npm - molstar - Versions diffs - 2.3.6 → 2.4.0 - Mend

molstar 2.3.6 → 2.4.0

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 (1610) hide show

package/lib/extensions/rcsb/assembly-symmetry/representation.js CHANGED Viewed

@@ -61,7 +61,7 @@ export var AssemblySymmetryParams = __assign(__assign(__assign({}, AxesParams),
 function getAssemblyName(s) {
     var _a;
     var id = ((_a = s.units[0].conformation.operator.assembly) === null || _a === void 0 ? void 0 : _a.id) || '';
-    return isInteger(id) ? "Assembly " + id : id;
+    return isInteger(id) ? "Assembly ".concat(id) : id;
 }
 var t = Mat4.identity();
 var tmpV = Vec3();
@@ -143,9 +143,9 @@ function getAxesShape(ctx, data, props, shape) {
         var type = assemblySymmetry.type, symbol = assemblySymmetry.symbol, kind = assemblySymmetry.kind, rotation_axes = assemblySymmetry.rotation_axes;
         var order = (_a = rotation_axes[groupId]) === null || _a === void 0 ? void 0 : _a.order;
         return [
-            "<small>" + data.model.entryId + "</small>",
-            "<small>" + getAssemblyName(data) + "</small>",
-            "Axis " + (groupId + 1) + " with Order " + order + " of " + type + " " + kind + " (" + symbol + ")"
+            "<small>".concat(data.model.entryId, "</small>"),
+            "<small>".concat(getAssemblyName(data), "</small>"),
+            "Axis ".concat(groupId + 1, " with Order ").concat(order, " of ").concat(type, " ").concat(kind, " (").concat(symbol, ")")
         ].join(' | ');
     };
     return Shape.create('Axes', data, geo, getColor, function () { return 1; }, getLabel);
@@ -346,9 +346,9 @@ function getCageShape(ctx, data, props, shape) {
         var type = assemblySymmetry.type, symbol = assemblySymmetry.symbol, kind = assemblySymmetry.kind;
         data.model.entryId;
         return [
-            "<small>" + data.model.entryId + "</small>",
-            "<small>" + getAssemblyName(data) + "</small>",
-            "Cage of " + type + " " + kind + " (" + symbol + ")"
+            "<small>".concat(data.model.entryId, "</small>"),
+            "<small>".concat(getAssemblyName(data), "</small>"),
+            "Cage of ".concat(type, " ").concat(kind, " (").concat(symbol, ")")
         ].join(' | ');
     };
     return Shape.create('Cage', data, geo, getColor, function () { return 1; }, getLabel);

package/lib/extensions/rcsb/assembly-symmetry/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/extensions/rcsb/graphql/types.d.ts CHANGED Viewed

@@ -1,4 +1,5 @@
 export declare type Maybe<T> = T | null;
+export declare type InputMaybe<T> = Maybe<T>;
 export declare type Exact<T extends {
     [key: string]: unknown;
 }> = {
@@ -6653,7 +6654,7 @@ export declare type Query = {
 };
 /** Query root */
 export declare type QueryAssembliesArgs = {
-    assembly_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    assembly_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryAssemblyArgs = {
@@ -6676,7 +6677,7 @@ export declare type QueryBranched_Entity_InstanceArgs = {
 };
 /** Query root */
 export declare type QueryBranched_Entity_InstancesArgs = {
-    instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    instance_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryChem_CompArgs = {
@@ -6684,7 +6685,7 @@ export declare type QueryChem_CompArgs = {
 };
 /** Query root */
 export declare type QueryChem_CompsArgs = {
-    comp_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    comp_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryEntriesArgs = {
@@ -6710,7 +6711,7 @@ export declare type QueryNonpolymer_Entity_InstanceArgs = {
 };
 /** Query root */
 export declare type QueryNonpolymer_Entity_InstancesArgs = {
-    instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    instance_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryPolymer_EntitiesArgs = {
@@ -6728,7 +6729,7 @@ export declare type QueryPolymer_Entity_InstanceArgs = {
 };
 /** Query root */
 export declare type QueryPolymer_Entity_InstancesArgs = {
-    instance_ids: ReadonlyArray<Maybe<Scalars['String']>>;
+    instance_ids: ReadonlyArray<InputMaybe<Scalars['String']>>;
 };
 /** Query root */
 export declare type QueryPubmedArgs = {
@@ -12849,25 +12850,25 @@ export declare type AssemblySymmetryQueryVariables = Exact<{
     entry_id: Scalars['String'];
 }>;
 export declare type AssemblySymmetryQuery = {
-    readonly assembly?: Maybe<{
-        readonly rcsb_struct_symmetry?: Maybe<ReadonlyArray<Maybe<{
+    readonly assembly?: {
+        readonly rcsb_struct_symmetry?: ReadonlyArray<{
             readonly kind: string;
             readonly oligomeric_state: string;
-            readonly stoichiometry: ReadonlyArray<Maybe<string>>;
+            readonly stoichiometry: ReadonlyArray<string | null | undefined>;
             readonly symbol: string;
             readonly type: string;
-            readonly clusters: ReadonlyArray<Maybe<{
-                readonly avg_rmsd?: Maybe<number>;
-                readonly members: ReadonlyArray<Maybe<{
+            readonly clusters: ReadonlyArray<{
+                readonly avg_rmsd?: number | null | undefined;
+                readonly members: ReadonlyArray<{
                     readonly asym_id: string;
-                    readonly pdbx_struct_oper_list_ids?: Maybe<ReadonlyArray<Maybe<string>>>;
-                }>>;
-            }>>;
-            readonly rotation_axes?: Maybe<ReadonlyArray<Maybe<{
-                readonly order?: Maybe<number>;
-                readonly start: ReadonlyArray<Maybe<number>>;
-                readonly end: ReadonlyArray<Maybe<number>>;
-            }>>>;
-        }>>>;
-    }>;
+                    readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null | undefined> | null | undefined;
+                } | null | undefined>;
+            } | null | undefined>;
+            readonly rotation_axes?: ReadonlyArray<{
+                readonly order?: number | null | undefined;
+                readonly start: ReadonlyArray<number | null | undefined>;
+                readonly end: ReadonlyArray<number | null | undefined>;
+            } | null | undefined> | null | undefined;
+        } | null | undefined> | null | undefined;
+    } | null | undefined;
 };

package/lib/extensions/rcsb/validation-report/behavior.js CHANGED Viewed

@@ -112,7 +112,7 @@ function geometryQualityLabel(loci) {
             }
             var summary_1 = [];
             issues_1.forEach(function (name) { return summary_1.push(name); });
-            return "Geometry Quality <small>(1 Atom)</small>: " + summary_1.join(', ');
+            return "Geometry Quality <small>(1 Atom)</small>: ".concat(summary_1.join(', '));
         }
         var hasValidationReport = false;
         var seen_1 = new Set();
@@ -149,15 +149,15 @@ function geometryQualityLabel(loci) {
         }
         if (!hasValidationReport)
             return;
-        var residueCount = "<small>(" + seen_1.size + " " + (seen_1.size > 1 ? 'Residues' : 'Residue') + ")</small>";
+        var residueCount = "<small>(".concat(seen_1.size, " ").concat(seen_1.size > 1 ? 'Residues' : 'Residue', ")</small>");
         if (cummulativeIssues_1.size === 0) {
-            return "Geometry Quality " + residueCount + ": no issues";
+            return "Geometry Quality ".concat(residueCount, ": no issues");
         }
         var summary_2 = [];
         cummulativeIssues_1.forEach(function (count, name) {
-            summary_2.push("" + name + (count > 1 ? " \u00D7 " + count : ''));
+            summary_2.push("".concat(name).concat(count > 1 ? " \u00D7 ".concat(count) : ''));
         });
-        return "Geometry Quality " + residueCount + ": " + summary_2.join(', ');
+        return "Geometry Quality ".concat(residueCount, ": ").concat(summary_2.join(', '));
     }
 }
 function densityFitLabel(loci) {
@@ -205,14 +205,14 @@ function densityFitLabel(loci) {
             return;
         var summary = [];
         if (rsrzSeen_1.size) {
-            var rsrzCount = "<small>(" + rsrzSeen_1.size + " " + (rsrzSeen_1.size > 1 ? 'Residues avg.' : 'Residue') + ")</small>";
+            var rsrzCount = "<small>(".concat(rsrzSeen_1.size, " ").concat(rsrzSeen_1.size > 1 ? 'Residues avg.' : 'Residue', ")</small>");
             var rsrzAvg = rsrzSum_1 / rsrzSeen_1.size;
-            summary.push("Real-Space R Z-score " + rsrzCount + ": " + rsrzAvg.toFixed(2));
+            summary.push("Real-Space R Z-score ".concat(rsrzCount, ": ").concat(rsrzAvg.toFixed(2)));
         }
         if (rsccSeen_1.size) {
-            var rsccCount = "<small>(" + rsccSeen_1.size + " " + (rsccSeen_1.size > 1 ? 'Residues avg.' : 'Residue') + ")</small>";
+            var rsccCount = "<small>(".concat(rsccSeen_1.size, " ").concat(rsccSeen_1.size > 1 ? 'Residues avg.' : 'Residue', ")</small>");
             var rsccAvg = rsccSum_1 / rsccSeen_1.size;
-            summary.push("Real-Space Correlation Coefficient " + rsccCount + ": " + rsccAvg.toFixed(2));
+            summary.push("Real-Space Correlation Coefficient ".concat(rsccCount, ": ").concat(rsccAvg.toFixed(2)));
         }
         if (summary.length) {
             return summary.join('</br>');
@@ -253,9 +253,9 @@ function randomCoilIndexLabel(loci) {
         }
         if (seen_3.size === 0)
             return;
-        var residueCount = "<small>(" + seen_3.size + " " + (seen_3.size > 1 ? 'Residues avg.' : 'Residue') + ")</small>";
+        var residueCount = "<small>(".concat(seen_3.size, " ").concat(seen_3.size > 1 ? 'Residues avg.' : 'Residue', ")</small>");
         var rciAvg = sum_1 / seen_3.size;
-        return "Random Coil Index " + residueCount + ": " + rciAvg.toFixed(2);
+        return "Random Coil Index ".concat(residueCount, ": ").concat(rciAvg.toFixed(2));
     }
 }
 //

package/lib/extensions/rcsb/validation-report/behavior.js.map CHANGED Viewed

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package/lib/extensions/rcsb/validation-report/prop.js CHANGED Viewed

@@ -33,7 +33,7 @@ var ValidationReport;
     ValidationReport.DefaultBaseUrl = '//ftp.rcsb.org/pub/pdb/validation_reports';
     function getEntryUrl(pdbId, baseUrl) {
         var id = pdbId.toLowerCase();
-        return baseUrl + "/" + id.substr(1, 2) + "/" + id + "/" + id + "_validation.xml.gz";
+        return "".concat(baseUrl, "/").concat(id.substr(1, 2), "/").concat(id, "/").concat(id, "_validation.xml.gz");
     }
     ValidationReport.getEntryUrl = getEntryUrl;
     function isApplicable(model) {
@@ -293,7 +293,7 @@ function ClashesBuilder(elementsCount) {
     var seen = new Map();
     return {
         add: function (element, id, magnitude, distance, isSymop) {
-            var hash = id + "|" + (isSymop ? 's' : '');
+            var hash = "".concat(id, "|").concat(isSymop ? 's' : '');
             var other = seen.get(hash);
             if (other !== undefined) {
                 aIndices[aIndices.length] = element;

package/lib/extensions/rcsb/validation-report/prop.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/extensions/rcsb/validation-report/representation.d.ts CHANGED Viewed

@@ -24,7 +24,7 @@ export declare const IntraUnitClashParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -49,7 +49,7 @@ export declare const InterUnitClashParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -62,7 +62,7 @@ export declare const InterUnitClashParams: {
 export declare type InterUnitClashParams = typeof InterUnitClashParams;
 export declare function InterUnitClashVisual(materialId: number): ComplexVisual<InterUnitClashParams>;
 export declare const ClashesParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     visuals: PD.MultiSelect<"intra-clash" | "inter-clash">;
     linkCap: PD.BooleanParam;
     sizeFactor: PD.Numeric;
@@ -87,7 +87,7 @@ export declare const ClashesParams: {
 };
 export declare type ClashesParams = typeof ClashesParams;
 export declare function getClashesParams(ctx: ThemeRegistryContext, structure: Structure): {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     visuals: PD.MultiSelect<"intra-clash" | "inter-clash">;
     linkCap: PD.BooleanParam;
     sizeFactor: PD.Numeric;
@@ -113,7 +113,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
 export declare type ClashesRepresentation = StructureRepresentation<ClashesParams>;
 export declare function ClashesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ClashesParams>): ClashesRepresentation;
 export declare const ClashesRepresentationProvider: StructureRepresentationProvider<{
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     visuals: PD.MultiSelect<"intra-clash" | "inter-clash">;
     linkCap: PD.BooleanParam;
     sizeFactor: PD.Numeric;

package/lib/extensions/rcsb/validation-report/representation.js CHANGED Viewed

@@ -74,7 +74,7 @@ function getIntraClashLabel(structure, unit, clashes, elements) {
     var mag = magnitude[idx].toFixed(2);
     var dist = distance[idx].toFixed(2);
     return [
-        "Clash id: " + id[idx] + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
+        "Clash id: ".concat(id[idx], " | Magnitude: ").concat(mag, " \u212B | Distance: ").concat(dist, " \u212B"),
         bondLabel(Bond.Location(structure, unit, clashes.a[idx], structure, unit, clashes.b[idx]))
     ].join('</br>');
 }
@@ -171,7 +171,7 @@ function getInterClashLabel(structure, clashes, elements) {
     var mag = c.props.magnitude.toFixed(2);
     var dist = c.props.distance.toFixed(2);
     return [
-        "Clash id: " + c.props.id + " | Magnitude: " + mag + " \u212B | Distance: " + dist + " \u212B",
+        "Clash id: ".concat(c.props.id, " | Magnitude: ").concat(mag, " \u212B | Distance: ").concat(dist, " \u212B"),
         bondLabel(Bond.Location(structure, uA, c.indexA, structure, uB, c.indexB))
     ].join('</br>');
 }

package/lib/extensions/rcsb/validation-report/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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