npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1829) hide show

package/lib/mol-model/structure/structure/symmetry.js.map CHANGED Viewed

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

@@ -66,7 +66,7 @@ function findIndexPairBonds(unit) {
             if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
-                orders[order.length] = order[i];
+                orders[orders.length] = order[i];
                 flags[flags.length] = flag[i];
             }
         }

package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-model/structure/structure/unit/bonds.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 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>
@@ -38,6 +38,7 @@ declare namespace Bond {
     function isLociEmpty(loci: Loci): boolean;
     function remapLoci(loci: Loci, structure: Structure): Loci;
     function toStructureElementLoci(loci: Loci): StructureElement.Loci;
+    function toFirstStructureElementLoci(loci: Loci): StructureElement.Loci;
     function getType(structure: Structure, location: Location<Unit.Atomic>): BondType;
     function getOrder(structure: Structure, location: Location<Unit.Atomic>): number;
     function getIntraUnitBondCount(structure: Structure): number;

package/lib/mol-model/structure/structure/unit/bonds.js CHANGED Viewed

@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 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>
  */
 import { Unit, StructureElement } from '../../structure';
 import { BondType } from '../../model/types';
-import { SortedArray } from '../../../../mol-data/int';
+import { SortedArray, OrderedSet } from '../../../../mol-data/int';
 import { CentroidHelper } from '../../../../mol-math/geometry/centroid-helper';
 export * from './bonds/data';
 export * from './bonds/intra-compute';
@@ -115,6 +115,11 @@ var Bond;
         return StructureElement.Loci(loci.structure, elements);
     }
     Bond.toStructureElementLoci = toStructureElementLoci;
+    function toFirstStructureElementLoci(loci) {
+        var _a = loci.bonds[0], aUnit = _a.aUnit, aIndex = _a.aIndex;
+        return StructureElement.Loci(loci.structure, [{ unit: aUnit, indices: OrderedSet.ofSingleton(aIndex) }]);
+    }
+    Bond.toFirstStructureElementLoci = toFirstStructureElementLoci;
     function getType(structure, location) {
         if (location.aUnit === location.bUnit) {
             var bonds = location.aUnit.bonds;

package/lib/mol-model/structure/structure/unit/bonds.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-model/structure/structure/unit.d.ts CHANGED Viewed

@@ -181,10 +181,10 @@ declare namespace Unit {
     export function areOperatorsEqual(a: Unit, b: Unit): boolean;
     export function areConformationsEqual(a: Unit, b: Unit): boolean;
     export function isSameConformation(u: Unit, model: Model): boolean;
-    export function getModelConformationOfKind(kind: Unit.Kind, model: Model): CoarseSphereConformation | CoarseGaussianConformation | import("../model/properties/atomic").AtomicConformation;
-    export function getConformation(u: Unit): CoarseSphereConformation | CoarseGaussianConformation | import("../model/properties/atomic").AtomicConformation;
-    export function getModelHierarchyOfKind(kind: Unit.Kind, model: Model): CoarseElements | import("../model/properties/atomic").AtomicHierarchy;
-    export function getHierarchy(u: Unit): CoarseElements | import("../model/properties/atomic").AtomicHierarchy;
+    export function getModelConformationOfKind(kind: Unit.Kind, model: Model): import("../model/properties/atomic").AtomicConformation | CoarseSphereConformation | CoarseGaussianConformation;
+    export function getConformation(u: Unit): import("../model/properties/atomic").AtomicConformation | CoarseSphereConformation | CoarseGaussianConformation;
+    export function getModelHierarchyOfKind(kind: Unit.Kind, model: Model): import("../model/properties/atomic").AtomicHierarchy | CoarseElements;
+    export function getHierarchy(u: Unit): import("../model/properties/atomic").AtomicHierarchy | CoarseElements;
     export {};
 }
 export { Unit };

package/lib/mol-model/structure/structure/util/superposition-db-mapping.js CHANGED Viewed

@@ -109,7 +109,7 @@ function buildIndex(structure, index, sI) {
                 var rI = residueOffset[eI];
                 if (!dbName[rI])
                     continue;
-                var key = dbName[rI] + "-" + accession[rI] + "-" + num[rI];
+                var key = "".concat(dbName[rI], "-").concat(accession[rI], "-").concat(num[rI]);
                 if (!index.has(key)) {
                     index.set(key, { key: key, pivots: (_a = {}, _a[sI] = [unit, eI, elements[residueSegment.end]], _a) });
                 }

package/lib/mol-model/structure/structure/util/superposition-db-mapping.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-model/volume/volume.js CHANGED Viewed

@@ -52,8 +52,8 @@ export var Volume;
         IsoValue.toRelative = toRelative;
         function toString(value) {
             return value.kind === 'relative'
-                ? value.relativeValue.toFixed(2) + " \u03C3"
-                : "" + value.absoluteValue.toPrecision(4);
+                ? "".concat(value.relativeValue.toFixed(2), " \u03C3")
+                : "".concat(value.absoluteValue.toPrecision(4));
         }
         IsoValue.toString = toString;
     })(IsoValue = Volume.IsoValue || (Volume.IsoValue = {}));

package/lib/mol-model/volume/volume.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-model-formats/shape/ply.d.ts CHANGED Viewed

@@ -12,12 +12,12 @@ import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 export declare const PlyShapeParams: {
     coloring: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        color: Color;
+    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
     }>, "material"> | PD.NamedParams<PD.Normalize<{
-        color: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
@@ -36,12 +36,12 @@ export declare const PlyShapeParams: {
 export declare type PlyShapeParams = typeof PlyShapeParams;
 export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapeProvider<PlyFile, Mesh, {
     coloring: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        color: Color;
+    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;
     }>, "material"> | PD.NamedParams<PD.Normalize<{
-        color: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         red: string;
         green: string;
         blue: string;

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

@@ -217,7 +217,7 @@ function createShape(plyFile, mesh, coloring, grouping) {
         return Color.fromRgb(red.value(idx), green.value(idx), blue.value(idx));
     }, function () { return 1; }, // size: constant
     function (groupId) {
-        return label + " " + ids[groupId];
+        return "".concat(label, " ").concat(ids[groupId]);
     });
 }
 function makeShapeGetter() {

package/lib/mol-model-formats/shape/ply.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-model-formats/structure/basic/atomic.js CHANGED Viewed

@@ -119,9 +119,9 @@ function createChainOperatorMappingAndSubstituteNames(hierarchy, format) {
         });
         var suffix = entries.suffix.value(i);
         var label = entries.label_asym_id.value(i);
-        labelMap.set("" + label + suffix, { name: label, operator: operator });
+        labelMap.set("".concat(label).concat(suffix), { name: label, operator: operator });
         var auth = entries.auth_asym_id.value(i);
-        authMap.set("" + auth + suffix, auth);
+        authMap.set("".concat(auth).concat(suffix), auth);
     }
     var _a = hierarchy.chains, label_asym_id = _a.label_asym_id, auth_asym_id = _a.auth_asym_id;
     var mappedLabel = new Array(label_asym_id.rowCount);

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

	@@ -1 +1 @@
1	- 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package/lib/mol-model-formats/structure/basic/properties.js CHANGED Viewed

@@ -11,7 +11,7 @@ import { Table } from '../../../mol-data/db';
 function getMissingResidues(data) {
     var map = new Map();
     var getKey = function (model_num, asym_id, seq_id) {
-        return model_num + "|" + asym_id + "|" + seq_id;
+        return "".concat(model_num, "|").concat(asym_id, "|").concat(seq_id);
     };
     var c = data.pdbx_unobs_or_zero_occ_residues;
     for (var i = 0, il = c._rowCount; i < il; ++i) {
@@ -61,7 +61,7 @@ function getSaccharideComponentMap(data) {
                     map.set(comp_id.value(i), saccharideComp);
                 }
                 else {
-                    console.warn("Unknown SNFG name '" + snfgName + "'");
+                    console.warn("Unknown SNFG name '".concat(snfgName, "'"));
                 }
             }
         }

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

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-model-formats/structure/basic/schema.d.ts CHANGED Viewed

@@ -60,7 +60,7 @@ export declare const BasicSchema: {
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;
         src_method: import("../../../mol-data/db/column").Column.Schema.Aliased<"nat" | "man" | "syn">;
-        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"polymer" | "water" | "branched" | "non-polymer" | "macrolide">;
+        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: import("../../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_number_of_molecules: import("../../../mol-data/db/column").Column.Schema.Int;
         pdbx_mutation: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -88,7 +88,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db/column").Column.Schema.Aliased<"oligosaccharide">;
     };
     chem_comp: {
-        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
         formula: import("../../../mol-data/db/column").Column.Schema.Str;
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;