molstar 3.0.0 → 3.2.0

package/lib/commonjs/mol-repr/structure/registry.d.ts

@@ -13,7 +13,7 @@ export declare namespace StructureRepresentationRegistry {
     export const BuiltIn: {
         cartoon: import("./representation").StructureRepresentationProvider<{
             sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
-            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
             bumpFrequency: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             unitKinds: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"spheres" | "gaussians" | "atomic">;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;

package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,7 +10,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
 export declare const CartoonParams: {
     sizeFactor: PD.Numeric;
-    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
     bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
@@ -48,7 +48,7 @@ export declare const CartoonParams: {
 export declare type CartoonParams = typeof CartoonParams;
 export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure): {
     sizeFactor: PD.Numeric;
-    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
     bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
@@ -87,7 +87,7 @@ export declare type CartoonRepresentation = StructureRepresentation<CartoonParam
 export declare function CartoonRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CartoonParams>): CartoonRepresentation;
 export declare const CartoonRepresentationProvider: StructureRepresentationProvider<{
     sizeFactor: PD.Numeric;
-    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-ring" | "nucleotide-block" | "direction-wedge">;
     bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;

package/lib/commonjs/mol-repr/structure/representation/cartoon.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -27,7 +27,7 @@ var CartoonVisuals = {
     'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
     'direction-wedge': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer direction wedge', ctx, getParams, polymer_direction_wedge_1.PolymerDirectionVisual); }
 };
-exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
+exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getCartoonParams(ctx, structure) {
     var params = param_definition_1.ParamDefinition.clone(exports.CartoonParams);
     var hasNucleotides = false;
@@ -40,7 +40,7 @@ function getCartoonParams(ctx, structure) {
     });
     params.visuals.defaultValue = ['polymer-trace'];
     if (hasNucleotides)
-        params.visuals.defaultValue.push('nucleotide-block');
+        params.visuals.defaultValue.push('nucleotide-ring');
     if (hasGaps)
         params.visuals.defaultValue.push('polymer-gap');
     return params;

package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -43,7 +43,7 @@ function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
                     mesh_1.Mesh.transform(surface, transform);
                     if (ctx.webgl && !ctx.webgl.isWebGL2)
                         mesh_1.Mesh.uniformTriangleGroup(surface);
-                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, props.probeRadius + (0, common_1.getUnitExtraRadius)(unit));
+                    sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, (0, common_1.getUnitExtraRadius)(unit));
                     surface.setBoundingSphere(sphere);
                     surface.meta.resolution = resolution;
                     return [2 /*return*/, surface];

package/lib/commonjs/mol-repr/structure/visual/util/bond.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-repr/structure/visual/util/bond.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -215,6 +215,7 @@ function getInterBondLoci(pickingId, structure, id) {
     return loci_1.EmptyLoci;
 }
 exports.getInterBondLoci = getInterBondLoci;
+var __unitMap = new Map();
 function eachInterBond(loci, structure, apply, isMarking) {
     var changed = false;
     if (structure_1.Bond.isLoci(loci)) {
@@ -234,17 +235,16 @@ function eachInterBond(loci, structure, apply, isMarking) {
             return false;
         if (isMarking && loci.elements.length === 1)
             return false; // only a single unit
-        var map_1 = new Map();
         for (var _b = 0, _c = loci.elements; _b < _c.length; _b++) {
             var e = _c[_b];
-            map_1.set(e.unit.id, e.indices);
+            __unitMap.set(e.unit.id, e.indices);
         }
         var _loop_2 = function (e) {
             var unit = e.unit;
             if (!structure_1.Unit.isAtomic(unit))
                 return "continue";
             structure.interUnitBonds.getConnectedUnits(unit.id).forEach(function (b) {
-                var otherLociIndices = map_1.get(b.unitB);
+                var otherLociIndices = __unitMap.get(b.unitB);
                 if (!isMarking || otherLociIndices) {
                     int_1.OrderedSet.forEach(e.indices, function (v) {
                         if (!b.connectedIndices.includes(v))
@@ -264,6 +264,7 @@ function eachInterBond(loci, structure, apply, isMarking) {
             var e = _e[_d];
             _loop_2(e);
         }
+        __unitMap.clear();
     }
     return changed;
 }

package/lib/commonjs/mol-script/language/builder.d.ts

@@ -10,6 +10,7 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
+            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;

package/lib/commonjs/mol-state/transform.js

@@ -56,7 +56,12 @@ var Transform;
             if (!!s === !!t)
                 continue;
             changed = true;
-            a[k] = s;
+            if (s !== void 0) {
+                a[k] = s;
+            }
+            else {
+                delete a[k];
+            }
         }
         for (var _b = 0, _c = Object.keys(a); _b < _c.length; _b++) {
             var k = _c[_b];
@@ -64,7 +69,12 @@ var Transform;
             if (!!s === !!t)
                 continue;
             changed = true;
-            a[k] = s;
+            if (s !== void 0) {
+                a[k] = s;
+            }
+            else {
+                delete a[k];
+            }
         }
         return changed;
     }

package/lib/commonjs/mol-theme/color/element-symbol.d.ts

@@ -154,7 +154,29 @@ export declare const ElementSymbolColorThemeParams: {
         }>, "generate"> | PD.NamedParams<PD.Normalize<{
             list: any;
         }>, "colors">;
-    }>, "operator-name">>;
+    }>, "operator-name"> | PD.NamedParams<PD.Normalize<{
+        palette: PD.NamedParams<PD.Normalize<{
+            maxCount: any;
+            hue: any;
+            chroma: any;
+            luminance: any;
+            clusteringStepCount: any;
+            minSampleCount: any;
+        }>, "generate"> | PD.NamedParams<PD.Normalize<{
+            list: any;
+        }>, "colors">;
+    }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
+        palette: PD.NamedParams<PD.Normalize<{
+            maxCount: any;
+            hue: any;
+            chroma: any;
+            luminance: any;
+            clusteringStepCount: any;
+            minSampleCount: any;
+        }>, "generate"> | PD.NamedParams<PD.Normalize<{
+            list: any;
+        }>, "colors">;
+    }>, "entity-source">>;
     saturation: PD.Numeric;
     lightness: PD.Numeric;
     colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
@@ -304,7 +326,29 @@ export declare function getElementSymbolColorThemeParams(ctx: ThemeDataContext):
         }>, "generate"> | PD.NamedParams<PD.Normalize<{
             list: any;
         }>, "colors">;
-    }>, "operator-name">>;
+    }>, "operator-name"> | PD.NamedParams<PD.Normalize<{
+        palette: PD.NamedParams<PD.Normalize<{
+            maxCount: any;
+            hue: any;
+            chroma: any;
+            luminance: any;
+            clusteringStepCount: any;
+            minSampleCount: any;
+        }>, "generate"> | PD.NamedParams<PD.Normalize<{
+            list: any;
+        }>, "colors">;
+    }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
+        palette: PD.NamedParams<PD.Normalize<{
+            maxCount: any;
+            hue: any;
+            chroma: any;
+            luminance: any;
+            clusteringStepCount: any;
+            minSampleCount: any;
+        }>, "generate"> | PD.NamedParams<PD.Normalize<{
+            list: any;
+        }>, "colors">;
+    }>, "entity-source">>;
     saturation: PD.Numeric;
     lightness: PD.Numeric;
     colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-theme/color/element-symbol.js

@@ -6,7 +6,6 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ElementSymbolColorThemeProvider = exports.ElementSymbolColorTheme = exports.elementSymbolColor = exports.getElementSymbolColorThemeParams = exports.ElementSymbolColorThemeParams = exports.ElementSymbolColors = void 0;
-var tslib_1 = require("tslib");
 var color_1 = require("../../mol-util/color");
 var structure_1 = require("../../mol-model/structure");
 var param_definition_1 = require("../../mol-util/param-definition");
@@ -15,18 +14,22 @@ var color_2 = require("../../mol-util/color/color");
 var params_1 = require("../../mol-util/color/params");
 var chain_id_1 = require("./chain-id");
 var operator_name_1 = require("./operator-name");
+var entity_id_1 = require("./entity-id");
+var type_helpers_1 = require("../../mol-util/type-helpers");
+var entity_source_1 = require("./entity-source");
 // from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
 exports.ElementSymbolColors = (0, color_1.ColorMap)({
     'H': 0xFFFFFF, 'D': 0xFFFFC0, 'T': 0xFFFFA0, 'HE': 0xD9FFFF, 'LI': 0xCC80FF, 'BE': 0xC2FF00, 'B': 0xFFB5B5, 'C': 0x909090, 'N': 0x3050F8, 'O': 0xFF0D0D, 'F': 0x90E050, 'NE': 0xB3E3F5, 'NA': 0xAB5CF2, 'MG': 0x8AFF00, 'AL': 0xBFA6A6, 'SI': 0xF0C8A0, 'P': 0xFF8000, 'S': 0xFFFF30, 'CL': 0x1FF01F, 'AR': 0x80D1E3, 'K': 0x8F40D4, 'CA': 0x3DFF00, 'SC': 0xE6E6E6, 'TI': 0xBFC2C7, 'V': 0xA6A6AB, 'CR': 0x8A99C7, 'MN': 0x9C7AC7, 'FE': 0xE06633, 'CO': 0xF090A0, 'NI': 0x50D050, 'CU': 0xC88033, 'ZN': 0x7D80B0, 'GA': 0xC28F8F, 'GE': 0x668F8F, 'AS': 0xBD80E3, 'SE': 0xFFA100, 'BR': 0xA62929, 'KR': 0x5CB8D1, 'RB': 0x702EB0, 'SR': 0x00FF00, 'Y': 0x94FFFF, 'ZR': 0x94E0E0, 'NB': 0x73C2C9, 'MO': 0x54B5B5, 'TC': 0x3B9E9E, 'RU': 0x248F8F, 'RH': 0x0A7D8C, 'PD': 0x006985, 'AG': 0xC0C0C0, 'CD': 0xFFD98F, 'IN': 0xA67573, 'SN': 0x668080, 'SB': 0x9E63B5, 'TE': 0xD47A00, 'I': 0x940094, 'XE': 0x940094, 'CS': 0x57178F, 'BA': 0x00C900, 'LA': 0x70D4FF, 'CE': 0xFFFFC7, 'PR': 0xD9FFC7, 'ND': 0xC7FFC7, 'PM': 0xA3FFC7, 'SM': 0x8FFFC7, 'EU': 0x61FFC7, 'GD': 0x45FFC7, 'TB': 0x30FFC7, 'DY': 0x1FFFC7, 'HO': 0x00FF9C, 'ER': 0x00E675, 'TM': 0x00D452, 'YB': 0x00BF38, 'LU': 0x00AB24, 'HF': 0x4DC2FF, 'TA': 0x4DA6FF, 'W': 0x2194D6, 'RE': 0x267DAB, 'OS': 0x266696, 'IR': 0x175487, 'PT': 0xD0D0E0, 'AU': 0xFFD123, 'HG': 0xB8B8D0, 'TL': 0xA6544D, 'PB': 0x575961, 'BI': 0x9E4FB5, 'PO': 0xAB5C00, 'AT': 0x754F45, 'RN': 0x428296, 'FR': 0x420066, 'RA': 0x007D00, 'AC': 0x70ABFA, 'TH': 0x00BAFF, 'PA': 0x00A1FF, 'U': 0x008FFF, 'NP': 0x0080FF, 'PU': 0x006BFF, 'AM': 0x545CF2, 'CM': 0x785CE3, 'BK': 0x8A4FE3, 'CF': 0xA136D4, 'ES': 0xB31FD4, 'FM': 0xB31FBA, 'MD': 0xB30DA6, 'NO': 0xBD0D87, 'LR': 0xC70066, 'RF': 0xCC0059, 'DB': 0xD1004F, 'SG': 0xD90045, 'BH': 0xE00038, 'HS': 0xE6002E, 'MT': 0xEB0026, 'DS': 0xFFFFFF, 'RG': 0xFFFFFF, 'CN': 0xFFFFFF, 'UUT': 0xFFFFFF, 'FL': 0xFFFFFF, 'UUP': 0xFFFFFF, 'LV': 0xFFFFFF, 'UUH': 0xFFFFFF
 });
 var DefaultElementSymbolColor = (0, color_1.Color)(0xFFFFFF);
 var Description = 'Assigns a color to every atom according to its chemical element.';
-// TODO generalise `carbonColor` param to all themes?
 exports.ElementSymbolColorThemeParams = {
     carbonColor: param_definition_1.ParamDefinition.MappedStatic('chain-id', {
-        'chain-id': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({}, chain_id_1.ChainIdColorThemeParams)),
-        'operator-name': param_definition_1.ParamDefinition.Group((0, tslib_1.__assign)({}, operator_name_1.OperatorNameColorThemeParams)),
-        'element-symbol': param_definition_1.ParamDefinition.Group({})
+        'chain-id': param_definition_1.ParamDefinition.Group(chain_id_1.ChainIdColorThemeParams),
+        'entity-id': param_definition_1.ParamDefinition.Group(entity_id_1.EntityIdColorThemeParams),
+        'entity-source': param_definition_1.ParamDefinition.Group(entity_source_1.EntitySourceColorThemeParams),
+        'operator-name': param_definition_1.ParamDefinition.Group(operator_name_1.OperatorNameColorThemeParams),
+        'element-symbol': param_definition_1.ParamDefinition.EmptyGroup()
     }, { description: 'Use chain-id coloring for carbon atoms.' }),
     saturation: param_definition_1.ParamDefinition.Numeric(0, { min: -6, max: 6, step: 0.1 }),
     lightness: param_definition_1.ParamDefinition.Numeric(0.2, { min: -6, max: 6, step: 0.1 }),
@@ -46,11 +49,13 @@ function elementSymbolColor(colorMap, element) {
 exports.elementSymbolColor = elementSymbolColor;
 function ElementSymbolColorTheme(ctx, props) {
     var colorMap = (0, color_2.getAdjustedColorMap)(props.colors.name === 'default' ? exports.ElementSymbolColors : props.colors.params, props.saturation, props.lightness);
-    var carbonColor = props.carbonColor.name === 'chain-id'
-        ? (0, chain_id_1.ChainIdColorTheme)(ctx, props.carbonColor.params).color
-        : props.carbonColor.name === 'operator-name'
-            ? (0, operator_name_1.OperatorNameColorTheme)(ctx, props.carbonColor.params).color
-            : undefined;
+    var pcc = props.carbonColor;
+    var carbonColor = pcc.name === 'chain-id' ? (0, chain_id_1.ChainIdColorTheme)(ctx, pcc.params).color :
+        pcc.name === 'entity-id' ? (0, entity_id_1.EntityIdColorTheme)(ctx, pcc.params).color :
+            pcc.name === 'entity-source' ? (0, entity_source_1.EntitySourceColorTheme)(ctx, pcc.params).color :
+                pcc.name === 'operator-name' ? (0, operator_name_1.OperatorNameColorTheme)(ctx, pcc.params).color :
+                    pcc.name === 'element-symbol' ? undefined :
+                        (0, type_helpers_1.assertUnreachable)(pcc);
     function elementColor(element, location) {
         return (carbonColor && element === 'C')
             ? carbonColor(location, false)

package/lib/commonjs/mol-theme/color/entity-id.js

@@ -32,17 +32,20 @@ function getEntityIdSerialMap(structure) {
             if (!map.has(k))
                 map.set(k, map.size);
         }
-        var spheres_entity_id = structure.models[i].coarseHierarchy.spheres.entity_id;
-        for (var j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
-            var k = key(spheres_entity_id.value(j), i);
-            if (!map.has(k))
-                map.set(k, map.size);
-        }
-        var gaussians_entity_id = structure.models[i].coarseHierarchy.gaussians.entity_id;
-        for (var j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
-            var k = key(gaussians_entity_id.value(j), i);
-            if (!map.has(k))
-                map.set(k, map.size);
+        var coarseHierarchy = structure.models[i].coarseHierarchy;
+        if (coarseHierarchy.isDefined) {
+            var spheres_entity_id = coarseHierarchy.spheres.entity_id;
+            for (var j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
+                var k = key(spheres_entity_id.value(j), i);
+                if (!map.has(k))
+                    map.set(k, map.size);
+            }
+            var gaussians_entity_id = coarseHierarchy.gaussians.entity_id;
+            for (var j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
+                var k = key(gaussians_entity_id.value(j), i);
+                if (!map.has(k))
+                    map.set(k, map.size);
+            }
         }
     }
     return map;

package/lib/commonjs/mol-theme/color/illustrative.d.ts

@@ -9,8 +9,6 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 export declare const IllustrativeColorThemeParams: {
     style: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        value: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         palette: PD.NamedParams<PD.Normalize<{
             maxCount: any;
             hue: any;
@@ -23,18 +21,6 @@ export declare const IllustrativeColorThemeParams: {
         }>, "colors">;
         asymId: "label" | "auth";
     }>, "chain-id"> | PD.NamedParams<PD.Normalize<{
-        saturation: number;
-        lightness: number;
-        colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
-            water: any;
-            ion: any;
-            protein: any;
-            RNA: any;
-            DNA: any;
-            PNA: any;
-            saccharide: any;
-        }>, "custom">;
-    }>, "molecule-type"> | PD.NamedParams<PD.Normalize<{
         palette: PD.NamedParams<PD.Normalize<{
             maxCount: any;
             hue: any;
@@ -45,7 +31,7 @@ export declare const IllustrativeColorThemeParams: {
         }>, "generate"> | PD.NamedParams<PD.Normalize<{
             list: any;
         }>, "colors">;
-    }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+    }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
         palette: PD.NamedParams<PD.Normalize<{
             maxCount: any;
             hue: any;
@@ -56,14 +42,26 @@ export declare const IllustrativeColorThemeParams: {
         }>, "generate"> | PD.NamedParams<PD.Normalize<{
             list: any;
         }>, "colors">;
-    }>, "entity-id">>;
+    }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+        value: Color;
+    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
+        saturation: number;
+        lightness: number;
+        colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+            water: any;
+            ion: any;
+            protein: any;
+            RNA: any;
+            DNA: any;
+            PNA: any;
+            saccharide: any;
+        }>, "custom">;
+    }>, "molecule-type">>;
     carbonLightness: PD.Numeric;
 };
 export declare type IllustrativeColorThemeParams = typeof IllustrativeColorThemeParams;
 export declare function getIllustrativeColorThemeParams(ctx: ThemeDataContext): {
     style: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        value: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
         palette: PD.NamedParams<PD.Normalize<{
             maxCount: any;
             hue: any;
@@ -76,18 +74,6 @@ export declare function getIllustrativeColorThemeParams(ctx: ThemeDataContext):
         }>, "colors">;
         asymId: "label" | "auth";
     }>, "chain-id"> | PD.NamedParams<PD.Normalize<{
-        saturation: number;
-        lightness: number;
-        colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
-            water: any;
-            ion: any;
-            protein: any;
-            RNA: any;
-            DNA: any;
-            PNA: any;
-            saccharide: any;
-        }>, "custom">;
-    }>, "molecule-type"> | PD.NamedParams<PD.Normalize<{
         palette: PD.NamedParams<PD.Normalize<{
             maxCount: any;
             hue: any;
@@ -98,7 +84,7 @@ export declare function getIllustrativeColorThemeParams(ctx: ThemeDataContext):
         }>, "generate"> | PD.NamedParams<PD.Normalize<{
             list: any;
         }>, "colors">;
-    }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+    }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
         palette: PD.NamedParams<PD.Normalize<{
             maxCount: any;
             hue: any;
@@ -109,7 +95,21 @@ export declare function getIllustrativeColorThemeParams(ctx: ThemeDataContext):
         }>, "generate"> | PD.NamedParams<PD.Normalize<{
             list: any;
         }>, "colors">;
-    }>, "entity-id">>;
+    }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+        value: Color;
+    }>, "uniform"> | PD.NamedParams<PD.Normalize<{
+        saturation: number;
+        lightness: number;
+        colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+            water: any;
+            ion: any;
+            protein: any;
+            RNA: any;
+            DNA: any;
+            PNA: any;
+            saccharide: any;
+        }>, "custom">;
+    }>, "molecule-type">>;
     carbonLightness: PD.Numeric;
 };
 export declare function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<IllustrativeColorThemeParams>): ColorTheme<IllustrativeColorThemeParams>;

package/lib/commonjs/mol-theme/color.d.ts

@@ -125,7 +125,29 @@ declare namespace ColorTheme {
                 }>, "generate"> | PD.NamedParams<PD.Normalize<{
                     list: any;
                 }>, "colors">;
-            }>, "operator-name">>;
+            }>, "operator-name"> | PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "entity-source">>;
             saturation: PD.Numeric;
             lightness: PD.Numeric;
             colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
@@ -286,8 +308,6 @@ declare namespace ColorTheme {
         }, "hydrophobicity">;
         illustrative: Provider<{
             style: PD.Mapped<PD.NamedParams<PD.Normalize<{
-                value: Color;
-            }>, "uniform"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
@@ -300,18 +320,6 @@ declare namespace ColorTheme {
                 }>, "colors">;
                 asymId: "label" | "auth";
             }>, "chain-id"> | PD.NamedParams<PD.Normalize<{
-                saturation: number;
-                lightness: number;
-                colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
-                    water: any;
-                    ion: any;
-                    protein: any;
-                    RNA: any;
-                    DNA: any;
-                    PNA: any;
-                    saccharide: any;
-                }>, "custom">;
-            }>, "molecule-type"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
@@ -322,7 +330,7 @@ declare namespace ColorTheme {
                 }>, "generate"> | PD.NamedParams<PD.Normalize<{
                     list: any;
                 }>, "colors">;
-            }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+            }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
@@ -333,7 +341,21 @@ declare namespace ColorTheme {
                 }>, "generate"> | PD.NamedParams<PD.Normalize<{
                     list: any;
                 }>, "colors">;
-            }>, "entity-id">>;
+            }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+                value: Color;
+            }>, "uniform"> | PD.NamedParams<PD.Normalize<{
+                saturation: number;
+                lightness: number;
+                colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+                    water: any;
+                    ion: any;
+                    protein: any;
+                    RNA: any;
+                    DNA: any;
+                    PNA: any;
+                    saccharide: any;
+                }>, "custom">;
+            }>, "molecule-type">>;
             carbonLightness: PD.Numeric;
         }, "illustrative">;
         'model-index': Provider<{

package/lib/commonjs/servers/volume/config.js

@@ -168,11 +168,11 @@ function configureLocal() {
         description: version_1.VOLUME_SERVER_HEADER
     });
     parser.add_argument('--jobs', { help: "Path to a JSON file with job specification.", required: false });
-    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });
+    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, action: 'store_true' });
     addJsonConfigArgs(parser);
     addLimitsArgs(parser);
     var config = parser.parse_args();
-    if (config.cfgTemplate !== null) {
+    if (config.cfgTemplate) {
         console.log(JSON.stringify(DefaultLimitsConfig, null, 2));
         process.exit(0);
     }
@@ -182,7 +182,7 @@ function configureLocal() {
             var cfg = JSON.parse(fs.readFileSync(config.cfg, 'utf8'));
             setLimitsConfig(cfg);
         }
-        if (config.printCfg !== null) {
+        if (config.printCfg) {
             console.log(JSON.stringify(exports.LimitsConfig, null, 2));
             process.exit(0);
         }

package/lib/commonjs/servers/volume/query.js

@@ -14,7 +14,7 @@ var fs = (0, tslib_1.__importStar)(require("fs"));
 var config_1 = require("./config");
 var LocalApi = (0, tslib_1.__importStar)(require("./server/local-api"));
 var config = (0, config_1.configureLocal)();
-if (config.jobsTemplate !== null) {
+if (config.jobsTemplate) {
     var exampleJobs = [{
             source: {
                 filename: "g:/test/mdb/xray-1tqn.mdb",