Unit;
 (function (Unit) {
     function isAtomic(u) { return u.kind === 0 /* Atomic */; }
@@ -149,8 +150,11 @@ var Unit;
             return new Atomic(id, this.invariantId, this.chainGroupId, this.traits, this.model, this.elements, symmetry_operator_1.SymmetryOperator.createMapping(op, this.model.atomicConformation, this.conformation.r), this.props);
         };
         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 ? undefined : tryRemapBonds(this, this.props.bonds, model) });
+                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)) {
                     props.boundary = undefined;
                     props.lookup3d = undefined;
@@ -160,7 +164,7 @@ var Unit;
             var operator = this.conformation.operator;
             var symmetry = symmetry_1.ModelSymmetry.Provider.get(model);
             if (operator.spgrOp !== -1 && symmetry && symmetry !== symmetry_1.ModelSymmetry.Provider.get(this.model)) {
-                var _a = operator.hkl, i = _a[0], j = _a[1], k = _a[2];
+                var _c = operator.hkl, i = _c[0], j = _c[1], k = _c[2];
                 var toFractional = symmetry.spacegroup.cell.toFractional;
                 var ref = linear_algebra_1.Vec3.transformMat4((0, linear_algebra_1.Vec3)(), model_1.Model.getCenter(model), toFractional);
                 operator = geometry_1.Spacegroup.getSymmetryOperatorRef(symmetry.spacegroup, operator.spgrOp, i, j, k, ref);
@@ -228,6 +232,16 @@ var Unit;
             enumerable: false,
             configurable: true
         });
+        Object.defineProperty(Atomic.prototype, "resonance", {
+            get: function () {
+                if (this.props.resonance)
+                    return this.props.resonance;
+                this.props.resonance = (0, resonance_1.getResonance)(this);
+                return this.props.resonance;
+            },
+            enumerable: false,
+            configurable: true
+        });
         Object.defineProperty(Atomic.prototype, "polymerElements", {
             get: function () {
                 if (this.props.polymerElements)
@@ -322,7 +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;
@@ -400,7 +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;
         }
@@ -408,7 +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;
         }
@@ -432,7 +446,7 @@ var Unit;
         return isSameConformation(a, b.model);
     }
     Unit.areConformationsEqual = areConformationsEqual;
-    function tryRemapBonds(a, old, model) {
+    function tryRemapBonds(a, old, model, dynamicBonds) {
         // TODO: should include additional checks?
         var _a;
         if (!old)
@@ -447,7 +461,7 @@ var Unit;
                 return old;
             return void 0;
         }
-        if ((_a = old.props) === null || _a === void 0 ? void 0 : _a.canRemap) {
+        if (((_a = old.props) === null || _a === void 0 ? void 0 : _a.canRemap) || !dynamicBonds) {
             return old;
         }
         return isSameConformation(a, model) ? old : void 0;
@@ -489,4 +503,3 @@ var Unit;
     Unit.getHierarchy = getHierarchy;
 })(Unit || (Unit = {}));
 exports.Unit = Unit;
-//# sourceMappingURL=unit.js.map

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

@@ -47,4 +47,3 @@ function computeStructureBoundary(s) {
     return { box: boundaryHelper.getBox(), sphere: boundaryHelper.getSphere() };
 }
 exports.computeStructureBoundary = computeStructureBoundary;
-//# sourceMappingURL=boundary.js.map

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

@@ -197,4 +197,3 @@ var StructureLookup3D = /** @class */ (function () {
     return StructureLookup3D;
 }());
 exports.StructureLookup3D = StructureLookup3D;
-//# sourceMappingURL=lookup3d.js.map

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

@@ -120,4 +120,3 @@ function getProteinElements(unit) {
     return int_1.SortedArray.ofSortedArray(indices);
 }
 exports.getProteinElements = getProteinElements;
-//# sourceMappingURL=polymer.js.map

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

@@ -25,4 +25,3 @@ function getPrincipalAxes(unit) {
     return principal_axes_1.PrincipalAxes.ofPositions(positions);
 }
 exports.getPrincipalAxes = getPrincipalAxes;
-//# sourceMappingURL=principal-axes.js.map

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

@@ -112,4 +112,3 @@ var StructureSubsetBuilder = /** @class */ (function () {
     return StructureSubsetBuilder;
 }());
 exports.StructureSubsetBuilder = StructureSubsetBuilder;
-//# sourceMappingURL=subset-builder.js.map

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

@@ -152,4 +152,3 @@ function buildIndex(structure, index, sI, traceOnly) {
         }
     }
 }
-//# sourceMappingURL=superposition-sifts-mapping.js.map

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 }));
@@ -88,4 +88,3 @@ function getMinSize(xs) {
     }
     return s;
 }
-//# sourceMappingURL=superposition.js.map

package/lib/commonjs/mol-model/structure/structure/util/unique-subset-builder.js

@@ -97,4 +97,3 @@ var StructureUniqueSubsetBuilder = /** @class */ (function () {
     return StructureUniqueSubsetBuilder;
 }());
 exports.StructureUniqueSubsetBuilder = StructureUniqueSubsetBuilder;
-//# sourceMappingURL=unique-subset-builder.js.map

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

@@ -70,4 +70,3 @@ var StructureUnitTransforms = /** @class */ (function () {
     return StructureUnitTransforms;
 }());
 exports.StructureUnitTransforms = StructureUnitTransforms;
-//# sourceMappingURL=unit-transforms.js.map

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

@@ -19,6 +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);
-//# sourceMappingURL=structure.js.map
+tslib_1.__exportStar(require("./structure/unit/rings"), exports);
+tslib_1.__exportStar(require("./export/mmcif"), exports);

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

@@ -21,4 +21,3 @@ var Topology;
     Topology.create = create;
 })(Topology || (Topology = {}));
 exports.Topology = Topology;
-//# sourceMappingURL=topology.js.map

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

@@ -6,5 +6,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./topology/topology"), exports);
-//# sourceMappingURL=topology.js.map
+tslib_1.__exportStar(require("./topology/topology"), exports);

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

@@ -19,4 +19,3 @@ var ArrayTrajectory = /** @class */ (function () {
     return ArrayTrajectory;
 }());
 exports.ArrayTrajectory = ArrayTrajectory;
-//# sourceMappingURL=trajectory.js.map

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

@@ -57,4 +57,3 @@ function getPositions(unit, indices) {
     return positions;
 }
 exports.getPositions = getPositions;
-//# sourceMappingURL=util.js.map

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

@@ -7,10 +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);
-//# sourceMappingURL=structure.js.map
+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/grid.js

@@ -64,4 +64,3 @@ var Grid;
     Grid.getHistogram = getHistogram;
 })(Grid || (Grid = {}));
 exports.Grid = Grid;
-//# sourceMappingURL=grid.js.map

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

@@ -189,4 +189,3 @@ var Volume;
         Cell.getBoundingSphere = getBoundingSphere;
     })(Cell = Volume.Cell || (Volume.Cell = {}));
 })(Volume = exports.Volume || (exports.Volume = {}));
-//# sourceMappingURL=volume.js.map

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

@@ -7,6 +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);
-//# sourceMappingURL=volume.js.map
+tslib_1.__exportStar(require("./volume/volume"), exports);
+tslib_1.__exportStar(require("./volume/grid"), exports);

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

@@ -6,4 +6,3 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-//# sourceMappingURL=format.js.map

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,
@@ -292,4 +292,3 @@ function shapeFromPly(source, params) {
     }); });
 }
 exports.shapeFromPly = shapeFromPly;
-//# sourceMappingURL=ply.js.map

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) {
@@ -171,4 +158,3 @@ function getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, che
     return { sameAsPrevious: sameAsPrevious, hierarchy: hierarchy, conformation: conformation, chainOperatorMapping: chainOperatorMapping };
 }
 exports.getAtomicHierarchyAndConformation = getAtomicHierarchyAndConformation;
-//# sourceMappingURL=atomic.js.map