npm - molstar - Versions diffs - 2.3.3 → 2.3.5 - Mend

molstar 2.3.3 → 2.3.5

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 (355) hide show

package/lib/apps/viewer/index.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -29,9 +29,11 @@ declare const DefaultViewerOptions: {
     layoutShowLog: boolean;
     layoutShowLeftPanel: boolean;
     collapseLeftPanel: boolean;
-    disableAntialiasing: boolean;
-    pixelScale: number;
-    enableWboit: boolean;
+    disableAntialiasing: boolean | undefined;
+    pixelScale: number | undefined;
+    pickScale: number | undefined;
+    pickPadding: number | undefined;
+    enableWboit: boolean | undefined;
     viewportShowExpand: boolean | undefined;
     viewportShowControls: boolean | undefined;
     viewportShowSettings: boolean | undefined;

package/lib/apps/viewer/index.html CHANGED Viewed

@@ -53,6 +53,9 @@
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+            var pickScale = getParam('pick-scale', '[^&]+').trim();
+            var pickPadding = getParam('pick-padding', '[^&]+').trim();
             var viewer = new molstar.Viewer('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
@@ -61,7 +64,10 @@
                 emdbProvider: emdbProvider || 'pdbe',
                 volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
                     ? 'https://maps.rcsb.org'
-                    : 'https://www.ebi.ac.uk/pdbe/densities'
+                    : 'https://www.ebi.ac.uk/pdbe/densities',
+                pixelScale: parseFloat(pixelScale) || 1,
+                pickScale: parseFloat(pickScale) || 0.25,
+                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
             });
             var snapshotId = getParam('snapshot-id', '[^&]+').trim();

package/lib/apps/viewer/index.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -56,9 +56,11 @@ var DefaultViewerOptions = {
     layoutShowLog: true,
     layoutShowLeftPanel: true,
     collapseLeftPanel: false,
-    disableAntialiasing: false,
-    pixelScale: 1,
-    enableWboit: true,
+    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: PluginConfig.General.PixelScale.defaultValue,
+    pickScale: PluginConfig.General.PickScale.defaultValue,
+    pickPadding: PluginConfig.General.PickPadding.defaultValue,
+    enableWboit: PluginConfig.General.EnableWboit.defaultValue,
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
     viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
@@ -99,6 +101,8 @@ var Viewer = /** @class */ (function () {
             config: [
                 [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
                 [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.PickScale, o.pickScale],
+                [PluginConfig.General.PickPadding, o.pickPadding],
                 [PluginConfig.General.EnableWboit, o.enableWboit],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],

package/lib/apps/viewer/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/cli/chem-comp-dict/util.d.ts CHANGED Viewed

@@ -16,7 +16,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        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">;
+        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">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -55,7 +55,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
         atom_id_2: import("../../mol-data/db/column").Column.Schema.Str;
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
         pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"E" | "Z" | "N">;
         pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
@@ -84,7 +84,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        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">;
+        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">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -123,7 +123,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
         atom_id_2: import("../../mol-data/db/column").Column.Schema.Str;
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
         pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"E" | "Z" | "N">;
         pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;

package/lib/commonjs/apps/viewer/index.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -20,7 +20,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("geo-export" | "g3d" | "cellpack" | "dnatco-confal-pyramids" | "pdbe-structure-quality-report" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "mp4-export")[];
+    extensions: ("g3d" | "cellpack" | "dnatco-confal-pyramids" | "pdbe-structure-quality-report" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "mp4-export" | "geo-export")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -29,9 +29,11 @@ declare const DefaultViewerOptions: {
     layoutShowLog: boolean;
     layoutShowLeftPanel: boolean;
     collapseLeftPanel: boolean;
-    disableAntialiasing: boolean;
-    pixelScale: number;
-    enableWboit: boolean;
+    disableAntialiasing: boolean | undefined;
+    pixelScale: number | undefined;
+    pickScale: number | undefined;
+    pickPadding: number | undefined;
+    enableWboit: boolean | undefined;
     viewportShowExpand: boolean | undefined;
     viewportShowControls: boolean | undefined;
     viewportShowSettings: boolean | undefined;

package/lib/commonjs/apps/viewer/index.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -62,9 +62,11 @@ var DefaultViewerOptions = {
     layoutShowLog: true,
     layoutShowLeftPanel: true,
     collapseLeftPanel: false,
-    disableAntialiasing: false,
-    pixelScale: 1,
-    enableWboit: true,
+    disableAntialiasing: config_1.PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: config_1.PluginConfig.General.PixelScale.defaultValue,
+    pickScale: config_1.PluginConfig.General.PickScale.defaultValue,
+    pickPadding: config_1.PluginConfig.General.PickPadding.defaultValue,
+    enableWboit: config_1.PluginConfig.General.EnableWboit.defaultValue,
     viewportShowExpand: config_1.PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: config_1.PluginConfig.Viewport.ShowControls.defaultValue,
     viewportShowSettings: config_1.PluginConfig.Viewport.ShowSettings.defaultValue,
@@ -105,6 +107,8 @@ var Viewer = /** @class */ (function () {
             config: [
                 [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
                 [config_1.PluginConfig.General.PixelScale, o.pixelScale],
+                [config_1.PluginConfig.General.PickScale, o.pickScale],
+                [config_1.PluginConfig.General.PickPadding, o.pickPadding],
                 [config_1.PluginConfig.General.EnableWboit, o.enableWboit],
                 [config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],

package/lib/commonjs/apps/viewer/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/cli/chem-comp-dict/util.d.ts CHANGED Viewed

@@ -16,7 +16,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        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">;
+        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">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -55,7 +55,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
         atom_id_2: import("../../mol-data/db/column").Column.Schema.Str;
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
         pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"E" | "Z" | "N">;
         pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
@@ -84,7 +84,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        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">;
+        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">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -123,7 +123,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
         atom_id_2: import("../../mol-data/db/column").Column.Schema.Str;
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
-        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"pi" | "sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo">;
+        value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
         pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"E" | "Z" | "N">;
         pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;

package/lib/commonjs/extensions/cellpack/model.d.ts CHANGED Viewed

@@ -19,7 +19,7 @@ export declare function createStructureFromCellPack(plugin: PluginContext, packi
     colors: Color[] | undefined;
 }>;
 export declare const LoadCellPackModel: StateAction<PSO.Root, void, PD.Normalize<{
-    source: PD.NamedParams<Asset.File | null, "file"> | PD.NamedParams<"InfluenzaModel2.json" | "blood_hiv_immature_inside.json" | "HIV_immature_model.json" | "BloodHIV1.0_mixed_fixed_nc1.cpr" | "HIV-1_0.1.6-8_mixed_radii_pdb.cpr" | "influenza_model1.json" | "ExosomeModel.json" | "Mycoplasma1.5_mixed_pdb_fixed.cpr" | "MycoplasmaModel.json", "id">;
+    source: PD.NamedParams<"InfluenzaModel2.json" | "blood_hiv_immature_inside.json" | "HIV_immature_model.json" | "BloodHIV1.0_mixed_fixed_nc1.cpr" | "HIV-1_0.1.6-8_mixed_radii_pdb.cpr" | "influenza_model1.json" | "ExosomeModel.json" | "Mycoplasma1.5_mixed_pdb_fixed.cpr" | "MycoplasmaModel.json", "id"> | PD.NamedParams<Asset.File | null, "file">;
     baseUrl: string;
     membrane: boolean;
     ingredients: Asset.File[] | null;

package/lib/commonjs/extensions/geo-export/mesh-exporter.d.ts CHANGED Viewed

@@ -36,7 +36,7 @@ export declare abstract class MeshExporter<D extends RenderObjectExportData> imp
         vertices: Float32Array;
         normals: Float32Array;
         indices: Uint32Array | undefined;
-        groups: Float32Array | Uint8Array;
+        groups: Uint8Array | Float32Array;
         vertexCount: number;
         drawCount: number;
     };

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts CHANGED Viewed

@@ -26,17 +26,17 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     xrayShaded: boolean;
     alpha: number;
     quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
-    axesColor: PD.NamedParams<PD.Normalize<{
+    axesColor: PD.NamedParams<PD.Normalize<unknown>, "byOrder"> | PD.NamedParams<PD.Normalize<{
         colorValue: any;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<unknown>, "byOrder">;
+    }>, "uniform">;
 }>>;
 export declare const AssemblySymmetryPresetParams: {
     ignoreHydrogens: PD.Base<boolean | undefined>;
     quality: PD.Base<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined>;
     theme: PD.Base<PD.Normalize<{
-        globalName: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
+        globalName: "occupancy" | "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
         carbonColor: "chain-id" | "operator-name" | "element-symbol" | undefined;
-        symmetryColor: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
+        symmetryColor: "occupancy" | "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
         focus: PD.Normalize<{
             name: any;
             params: any;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts CHANGED Viewed

@@ -9,34 +9,34 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { AssemblySymmetry } from './prop';
 export declare const AssemblySymmetryClusterColorThemeParams: {
     palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        list: {
-            kind: "interpolate" | "set";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "colors"> | PD.NamedParams<PD.Normalize<{
         maxCount: number;
         hue: [number, number];
         chroma: [number, number];
         luminance: [number, number];
         clusteringStepCount: number;
         minSampleCount: number;
-    }>, "generate">>;
+    }>, "generate"> | PD.NamedParams<PD.Normalize<{
+        list: {
+            kind: "set" | "interpolate";
+            colors: import("../../../mol-util/color/color").ColorListEntry[];
+        };
+    }>, "colors">>;
 };
 export declare type AssemblySymmetryClusterColorThemeParams = typeof AssemblySymmetryClusterColorThemeParams;
 export declare function getAssemblySymmetryClusterColorThemeParams(ctx: ThemeDataContext): {
     palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        list: {
-            kind: "interpolate" | "set";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "colors"> | PD.NamedParams<PD.Normalize<{
         maxCount: number;
         hue: [number, number];
         chroma: [number, number];
         luminance: [number, number];
         clusteringStepCount: number;
         minSampleCount: number;
-    }>, "generate">>;
+    }>, "generate"> | PD.NamedParams<PD.Normalize<{
+        list: {
+            kind: "set" | "interpolate";
+            colors: import("../../../mol-util/color/color").ColorListEntry[];
+        };
+    }>, "colors">>;
 };
 export declare function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props: PD.Values<AssemblySymmetryClusterColorThemeParams>): ColorTheme<AssemblySymmetryClusterColorThemeParams>;
 export declare const AssemblySymmetryClusterColorThemeProvider: ColorTheme.Provider<AssemblySymmetryClusterColorThemeParams, AssemblySymmetry.Tag.Cluster>;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts CHANGED Viewed

@@ -18,9 +18,9 @@ export declare const AssemblySymmetryParams: {
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
-    axesColor: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    axesColor: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "byOrder"> | PD.NamedParams<PD.Normalize<{
         colorValue: Color;
-    }>, "uniform"> | PD.NamedParams<PD.Normalize<unknown>, "byOrder">>;
+    }>, "uniform">>;
 };
 export declare type AssemblySymmetryParams = typeof AssemblySymmetryParams;
 export declare type AssemblySymmetryProps = PD.Values<AssemblySymmetryParams>;

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

@@ -41,7 +41,7 @@ function createIntraUnitClashCylinderMesh(ctx, unit, structure, theme, props, me
             pos(elements[a[edgeIndex]], posA);
             pos(elements[b[edgeIndex]], posB);
         },
-        style: function (edgeIndex) { return 4 /* Disk */; },
+        style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return magnitude[edgeIndex] * sizeFactor; },
     };
     return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);
@@ -134,7 +134,7 @@ function createInterUnitClashCylinderMesh(ctx, structure, theme, props, mesh) {
             uA.conformation.position(uA.elements[b.indexA], posA);
             uB.conformation.position(uB.elements[b.indexB], posB);
         },
-        style: function (edgeIndex) { return 4 /* Disk */; },
+        style: function (edgeIndex) { return 6 /* Disk */; },
         radius: function (edgeIndex) { return edges[edgeIndex].props.magnitude * sizeFactor; }
     };
     return (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh);

package/lib/commonjs/mol-canvas3d/camera/util.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,6 +25,7 @@ declare namespace Viewport {
 export declare function cameraProject(out: Vec4, point: Vec3, viewport: Viewport, projectionView: Mat4): Vec4;
 /**
  * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
  */
-export declare function cameraUnproject(out: Vec3, point: Vec3, viewport: Viewport, inverseProjectionView: Mat4): Vec3;
+export declare function cameraUnproject(out: Vec3, point: Vec3 | Vec4, viewport: Viewport, inverseProjectionView: Mat4): Vec3;

package/lib/commonjs/mol-canvas3d/camera/util.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -52,12 +52,10 @@ exports.Viewport = Viewport;
 })(Viewport || (Viewport = {}));
 exports.Viewport = Viewport;
 //
-var NEAR_RANGE = 0;
-var FAR_RANGE = 1;
 var tmpVec4 = (0, linear_algebra_1.Vec4)();
 /** Transform point into 2D window coordinates. */
 function cameraProject(out, point, viewport, projectionView) {
-    var vX = viewport.x, vY = viewport.y, vWidth = viewport.width, vHeight = viewport.height;
+    var x = viewport.x, y = viewport.y, width = viewport.width, height = viewport.height;
     // clip space -> NDC -> window coordinates, implicit 1.0 for w component
     linear_algebra_1.Vec4.set(tmpVec4, point[0], point[1], point[2], 1.0);
     // transform into clip space
@@ -69,26 +67,27 @@ function cameraProject(out, point, viewport, projectionView) {
         tmpVec4[1] /= w;
         tmpVec4[2] /= w;
     }
-    // transform into window coordinates, set fourth component is (1/clip.w) as in gl_FragCoord.w
-    out[0] = vX + vWidth / 2 * tmpVec4[0] + (0 + vWidth / 2);
-    out[1] = vY + vHeight / 2 * tmpVec4[1] + (0 + vHeight / 2);
-    out[2] = (FAR_RANGE - NEAR_RANGE) / 2 * tmpVec4[2] + (FAR_RANGE + NEAR_RANGE) / 2;
+    // transform into window coordinates, set fourth component to 1 / clip.w as in gl_FragCoord.w
+    out[0] = (tmpVec4[0] + 1) * width * 0.5 + x;
+    out[1] = (1 - tmpVec4[1]) * height * 0.5 + y; // flip Y
+    out[2] = (tmpVec4[2] + 1) * 0.5;
     out[3] = w === 0 ? 0 : 1 / w;
     return out;
 }
 exports.cameraProject = cameraProject;
 /**
  * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
  */
 function cameraUnproject(out, point, viewport, inverseProjectionView) {
-    var vX = viewport.x, vY = viewport.y, vWidth = viewport.width, vHeight = viewport.height;
-    var x = point[0] - vX;
-    var y = (vHeight - point[1] - 1) - vY;
-    var z = point[2];
-    out[0] = (2 * x) / vWidth - 1;
-    out[1] = (2 * y) / vHeight - 1;
-    out[2] = 2 * z - 1;
+    var x = viewport.x, y = viewport.y, width = viewport.width, height = viewport.height;
+    var px = point[0] - x;
+    var py = (height - point[1] - 1) - y;
+    var pz = point[2];
+    out[0] = (2 * px) / width - 1;
+    out[1] = (2 * py) / height - 1;
+    out[2] = 2 * pz - 1;
     return linear_algebra_1.Vec3.transformMat4(out, out, inverseProjectionView);
 }
 exports.cameraUnproject = cameraUnproject;

package/lib/commonjs/mol-canvas3d/camera/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/mol-canvas3d/camera.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -57,8 +57,16 @@ declare class Camera implements ICamera {
     getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot>;
     getInvariantFocus(target: Vec3, radius: number, up: Vec3, dir: Vec3): Partial<Camera.Snapshot>;
     focus(target: Vec3, radius: number, durationMs?: number, up?: Vec3, dir?: Vec3): void;
+    /** Transform point into 2D window coordinates. */
     project(out: Vec4, point: Vec3): Vec4;
-    unproject(out: Vec3, point: Vec3): Vec3;
+    /**
+     * Transform point from screen space to 3D coordinates.
+     * The point must have `x` and `y` set to 2D window coordinates
+     * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+     */
+    unproject(out: Vec3, point: Vec3 | Vec4): Vec3;
+    /** World space pixel size at given `point` */
+    getPixelSize(point: Vec3): number;
     constructor(state?: Partial<Camera.Snapshot>, viewport?: Viewport, props?: Partial<{
         pixelScale: number;
     }>);
@@ -69,7 +77,7 @@ declare namespace Camera {
     /**
      * Sets an offseted view in a larger frustum. This is useful for
      * - multi-window or multi-monitor/multi-machine setups
-     * - jittering the camera position for
+     * - jittering the camera position for sampling
      */
     interface ViewOffset {
         enabled: boolean;