molstar 3.2.0 → 3.4.0

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

@@ -23,11 +23,13 @@ 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: '',
@@ -41,16 +43,24 @@ 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 = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
     var size = 0;
@@ -60,8 +70,16 @@ 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
@@ -75,12 +93,14 @@ function processResidue(state, start, end) {
         arraySetAdd(altLocs, altLoc);
     }
     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 {
@@ -89,13 +109,14 @@ 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);
             }
         }
     }
@@ -103,15 +124,15 @@ 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)
@@ -120,7 +141,7 @@ 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;
@@ -132,10 +153,10 @@ 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;
@@ -146,46 +167,45 @@ 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;
+    }
     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 (SortedArray.areEqual(ring, r))
+                return false;
+        }
+        else if (ring.length > r.length) {
+            if (SortedArray.isSubset(ring, r))
+                return false;
         }
     }
     state.currentRings.push(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++) {
@@ -199,17 +219,24 @@ 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;
 }
 export function getFingerprint(elements) {
     var len = elements.length;
@@ -328,4 +355,3 @@ export function createIndex(rings, aromaticRings) {
     }
     return { elementRingIndices: elementRingIndices, elementAromaticRingIndices: elementAromaticRingIndices, ringComponentIndex: ringComponentIndex, ringComponents: ringComponents };
 }
-//# sourceMappingURL=compute.js.map

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

@@ -210,4 +210,3 @@ function getAromaticRings(unit, rings) {
     return aromaticRings;
 }
 export { UnitRing, UnitRings };
-//# sourceMappingURL=rings.js.map

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

@@ -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>
@@ -20,6 +20,7 @@ import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
 import { ElementSetIntraBondCache } from './unit/bonds/element-set-intra-bond-cache';
 import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { getResonance } from './unit/resonance';
 var Unit;
 (function (Unit) {
     function isAtomic(u) { return u.kind === 0 /* Atomic */; }
@@ -146,8 +147,11 @@ var Unit;
             return new Atomic(id, this.invariantId, this.chainGroupId, this.traits, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomicConformation, this.conformation.r), this.props);
         };
         Atomic.prototype.remapModel = function (model, dynamicBonds, props) {
+            var _a, _b;
             if (!props) {
-                props = __assign(__assign({}, this.props), { bonds: dynamicBonds ? undefined : tryRemapBonds(this, this.props.bonds, model) });
+                props = __assign(__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;
@@ -157,7 +161,7 @@ var Unit;
             var operator = this.conformation.operator;
             var symmetry = ModelSymmetry.Provider.get(model);
             if (operator.spgrOp !== -1 && symmetry && symmetry !== 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 = Vec3.transformMat4(Vec3(), Model.getCenter(model), toFractional);
                 operator = Spacegroup.getSymmetryOperatorRef(symmetry.spacegroup, operator.spgrOp, i, j, k, ref);
@@ -225,6 +229,16 @@ var Unit;
             enumerable: false,
             configurable: true
         });
+        Object.defineProperty(Atomic.prototype, "resonance", {
+            get: function () {
+                if (this.props.resonance)
+                    return this.props.resonance;
+                this.props.resonance = getResonance(this);
+                return this.props.resonance;
+            },
+            enumerable: false,
+            configurable: true
+        });
         Object.defineProperty(Atomic.prototype, "polymerElements", {
             get: function () {
                 if (this.props.polymerElements)
@@ -429,7 +443,7 @@ 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)
@@ -444,7 +458,7 @@ 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;
@@ -486,4 +500,3 @@ var Unit;
     Unit.getHierarchy = getHierarchy;
 })(Unit || (Unit = {}));
 export { Unit };
-//# sourceMappingURL=unit.js.map

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

@@ -43,4 +43,3 @@ export function computeStructureBoundary(s) {
     }
     return { box: boundaryHelper.getBox(), sphere: boundaryHelper.getSphere() };
 }
-//# sourceMappingURL=boundary.js.map

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

@@ -193,4 +193,3 @@ var StructureLookup3D = /** @class */ (function () {
     return StructureLookup3D;
 }());
 export { StructureLookup3D };
-//# sourceMappingURL=lookup3d.js.map

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

@@ -111,4 +111,3 @@ export function getProteinElements(unit) {
     }
     return SortedArray.ofSortedArray(indices);
 }
-//# sourceMappingURL=polymer.js.map

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

@@ -20,4 +20,3 @@ export function getPrincipalAxes(unit) {
     var positions = toPositionsArray(unit);
     return PrincipalAxes.ofPositions(positions);
 }
-//# sourceMappingURL=principal-axes.js.map

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

@@ -109,4 +109,3 @@ var StructureSubsetBuilder = /** @class */ (function () {
     return StructureSubsetBuilder;
 }());
 export { StructureSubsetBuilder };
-//# sourceMappingURL=subset-builder.js.map

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

@@ -148,4 +148,3 @@ function buildIndex(structure, index, sI, traceOnly) {
         }
     }
 }
-//# sourceMappingURL=superposition-sifts-mapping.js.map

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

@@ -83,4 +83,3 @@ function getMinSize(xs) {
     }
     return s;
 }
-//# sourceMappingURL=superposition.js.map

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

@@ -94,4 +94,3 @@ var StructureUniqueSubsetBuilder = /** @class */ (function () {
     return StructureUniqueSubsetBuilder;
 }());
 export { StructureUniqueSubsetBuilder };
-//# sourceMappingURL=unique-subset-builder.js.map

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

@@ -67,4 +67,3 @@ var StructureUnitTransforms = /** @class */ (function () {
     return StructureUnitTransforms;
 }());
 export { StructureUnitTransforms };
-//# sourceMappingURL=unit-transforms.js.map

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

@@ -12,4 +12,3 @@ import { StructureProperties } from './structure/properties';
 export { StructureElement, Bond, Structure, Unit, StructureSymmetry, StructureProperties };
 export * from './structure/unit/rings';
 export * from './export/mmcif';
-//# sourceMappingURL=structure.js.map

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

@@ -18,4 +18,3 @@ var Topology;
     }
     Topology.create = create;
 })(Topology || (Topology = {}));
-//# sourceMappingURL=topology.js.map

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

@@ -4,4 +4,3 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 export * from './topology/topology';
-//# sourceMappingURL=topology.js.map

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

@@ -16,4 +16,3 @@ var ArrayTrajectory = /** @class */ (function () {
     return ArrayTrajectory;
 }());
 export { ArrayTrajectory };
-//# sourceMappingURL=trajectory.js.map

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

@@ -49,4 +49,3 @@ export function getPositions(unit, indices) {
     }
     return positions;
 }
-//# sourceMappingURL=util.js.map

package/lib/mol-model/structure.js

@@ -10,4 +10,3 @@ export * from './structure/model';
 export * from './structure/structure';
 export * from './structure/query';
 export * from './structure/trajectory';
-//# sourceMappingURL=structure.js.map

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

@@ -61,4 +61,3 @@ var Grid;
     Grid.getHistogram = getHistogram;
 })(Grid || (Grid = {}));
 export { Grid };
-//# sourceMappingURL=grid.js.map

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

@@ -186,4 +186,3 @@ export var Volume;
         Cell.getBoundingSphere = getBoundingSphere;
     })(Cell = Volume.Cell || (Volume.Cell = {}));
 })(Volume || (Volume = {}));
-//# sourceMappingURL=volume.js.map

package/lib/mol-model/volume.js

@@ -6,4 +6,3 @@
  */
 export * from './volume/volume';
 export * from './volume/grid';
-//# sourceMappingURL=volume.js.map

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

@@ -5,4 +5,3 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 export {};
-//# sourceMappingURL=format.js.map

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

@@ -288,4 +288,3 @@ export function shapeFromPly(source, params) {
         });
     }); });
 }
-//# sourceMappingURL=ply.js.map

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

@@ -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>
@@ -37,14 +37,6 @@ 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 = Table.ofColumns(AtomsSchema, {
         type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased(Column.Schema.str) }),
@@ -74,11 +66,6 @@ function createHierarchyData(atom_site, sourceIndex, offsets) {
     // Optimize the numeric columns
     Table.columnToArray(residues, 'label_seq_id', Int32Array);
     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) {
@@ -167,4 +154,3 @@ export function getAtomicHierarchyAndConformation(atom_site, sourceIndex, entiti
     var conformation = getConformation(atom_site);
     return { sameAsPrevious: sameAsPrevious, hierarchy: hierarchy, conformation: conformation, chainOperatorMapping: chainOperatorMapping };
 }
-//# sourceMappingURL=atomic.js.map

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

@@ -77,4 +77,3 @@ function getData(data) {
     var entity_id = data.entity_id, seq_id_begin = data.seq_id_begin, seq_id_end = data.seq_id_end, asym_id = data.asym_id;
     return __assign({ count: entity_id.rowCount, entity_id: entity_id, asym_id: asym_id, seq_id_begin: seq_id_begin, seq_id_end: seq_id_end }, getSegments(asym_id, seq_id_begin, seq_id_end));
 }
-//# sourceMappingURL=coarse.js.map

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

@@ -129,4 +129,3 @@ export function getEntitiesWithPRD(data, entities, structAsymMap) {
     var prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
     return __assign(__assign({}, entities), { prd_id: prdIdColumn });
 }
-//# sourceMappingURL=entities.js.map

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

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

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -238,4 +238,3 @@ function readIntegrative(ctx, data, properties, format) {
         });
     });
 }
-//# sourceMappingURL=parser.js.map

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

@@ -122,4 +122,3 @@ export function getStructAsymMap(atomic, data) {
     }
     return map;
 }
-//# sourceMappingURL=properties.js.map

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -196,4 +196,4 @@ export interface BasicData {
     pdbx_unobs_or_zero_occ_residues: UnobsOrZeroOccResidues;
     pdbx_molecule: Molecule;
 }
-export declare function createBasic(data: Partial<BasicData>): BasicData;
+export declare function createBasic(data: Partial<BasicData>, normalize?: boolean): BasicData;

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

@@ -1,11 +1,12 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { getNormalizedAtomSite } from './util';
 export var BasicSchema = {
     entry: mmCIF_Schema.entry,
     struct: mmCIF_Schema.struct,
@@ -25,7 +26,8 @@ export var BasicSchema = {
     pdbx_unobs_or_zero_occ_residues: mmCIF_Schema.pdbx_unobs_or_zero_occ_residues,
     pdbx_molecule: mmCIF_Schema.pdbx_molecule,
 };
-export function createBasic(data) {
+export function createBasic(data, normalize) {
+    if (normalize === void 0) { normalize = false; }
     var basic = Object.create(null);
     for (var _i = 0, _a = Object.keys(BasicSchema); _i < _a.length; _i++) {
         var name_1 = _a[_i];
@@ -36,6 +38,8 @@ export function createBasic(data) {
             basic[name_1] = Table.ofUndefinedColumns(BasicSchema[name_1], 0);
         }
     }
+    if (normalize) {
+        basic.atom_site = getNormalizedAtomSite(basic.atom_site);
+    }
     return basic;
 }
-//# sourceMappingURL=schema.js.map

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

@@ -33,4 +33,3 @@ export function getSequence(data, entities, atomicHierarchy, coarseHierarchy) {
     }
     return { byEntityKey: byEntityKey, sequences: sequences };
 }
-//# sourceMappingURL=sequence.js.map

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

@@ -65,4 +65,3 @@ export function sortAtomSite(ctx, atom_site, start, end) {
         });
     });
 }
-//# sourceMappingURL=sort.js.map