molstar 3.0.0 → 3.2.0

package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        label: string; /** Precision data the server can show. */
+        /** Precision data the server can show. */
+        label: string;
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,7 +23,6 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
-        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

package/lib/commonjs/mol-plugin/behavior/static/representation.js

@@ -89,7 +89,7 @@ function UpdateRepresentationVisibility(ctx) {
 }
 exports.UpdateRepresentationVisibility = UpdateRepresentationVisibility;
 function updateVisibility(cell, r) {
-    if (r.state.visible === cell.state.isHidden) {
+    if (r.state.visible === !!cell.state.isHidden) {
         r.setState({ visible: !cell.state.isHidden });
         return true;
     }

package/lib/commonjs/mol-plugin-state/actions/volume.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/commonjs/mol-plugin-state/actions/volume.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -74,8 +74,8 @@ var DownloadDensity = mol_state_1.StateAction.build({
                         case 'pdb-xray':
                             downloadParams = src.params.provider.server === 'pdbe' ? {
                                 url: assets_1.Asset.Url(src.params.type === '2fofc'
-                                    ? "http://www.ebi.ac.uk/pdbe/coordinates/files/".concat(src.params.provider.id.toLowerCase(), ".ccp4")
-                                    : "http://www.ebi.ac.uk/pdbe/coordinates/files/".concat(src.params.provider.id.toLowerCase(), "_diff.ccp4")),
+                                    ? "https://www.ebi.ac.uk/pdbe/coordinates/files/".concat(src.params.provider.id.toLowerCase(), ".ccp4")
+                                    : "https://www.ebi.ac.uk/pdbe/coordinates/files/".concat(src.params.provider.id.toLowerCase(), "_diff.ccp4")),
                                 isBinary: true,
                                 label: "PDBe X-ray map: ".concat(src.params.provider.id)
                             } : {

package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy-preset.d.ts

@@ -66,6 +66,7 @@ export declare const PresetTrajectoryHierarchy: {
         }>, "symmetry-assembly"> | undefined;
         representationPresetParams: PD.Normalize<{
             ignoreHydrogens: any;
+            ignoreLight: any;
             quality: any;
             theme: any;
         }> | undefined;
@@ -90,6 +91,7 @@ export declare const PresetTrajectoryHierarchy: {
         useDefaultIfSingleModel: boolean | undefined;
         representationPresetParams: PD.Normalize<{
             ignoreHydrogens: any;
+            ignoreLight: any;
             quality: any;
             theme: any;
         }> | undefined;

package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts

@@ -48,6 +48,7 @@ export declare class TrajectoryHierarchyBuilder {
         }>, "symmetry-assembly"> | undefined;
         representationPresetParams: PD.Normalize<{
             ignoreHydrogens: any;
+            ignoreLight: any;
             quality: any;
             theme: any;
         }> | undefined;

package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.d.ts

@@ -13,7 +13,6 @@ import { PluginContext } from '../../../mol-plugin/context';
 import { StateObjectRef, StateObjectSelector } from '../../../mol-state';
 import { StaticStructureComponentType } from '../../helpers/structure-component';
 import { StructureSelectionQueries as Q } from '../../helpers/structure-selection-query';
-import { Color } from '../../../mol-util/color';
 export interface StructureRepresentationPresetProvider<P = any, S extends _Result = _Result> extends PresetProvider<PluginStateObject.Molecule.Structure, P, S> {
 }
 export declare function StructureRepresentationPresetProvider<P, S extends _Result>(repr: StructureRepresentationPresetProvider<P, S>): StructureRepresentationPresetProvider<P, S>;
@@ -30,11 +29,12 @@ export declare namespace StructureRepresentationPresetProvider {
     };
     const CommonParams: {
         ignoreHydrogens: PD.Base<boolean | undefined>;
+        ignoreLight: PD.Base<boolean | undefined>;
         quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
         theme: PD.Base<PD.Normalize<{
-            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
             carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
-            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
             focus: PD.Normalize<{
                 name: any;
                 params: any;
@@ -45,11 +45,12 @@ export declare namespace StructureRepresentationPresetProvider {
     function reprBuilder(plugin: PluginContext, params: CommonParams, structure?: Structure): {
         update: import("../../../mol-state/state/builder").StateBuilder.Root;
         builder: import("./representation").StructureRepresentationBuilder;
-        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
-        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
         typeParams: {
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             ignoreHydrogens: boolean;
+            ignoreLight: boolean;
         };
         ballAndStickColor: Partial<PD.Values<{
             carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "element-symbol"> | PD.NamedParams<PD.Normalize<{
@@ -75,129 +76,151 @@ export declare namespace StructureRepresentationPresetProvider {
                 }>, "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<{
-                H: Color;
-                D: Color;
-                T: Color;
-                HE: Color;
-                LI: Color;
-                BE: Color;
-                B: Color;
-                C: Color;
-                N: Color;
-                O: Color;
-                F: Color;
-                NE: Color;
-                NA: Color;
-                MG: Color;
-                AL: Color;
-                SI: Color;
-                P: Color;
-                S: Color;
-                CL: Color;
-                AR: Color;
-                K: Color;
-                CA: Color;
-                SC: Color;
-                TI: Color;
-                V: Color;
-                CR: Color;
-                MN: Color;
-                FE: Color;
-                CO: Color;
-                NI: Color;
-                CU: Color;
-                ZN: Color;
-                GA: Color;
-                GE: Color;
-                AS: Color;
-                SE: Color;
-                BR: Color;
-                KR: Color;
-                RB: Color;
-                SR: Color;
-                Y: Color;
-                ZR: Color;
-                NB: Color;
-                MO: Color;
-                TC: Color;
-                RU: Color;
-                RH: Color;
-                PD: Color;
-                AG: Color;
-                CD: Color;
-                IN: Color;
-                SN: Color;
-                SB: Color;
-                TE: Color;
-                I: Color;
-                XE: Color;
-                CS: Color;
-                BA: Color;
-                LA: Color;
-                CE: Color;
-                PR: Color;
-                ND: Color;
-                PM: Color;
-                SM: Color;
-                EU: Color;
-                GD: Color;
-                TB: Color;
-                DY: Color;
-                HO: Color;
-                ER: Color;
-                TM: Color;
-                YB: Color;
-                LU: Color;
-                HF: Color;
-                TA: Color;
-                W: Color;
-                RE: Color;
-                OS: Color;
-                IR: Color;
-                PT: Color;
-                AU: Color;
-                HG: Color;
-                TL: Color;
-                PB: Color;
-                BI: Color;
-                PO: Color;
-                AT: Color;
-                RN: Color;
-                FR: Color;
-                RA: Color;
-                AC: Color;
-                TH: Color;
-                PA: Color;
-                U: Color;
-                NP: Color;
-                PU: Color;
-                AM: Color;
-                CM: Color;
-                BK: Color;
-                CF: Color;
-                ES: Color;
-                FM: Color;
-                MD: Color;
-                NO: Color;
-                LR: Color;
-                RF: Color;
-                DB: Color;
-                SG: Color;
-                BH: Color;
-                HS: Color;
-                MT: Color;
-                DS: Color;
-                RG: Color;
-                CN: Color;
-                UUT: Color;
-                FL: Color;
-                UUP: Color;
-                LV: Color;
-                UUH: Color;
+                H: import("../../../mol-util/color").Color;
+                D: import("../../../mol-util/color").Color;
+                T: import("../../../mol-util/color").Color;
+                HE: import("../../../mol-util/color").Color;
+                LI: import("../../../mol-util/color").Color;
+                BE: import("../../../mol-util/color").Color;
+                B: import("../../../mol-util/color").Color;
+                C: import("../../../mol-util/color").Color;
+                N: import("../../../mol-util/color").Color;
+                O: import("../../../mol-util/color").Color;
+                F: import("../../../mol-util/color").Color;
+                NE: import("../../../mol-util/color").Color;
+                NA: import("../../../mol-util/color").Color;
+                MG: import("../../../mol-util/color").Color;
+                AL: import("../../../mol-util/color").Color;
+                SI: import("../../../mol-util/color").Color;
+                P: import("../../../mol-util/color").Color;
+                S: import("../../../mol-util/color").Color;
+                CL: import("../../../mol-util/color").Color;
+                AR: import("../../../mol-util/color").Color;
+                K: import("../../../mol-util/color").Color;
+                CA: import("../../../mol-util/color").Color;
+                SC: import("../../../mol-util/color").Color;
+                TI: import("../../../mol-util/color").Color;
+                V: import("../../../mol-util/color").Color;
+                CR: import("../../../mol-util/color").Color;
+                MN: import("../../../mol-util/color").Color;
+                FE: import("../../../mol-util/color").Color;
+                CO: import("../../../mol-util/color").Color;
+                NI: import("../../../mol-util/color").Color;
+                CU: import("../../../mol-util/color").Color;
+                ZN: import("../../../mol-util/color").Color;
+                GA: import("../../../mol-util/color").Color;
+                GE: import("../../../mol-util/color").Color;
+                AS: import("../../../mol-util/color").Color;
+                SE: import("../../../mol-util/color").Color;
+                BR: import("../../../mol-util/color").Color;
+                KR: import("../../../mol-util/color").Color;
+                RB: import("../../../mol-util/color").Color;
+                SR: import("../../../mol-util/color").Color;
+                Y: import("../../../mol-util/color").Color;
+                ZR: import("../../../mol-util/color").Color;
+                NB: import("../../../mol-util/color").Color;
+                MO: import("../../../mol-util/color").Color;
+                TC: import("../../../mol-util/color").Color;
+                RU: import("../../../mol-util/color").Color;
+                RH: import("../../../mol-util/color").Color;
+                PD: import("../../../mol-util/color").Color;
+                AG: import("../../../mol-util/color").Color;
+                CD: import("../../../mol-util/color").Color;
+                IN: import("../../../mol-util/color").Color;
+                SN: import("../../../mol-util/color").Color;
+                SB: import("../../../mol-util/color").Color;
+                TE: import("../../../mol-util/color").Color;
+                I: import("../../../mol-util/color").Color;
+                XE: import("../../../mol-util/color").Color;
+                CS: import("../../../mol-util/color").Color;
+                BA: import("../../../mol-util/color").Color;
+                LA: import("../../../mol-util/color").Color;
+                CE: import("../../../mol-util/color").Color;
+                PR: import("../../../mol-util/color").Color;
+                ND: import("../../../mol-util/color").Color;
+                PM: import("../../../mol-util/color").Color;
+                SM: import("../../../mol-util/color").Color;
+                EU: import("../../../mol-util/color").Color;
+                GD: import("../../../mol-util/color").Color;
+                TB: import("../../../mol-util/color").Color;
+                DY: import("../../../mol-util/color").Color;
+                HO: import("../../../mol-util/color").Color;
+                ER: import("../../../mol-util/color").Color;
+                TM: import("../../../mol-util/color").Color;
+                YB: import("../../../mol-util/color").Color;
+                LU: import("../../../mol-util/color").Color;
+                HF: import("../../../mol-util/color").Color;
+                TA: import("../../../mol-util/color").Color;
+                W: import("../../../mol-util/color").Color;
+                RE: import("../../../mol-util/color").Color;
+                OS: import("../../../mol-util/color").Color;
+                IR: import("../../../mol-util/color").Color;
+                PT: import("../../../mol-util/color").Color;
+                AU: import("../../../mol-util/color").Color;
+                HG: import("../../../mol-util/color").Color;
+                TL: import("../../../mol-util/color").Color;
+                PB: import("../../../mol-util/color").Color;
+                BI: import("../../../mol-util/color").Color;
+                PO: import("../../../mol-util/color").Color;
+                AT: import("../../../mol-util/color").Color;
+                RN: import("../../../mol-util/color").Color;
+                FR: import("../../../mol-util/color").Color;
+                RA: import("../../../mol-util/color").Color;
+                AC: import("../../../mol-util/color").Color;
+                TH: import("../../../mol-util/color").Color;
+                PA: import("../../../mol-util/color").Color;
+                U: import("../../../mol-util/color").Color;
+                NP: import("../../../mol-util/color").Color;
+                PU: import("../../../mol-util/color").Color;
+                AM: import("../../../mol-util/color").Color;
+                CM: import("../../../mol-util/color").Color;
+                BK: import("../../../mol-util/color").Color;
+                CF: import("../../../mol-util/color").Color;
+                ES: import("../../../mol-util/color").Color;
+                FM: import("../../../mol-util/color").Color;
+                MD: import("../../../mol-util/color").Color;
+                NO: import("../../../mol-util/color").Color;
+                LR: import("../../../mol-util/color").Color;
+                RF: import("../../../mol-util/color").Color;
+                DB: import("../../../mol-util/color").Color;
+                SG: import("../../../mol-util/color").Color;
+                BH: import("../../../mol-util/color").Color;
+                HS: import("../../../mol-util/color").Color;
+                MT: import("../../../mol-util/color").Color;
+                DS: import("../../../mol-util/color").Color;
+                RG: import("../../../mol-util/color").Color;
+                CN: import("../../../mol-util/color").Color;
+                UUT: import("../../../mol-util/color").Color;
+                FL: import("../../../mol-util/color").Color;
+                UUP: import("../../../mol-util/color").Color;
+                LV: import("../../../mol-util/color").Color;
+                UUH: import("../../../mol-util/color").Color;
             }>, "custom">>;
         }>>;
     };
@@ -216,6 +239,7 @@ export declare const PresetStructureRepresentations: {
     empty: StructureRepresentationPresetProvider<unknown, {}>;
     auto: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -245,6 +269,7 @@ export declare const PresetStructureRepresentations: {
     'atomic-detail': StructureRepresentationPresetProvider<{
         showCarbohydrateSymbol: boolean;
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -266,6 +291,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-cartoon': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -286,6 +312,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-and-ligand': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -321,6 +348,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'protein-and-nucleic': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -343,6 +371,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'coarse-surface': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -366,6 +395,7 @@ export declare const PresetStructureRepresentations: {
     illustrative: StructureRepresentationPresetProvider<{
         showCarbohydrateSymbol: boolean;
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;

package/lib/commonjs/mol-plugin-state/builder/structure/representation-preset.js

@@ -21,13 +21,12 @@ var operator_name_1 = require("../../../mol-theme/color/operator-name");
 var index_pair_1 = require("../../../mol-model-formats/structure/property/bonds/index-pair");
 var struct_conn_1 = require("../../../mol-model-formats/structure/property/bonds/struct_conn");
 var type_helpers_1 = require("../../../mol-util/type-helpers");
-var color_1 = require("../../../mol-util/color");
-var postprocessing_1 = require("../../../mol-canvas3d/passes/postprocessing");
 function StructureRepresentationPresetProvider(repr) { return repr; }
 exports.StructureRepresentationPresetProvider = StructureRepresentationPresetProvider;
 (function (StructureRepresentationPresetProvider) {
     StructureRepresentationPresetProvider.CommonParams = {
         ignoreHydrogens: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)),
+        ignoreLight: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false)),
         quality: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Select('auto', base_1.VisualQualityOptions)),
         theme: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Group({
             globalName: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Text('')),
@@ -56,11 +55,14 @@ exports.StructureRepresentationPresetProvider = StructureRepresentationPresetPro
         var typeParams = {
             quality: plugin.managers.structure.component.state.options.visualQuality,
             ignoreHydrogens: !plugin.managers.structure.component.state.options.showHydrogens,
+            ignoreLight: plugin.managers.structure.component.state.options.ignoreLight,
         };
         if (params.quality && params.quality !== 'auto')
             typeParams.quality = params.quality;
         if (params.ignoreHydrogens !== void 0)
             typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
+        if (params.ignoreLight !== void 0)
+            typeParams.ignoreLight = !!params.ignoreLight;
         var color = ((_a = params.theme) === null || _a === void 0 ? void 0 : _a.globalName) ? (_b = params.theme) === null || _b === void 0 ? void 0 : _b.globalName : void 0;
         var ballAndStickColor = ((_c = params.theme) === null || _c === void 0 ? void 0 : _c.carbonColor) !== undefined
             ? { carbonColor: getCarbonColorParams((_d = params.theme) === null || _d === void 0 ? void 0 : _d.carbonColor) }
@@ -83,14 +85,6 @@ exports.StructureRepresentationPresetProvider = StructureRepresentationPresetPro
 var CommonParams = StructureRepresentationPresetProvider.CommonParams;
 var reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 var updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
-function resetPostprocessingProps(plugin) {
-    if (plugin.canvas3d) {
-        var p = param_definition_1.ParamDefinition.getDefaultValues(postprocessing_1.PostprocessingParams);
-        plugin.canvas3d.setProps({
-            postprocessing: { outline: p.outline, occlusion: p.occlusion }
-        });
-    }
-}
 var auto = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-auto',
     display: {
@@ -130,7 +124,6 @@ var empty = StructureRepresentationPresetProvider({
     apply: function (ref, params, plugin) {
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
             return (0, tslib_1.__generator)(this, function (_a) {
-                resetPostprocessingProps(plugin);
                 return [2 /*return*/, {}];
             });
         });
@@ -205,7 +198,6 @@ var polymerAndLigand = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_h = (_g = params.theme) === null || _g === void 0 ? void 0 : _g.focus) === null || _h === void 0 ? void 0 : _h.name, (_k = (_j = params.theme) === null || _j === void 0 ? void 0 : _j.focus) === null || _k === void 0 ? void 0 : _k.params)];
                     case 10:
                         _o.sent();
-                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -257,7 +249,6 @@ var proteinAndNucleic = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name, (_d = (_c = params.theme) === null || _c === void 0 ? void 0 : _c.focus) === null || _d === void 0 ? void 0 : _d.params)];
                     case 4:
                         _g.sent();
-                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -324,7 +315,6 @@ var coarseSurface = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name, (_d = (_c = params.theme) === null || _c === void 0 ? void 0 : _c.focus) === null || _d === void 0 ? void 0 : _d.params)];
                     case 4:
                         _g.sent();
-                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -368,7 +358,6 @@ var polymerCartoon = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name, (_d = (_c = params.theme) === null || _c === void 0 ? void 0 : _c.focus) === null || _d === void 0 ? void 0 : _d.params)];
                     case 3:
                         _g.sent();
-                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -446,7 +435,6 @@ var atomicDetail = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_c = (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name) !== null && _c !== void 0 ? _c : color, (_f = (_e = (_d = params.theme) === null || _d === void 0 ? void 0 : _d.focus) === null || _e === void 0 ? void 0 : _e.params) !== null && _f !== void 0 ? _f : colorParams)];
                     case 5:
                         _o.sent();
-                        resetPostprocessingProps(plugin);
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -488,20 +476,6 @@ var illustrative = StructureRepresentationPresetProvider({
                         return [4 /*yield*/, updateFocusRepr(plugin, structure, (_c = (_b = (_a = params.theme) === null || _a === void 0 ? void 0 : _a.focus) === null || _b === void 0 ? void 0 : _b.name) !== null && _c !== void 0 ? _c : color, (_e = (_d = params.theme) === null || _d === void 0 ? void 0 : _d.focus) === null || _e === void 0 ? void 0 : _e.params)];
                     case 3:
                         _h.sent();
-                        if (plugin.canvas3d) {
-                            plugin.canvas3d.setProps({
-                                postprocessing: {
-                                    outline: {
-                                        name: 'on',
-                                        params: { scale: 1, color: (0, color_1.Color)(0x000000), threshold: 0.25 }
-                                    },
-                                    occlusion: {
-                                        name: 'on',
-                                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
-                                    },
-                                }
-                            });
-                        }
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });
@@ -524,6 +498,6 @@ exports.PresetStructureRepresentations = {
     'polymer-and-ligand': polymerAndLigand,
     'protein-and-nucleic': proteinAndNucleic,
     'coarse-surface': coarseSurface,
-    'illustrative': illustrative,
+    illustrative: illustrative,
 };
 //# sourceMappingURL=representation-preset.js.map

package/lib/commonjs/mol-plugin-state/builder/structure/representation.d.ts

@@ -17,6 +17,7 @@ export declare class StructureRepresentationBuilder {
     private get dataState();
     readonly defaultProvider: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
+        ignoreLight: boolean | undefined;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
@@ -43,7 +44,7 @@ export declare class StructureRepresentationBuilder {
             all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
         };
     }>;
-    private resolveProvider;
+    resolveProvider(ref: StructureRepresentationPresetProviderRef): StructureRepresentationPresetProvider<unknown, {}>;
     hasPreset(s: PluginStateObject.Molecule.Structure): boolean;
     get providers(): ReadonlyArray<StructureRepresentationPresetProvider>;
     getPresets(s?: PluginStateObject.Molecule.Structure): readonly StructureRepresentationPresetProvider<any, StructureRepresentationPresetProvider.Result>[];

package/lib/commonjs/mol-plugin-state/formats/volume.js

@@ -18,7 +18,6 @@ var object_1 = require("../../mol-util/object");
 var property_1 = require("../../mol-model-formats/volume/property");
 var util_1 = require("../../mol-plugin/behavior/dynamic/volume-streaming/util");
 var mol_task_1 = require("../../mol-task");
-var density_server_1 = require("../../mol-model-formats/volume/density-server");
 exports.VolumeFormatCategory = 'Volume';
 function tryObtainRecommendedIsoValue(plugin, volume) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
@@ -58,16 +57,7 @@ function tryGetRecomendedIsoValue(volume) {
         return;
     if (recommendedIsoValue.kind === 'relative')
         return recommendedIsoValue;
-    var stats = volume.grid.stats;
-    if (density_server_1.DscifFormat.is(volume.sourceData)) {
-        stats = {
-            min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
-            max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
-            mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
-            sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
-        };
-    }
-    return volume_1.Volume.IsoValue.toRelative(recommendedIsoValue, stats);
+    return volume_1.Volume.adjustedIsoValue(volume, recommendedIsoValue.absoluteValue, 'absolute');
 }
 function defaultVisuals(plugin, data) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {