molstar 2.3.3 → 2.3.5

package/lib/mol-model-formats/structure/common/component.d.ts

@@ -19,29 +19,29 @@ export declare class ComponentBuilder {
     private getType;
     has(compId: string): boolean;
     get(compId: string): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
-        mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
         name: Column.Schema.Str;
         pdbx_synonyms: Column.Schema.List<string>;
-    }, "type" | "name" | "id">> | undefined;
+    }, "id" | "type" | "name">> | undefined;
     add(compId: string, index: number): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
-        mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
         name: Column.Schema.Str;
         pdbx_synonyms: Column.Schema.List<string>;
-    }, "type" | "name" | "id">>;
+    }, "id" | "type" | "name">>;
     getChemCompTable(): Table<{
-        type: Column.Schema.Aliased<"non-polymer" | "other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: Column.Schema.Aliased<"D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "other" | "Ion" | "Lipid">;
         formula: Column.Schema.Str;
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
-        mon_nstd_flag: Column.Schema.Aliased<"y" | "no" | "n" | "yes">;
+        mon_nstd_flag: Column.Schema.Aliased<"no" | "n" | "yes" | "y">;
         name: Column.Schema.Str;
         pdbx_synonyms: Column.Schema.List<string>;
     }>;

package/lib/mol-model-formats/structure/common/entity.d.ts

@@ -28,7 +28,7 @@ export declare class EntityBuilder {
         formula_weight: Column.Schema.Float;
         id: Column.Schema.Str;
         src_method: Column.Schema.Aliased<"nat" | "man" | "syn">;
-        type: Column.Schema.Aliased<"polymer" | "water" | "branched" | "non-polymer" | "macrolide">;
+        type: Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
         pdbx_description: Column.Schema.List<string>;
         pdbx_number_of_molecules: Column.Schema.Int;
         pdbx_mutation: Column.Schema.Str;

package/lib/mol-model-formats/structure/pdb/entity.js

@@ -18,7 +18,7 @@ export function parseCmpnd(lines, lineStart, lineEnd) {
     var getLine = function (n) { return lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]); };
     var currentSpec;
     var currentCompound = { chains: [], description: '' };
-    var Compounds = [];
+    var compounds = [];
     for (var i = lineStart; i < lineEnd; i++) {
         var line = getLine(i);
         // COLUMNS       DATA TYPE       FIELD         DEFINITION
@@ -44,7 +44,7 @@ export function parseCmpnd(lines, lineStart, lineEnd) {
                 chains: [],
                 description: ''
             };
-            Compounds.push(currentCompound);
+            compounds.push(currentCompound);
         }
         else if (currentSpec === 'MOLECULE') {
             if (currentCompound.description)
@@ -55,7 +55,33 @@ export function parseCmpnd(lines, lineStart, lineEnd) {
             Array.prototype.push.apply(currentCompound.chains, value.split(/\s*,\s*/));
         }
     }
-    return Compounds;
+    // Define a seprate entity for each chain
+    // --------------------------------------
+    //
+    // This is a workaround for how sequences are currently determined for PDB files.
+    //
+    // The current approach infers the "observed sequence" from the atomic hierarchy.
+    // However, for example for PDB ID 3HHR, this approach fails, since chains B and C
+    // belong to the same entity but contain different observed sequence, which causes display
+    // errors in the sequence viewer (since the sequences are determined "per entity").
+    //
+    // A better approach could be to parse SEQRES categories and use it to construct
+    // entity_poly_seq category. However, this would require constructing label_seq_id (with gaps)
+    // from RES ID pdb column (auth_seq_id), which isn't a trivial exercise.
+    //
+    // (properly formatted) mmCIF structures do not exhibit this issue.
+    var singletons = [];
+    for (var _i = 0, compounds_1 = compounds; _i < compounds_1.length; _i++) {
+        var comp = compounds_1[_i];
+        for (var _a = 0, _b = comp.chains; _a < _b.length; _a++) {
+            var chain = _b[_a];
+            singletons.push({
+                description: comp.description,
+                chains: [chain]
+            });
+        }
+    }
+    return singletons;
 }
 export function parseHetnam(lines, lineStart, lineEnd) {
     var getLine = function (n) { return lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]); };

package/lib/mol-model-formats/structure/pdb/entity.js.map

@@ -1 +1 @@
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+{"version":3,"file":"entity.js","sourceRoot":"","sources":["../../../../src/mol-model-formats/structure/pdb/entity.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,IAAM,IAAI,GAAG;IACT,QAAQ,EAAE,EAAE;IACZ,UAAU,EAAE,EAAE;IACd,OAAO,EAAE,EAAE;IACX,UAAU,EAAE,EAAE;IACd,SAAS,EAAE,EAAE;IACb,IAAI,EAAE,EAAE;IACR,YAAY,EAAE,EAAE;IAChB,UAAU,EAAE,EAAE;IACd,eAAe,EAAE,EAAE;CACtB,CAAC;AAGF,MAAM,UAAU,UAAU,CAAC,KAAa,EAAE,SAAiB,EAAE,OAAe;IACxE,IAAM,OAAO,GAAG,UAAC,CAAS,IAAK,OAAA,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAApE,CAAoE,CAAC;IAEpG,IAAI,WAA6B,CAAC;IAClC,IAAI,eAAe,GAAmB,EAAE,MAAM,EAAE,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,CAAC;IACtE,IAAM,SAAS,GAAqB,EAAE,CAAC;IAEvC,KAAK,IAAI,CAAC,GAAG,SAAS,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;QACtC,IAAM,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QACxB,yDAAyD;QACzD,qFAAqF;QACrF,yCAAyC;QACzC,wFAAwF;QACxF,uFAAuF;QACvF,qBAAqB;QAErB,IAAM,KAAK,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;QACzC,IAAM,YAAY,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;QACxC,IAAM,SAAS,GAAG,KAAK,CAAC,SAAS,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC;QAEnD,IAAI,KAAK,SAAQ,CAAC;QAElB,IAAI,SAAS,IAAI,IAAI,EAAE;YACnB,WAAW,GAAG,SAAiB,CAAC;YAChC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC;SAC7C;aAAM;YACH,KAAK,GAAG,KAAK,CAAC;SACjB;QACD,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;QAEhC,IAAI,WAAW,KAAK,QAAQ,EAAE;YAC1B,eAAe,GAAG;gBACd,MAAM,EAAE,EAAE;gBACV,WAAW,EAAE,EAAE;aAClB,CAAC;YACF,SAAS,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC;SACnC;aAAM,IAAI,WAAW,KAAK,UAAU,EAAE;YACnC,IAAI,eAAe,CAAC,WAAW;gBAAE,eAAe,CAAC,WAAW,IAAI,GAAG,CAAC;YACpE,eAAe,CAAC,WAAW,IAAI,KAAK,CAAC;SACxC;aAAM,IAAI,WAAW,KAAK,OAAO,EAAE;YAChC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC;SAC9E;KACJ;IAED,yCAAyC;IACzC,yCAAyC;IACzC,EAAE;IACF,iFAAiF;IACjF,EAAE;IACF,iFAAiF;IACjF,kFAAkF;IAClF,0FAA0F;IAC1F,mFAAmF;IACnF,EAAE;IACF,gFAAgF;IAChF,8FAA8F;IAC9F,wEAAwE;IACxE,EAAE;IACF,mEAAmE;IACnE,IAAM,UAAU,GAAqB,EAAE,CAAC;IACxC,KAAmB,UAAS,EAAT,uBAAS,EAAT,uBAAS,EAAT,IAAS,EAAE;QAAzB,IAAM,IAAI,kBAAA;QACX,KAAoB,UAAW,EAAX,KAAA,IAAI,CAAC,MAAM,EAAX,cAAW,EAAX,IAAW,EAAE;YAA5B,IAAM,KAAK,SAAA;YACZ,UAAU,CAAC,IAAI,CAAC;gBACZ,WAAW,EAAE,IAAI,CAAC,WAAW;gBAC7B,MAAM,EAAE,CAAC,KAAK,CAAC;aAClB,CAAC,CAAC;SACN;KACJ;IACD,OAAO,UAAU,CAAC;AACtB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAa,EAAE,SAAiB,EAAE,OAAe;IACzE,IAAM,OAAO,GAAG,UAAC,CAAS,IAAK,OAAA,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAApE,CAAoE,CAAC;IAEpG,IAAM,OAAO,GAAG,IAAI,GAAG,EAAkB,CAAC;IAE1C,KAAK,IAAI,CAAC,GAAG,SAAS,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;QACtC,IAAM,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QACxB,yDAAyD;QACzD,+EAA+E;QAC/E,uCAAuC;QACvC,wFAAwF;QACxF,+EAA+E;QAC/E,6DAA6D;QAE7D,IAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;QACtC,IAAM,MAAI,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;QAEpC,IAAI,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;YAClB,OAAO,CAAC,GAAG,CAAC,GAAG,EAAK,OAAO,CAAC,GAAG,CAAC,GAAG,CAAE,SAAI,MAAM,CAAC,CAAC;SACpD;aAAM;YACH,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,MAAI,CAAC,CAAC;SAC1B;KACJ;IAED,OAAO,OAAO,CAAC;AACnB,CAAC"}

package/lib/mol-model-props/sequence/themes/best-database-mapping.d.ts

@@ -8,34 +8,34 @@ import { ThemeDataContext } from '../../../mol-theme/theme';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 export declare const BestDatabaseSequenceMappingColorThemeParams: {
     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 BestDatabaseSequenceMappingColorThemeParams = typeof BestDatabaseSequenceMappingColorThemeParams;
 export declare function getBestDatabaseSequenceMappingColorThemeParams(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 BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<BestDatabaseSequenceMappingColorThemeParams>): ColorTheme<BestDatabaseSequenceMappingColorThemeParams>;
 export declare const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<BestDatabaseSequenceMappingColorThemeParams, 'best-sequence-database-mapping'>;

package/lib/mol-plugin/behavior/behavior.d.ts

@@ -114,7 +114,7 @@ declare namespace PluginBehavior {
     export const CreateCategory: StateTransformer<Root, Category, ParamDefinition.Normalize<{
         label: string;
     }>>;
-    export function getCategoryId(t: StateTransformer): "common" | "representation" | "interaction" | "custom-props" | "misc";
+    export function getCategoryId(t: StateTransformer): "representation" | "custom-props" | "common" | "interaction" | "misc";
     export function create<P>(params: CreateParams<P>): StateTransformer<Category, Behavior, P>;
     export function simpleCommandHandler<T>(cmd: PluginCommand<T>, action: (data: T, ctx: PluginContext) => void | Promise<void>): {
         new (ctx: PluginContext): {

package/lib/mol-plugin/behavior/dynamic/representation.d.ts

@@ -12,7 +12,8 @@ export declare const HighlightLoci: import("../../../mol-state/transformer").Sta
         hoverHighlightOnly: Binding;
         hoverHighlightOnlyExtend: Binding;
     }>;
-    ignore: PD.Value<("volume-loci" | "isosurface-loci" | "empty-loci" | "cell-loci" | "every-loci" | "element-loci" | "structure-loci" | "bond-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
+    ignore: PD.Value<("every-loci" | "empty-loci" | "element-loci" | "structure-loci" | "bond-loci" | "data-loci" | "shape-loci" | "group-loci" | "volume-loci" | "isosurface-loci" | "cell-loci")[]>;
+    preferAtoms: PD.BooleanParam;
     mark: PD.BooleanParam;
 }>>;
 export declare const SelectLoci: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, PD.Values<{
@@ -24,7 +25,8 @@ export declare const SelectLoci: import("../../../mol-state/transformer").StateT
         clickDeselect: Binding;
         clickDeselectAllOnEmpty: Binding;
     }>;
-    ignore: PD.Value<("volume-loci" | "isosurface-loci" | "empty-loci" | "cell-loci" | "every-loci" | "element-loci" | "structure-loci" | "bond-loci" | "data-loci" | "shape-loci" | "group-loci")[]>;
+    ignore: PD.Value<("every-loci" | "empty-loci" | "element-loci" | "structure-loci" | "bond-loci" | "data-loci" | "shape-loci" | "group-loci" | "volume-loci" | "isosurface-loci" | "cell-loci")[]>;
+    preferAtoms: PD.BooleanParam;
     mark: PD.BooleanParam;
 }>>;
 export declare const DefaultLociLabelProvider: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, unknown>;

package/lib/mol-plugin/behavior/dynamic/representation.js

@@ -15,7 +15,7 @@ import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observ
 import { Binding } from '../../../mol-util/binding';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
+import { Bond, Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
 import { arrayMax } from '../../../mol-util/array';
 var B = ButtonsType;
 var M = ModifiersKeys;
@@ -28,6 +28,7 @@ var DefaultHighlightLociBindings = {
 var HighlightLociParams = {
     bindings: PD.Value(DefaultHighlightLociBindings, { isHidden: true }),
     ignore: PD.Value([], { isHidden: true }),
+    preferAtoms: PD.Boolean(false, { description: 'Always prefer atoms over bonds' }),
     mark: PD.Boolean(true)
 };
 export var HighlightLoci = PluginBehavior.create({
@@ -44,6 +45,11 @@ export var HighlightLoci = PluginBehavior.create({
             };
             return _this;
         }
+        class_1.prototype.getLoci = function (loci) {
+            return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
+                ? Bond.toFirstStructureElementLoci(loci)
+                : loci;
+        };
         class_1.prototype.register = function () {
             var _this = this;
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, function (_a) {
@@ -51,19 +57,20 @@ export var HighlightLoci = PluginBehavior.create({
                 var current = _a.current, buttons = _a.buttons, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy)
                     return;
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(current.loci.kind)) >= 0) {
+                var loci = _this.getLoci(current.loci);
+                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0) {
                     _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EmptyLoci });
                     return;
                 }
                 var matched = false;
                 if (Binding.match(_this.params.bindings.hoverHighlightOnly, buttons, modifiers)) {
                     // remove repr to highlight loci everywhere on hover
-                    _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci: current.loci });
+                    _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci: loci });
                     matched = true;
                 }
                 if (Binding.match(_this.params.bindings.hoverHighlightOnlyExtend, buttons, modifiers)) {
                     // remove repr to highlight loci everywhere on hover
-                    _this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci: current.loci });
+                    _this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci: loci });
                     matched = true;
                 }
                 if (!matched) {
@@ -92,6 +99,7 @@ var DefaultSelectLociBindings = {
 var SelectLociParams = {
     bindings: PD.Value(DefaultSelectLociBindings, { isHidden: true }),
     ignore: PD.Value([], { isHidden: true }),
+    preferAtoms: PD.Boolean(false, { description: 'Always prefer atoms over bonds' }),
     mark: PD.Boolean(true)
 };
 export var SelectLoci = PluginBehavior.create({
@@ -109,6 +117,11 @@ export var SelectLoci = PluginBehavior.create({
             _this.spine = new StateTreeSpine.Impl(ctx.state.data.cells);
             return _this;
         }
+        class_2.prototype.getLoci = function (loci) {
+            return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
+                ? Bond.toFirstStructureElementLoci(loci)
+                : loci;
+        };
         class_2.prototype.applySelectMark = function (ref, clear) {
             var cell = this.ctx.state.data.cells.get(ref);
             if (cell && SO.isRepresentation3D(cell.obj)) {
@@ -125,8 +138,8 @@ export var SelectLoci = PluginBehavior.create({
         };
         class_2.prototype.register = function () {
             var _this = this;
-            var lociIsEmpty = function (current) { return Loci.isEmpty(current.loci); };
-            var lociIsNotEmpty = function (current) { return !Loci.isEmpty(current.loci); };
+            var lociIsEmpty = function (loci) { return Loci.isEmpty(loci); };
+            var lociIsNotEmpty = function (loci) { return !Loci.isEmpty(loci); };
             var actions = [
                 ['clickSelect', function (current) { return _this.ctx.managers.interactivity.lociSelects.select(current); }, lociIsNotEmpty],
                 ['clickToggle', function (current) { return _this.ctx.managers.interactivity.lociSelects.toggle(current); }, lociIsNotEmpty],
@@ -147,13 +160,14 @@ export var SelectLoci = PluginBehavior.create({
                 var current = _a.current, button = _a.button, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy || !_this.ctx.selectionMode)
                     return;
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(current.loci.kind)) >= 0)
+                var loci = _this.getLoci(current.loci);
+                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0)
                     return;
                 // only trigger the 1st action that matches
                 for (var _i = 0, actions_1 = actions; _i < actions_1.length; _i++) {
                     var _c = actions_1[_i], binding = _c[0], action = _c[1], condition = _c[2];
-                    if (Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(current))) {
-                        action(current);
+                    if (Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
+                        action({ repr: current.repr, loci: loci });
                         break;
                     }
                 }

package/lib/mol-plugin/behavior/dynamic/representation.js.map

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

@@ -49,16 +49,16 @@ export declare namespace VolumeStreaming {
         channelParams?: DefaultChannelParams;
     }): {
         entry: PD.Mapped<PD.NamedParams<PD.Values<{
-            view: PD.Mapped<PD.NamedParams<PD.Normalize<{
-                bottomLeft: Vec3;
-                topRight: Vec3;
-            }>, "box"> | PD.NamedParams<PD.Normalize<{
+            view: PD.Mapped<PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
                 radius: number;
                 selectionDetailLevel: number;
                 isSelection: boolean;
                 bottomLeft: Vec3;
                 topRight: Vec3;
-            }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+            }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
+                bottomLeft: Vec3;
+                topRight: Vec3;
+            }>, "box"> | PD.NamedParams<PD.Normalize<{
                 radius: number;
                 bottomLeft: Vec3;
                 topRight: Vec3;
@@ -81,16 +81,16 @@ export declare namespace VolumeStreaming {
         structure?: Structure;
         channelParams?: DefaultChannelParams;
     }): {
-        view: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            bottomLeft: Vec3;
-            topRight: Vec3;
-        }>, "box"> | PD.NamedParams<PD.Normalize<{
+        view: PD.Mapped<PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
             radius: number;
             selectionDetailLevel: number;
             isSelection: boolean;
             bottomLeft: Vec3;
             topRight: Vec3;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
+            bottomLeft: Vec3;
+            topRight: Vec3;
+        }>, "box"> | PD.NamedParams<PD.Normalize<{
             radius: number;
             bottomLeft: Vec3;
             topRight: Vec3;

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

@@ -29,25 +29,25 @@ declare const CreateVolumeStreamingInfo: StateTransformer<SO.Molecule.Structure,
     serverUrl: string;
     entries: PD.Normalize<PD.Values<{
         dataId: PD.Text<string>;
-        source: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "x-ray"> | PD.NamedParams<PD.Normalize<{
+        source: PD.Mapped<PD.NamedParams<PD.Normalize<{
             isoValue: any;
-        }>, "em">>;
+        }>, "em"> | PD.NamedParams<PD.Normalize<unknown>, "x-ray">>;
     }>>[];
 }>>;
 export { CreateVolumeStreamingBehavior };
 declare type CreateVolumeStreamingBehavior = typeof CreateVolumeStreamingBehavior;
 declare const CreateVolumeStreamingBehavior: StateTransformer<VolumeServerInfo, VolumeStreaming, PD.Normalize<{
     entry: PD.NamedParams<PD.Values<{
-        view: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            bottomLeft: any;
-            topRight: any;
-        }>, "box"> | PD.NamedParams<PD.Normalize<{
+        view: PD.Mapped<PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
             radius: any;
             selectionDetailLevel: any;
             isSelection: any;
             bottomLeft: any;
             topRight: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
+            bottomLeft: any;
+            topRight: any;
+        }>, "box"> | PD.NamedParams<PD.Normalize<{
             radius: any;
             bottomLeft: any;
             topRight: any;

package/lib/mol-plugin/commands.d.ts

@@ -259,13 +259,13 @@ export declare const PluginCommands: {
                     selectStrength: number;
                     markerPriority: number;
                     xrayEdgeFalloff: number;
-                    style: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                    style: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "flat"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "metallic"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         lightIntensity: any;
                         ambientIntensity: any;
                         metalness: any;
                         roughness: any;
                         reflectivity: any;
-                    }>, "custom"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "matte"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "flat"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "glossy"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "metallic"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "plastic">;
+                    }>, "custom"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "matte"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "glossy"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "plastic">;
                     clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         variant: any;
                         objects: any;
@@ -302,6 +302,10 @@ export declare const PluginCommands: {
                         maxDistanceMin: any;
                     }>, "on">;
                 }>>;
+                interaction: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                    maxFps: number;
+                    preferAtomPixelPadding: number;
+                }>>;
                 debug: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                     sceneBoundingSpheres: boolean;
                     visibleSceneBoundingSpheres: boolean;

package/lib/mol-plugin/config.d.ts

@@ -24,6 +24,7 @@ export declare const PluginConfig: {
         DisablePreserveDrawingBuffer: PluginConfigItem<boolean>;
         PixelScale: PluginConfigItem<number>;
         PickScale: PluginConfigItem<number>;
+        PickPadding: PluginConfigItem<number>;
         EnableWboit: PluginConfigItem<boolean>;
         PreferWebGl1: PluginConfigItem<boolean>;
     };

package/lib/mol-plugin/config.js

@@ -33,6 +33,7 @@ export var PluginConfig = {
         DisablePreserveDrawingBuffer: item('plugin-config.disable-preserve-drawing-buffer', false),
         PixelScale: item('plugin-config.pixel-scale', 1),
         PickScale: item('plugin-config.pick-scale', 0.25),
+        PickPadding: item('plugin-config.pick-padding', 3),
         EnableWboit: item('plugin-config.enable-wboit', true),
         // as of Oct 1 2021, WebGL 2 doesn't work on iOS 15.
         // TODO: check back in a few weeks to see if it was fixed

package/lib/mol-plugin/config.js.map

@@ -1 +1 @@
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+{"version":3,"file":"config.js","sourceRoot":"","sources":["../../src/mol-plugin/config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,wBAAwB,CAAC;AAM1D;IAGI,0BAAmB,GAAW,EAAS,YAAgB;QAApC,QAAG,GAAH,GAAG,CAAQ;QAAS,iBAAY,GAAZ,YAAY,CAAI;IAAI,CAAC;IAF5D,mCAAQ,GAAR,cAAa,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;IAC/B,kCAAO,GAAP,cAAY,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;IAElC,uBAAC;AAAD,CAAC,AAJD,IAIC;;AAED,SAAS,IAAI,CAAI,GAAW,EAAE,YAAgB,IAAI,OAAO,IAAI,gBAAgB,CAAC,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,CAAC;AAGnG,mFAAmF;AACnF,SAAS,MAAM;IACX,IAAI,OAAO,SAAS,KAAK,WAAW,IAAI,OAAO,MAAM,KAAK,WAAW;QAAE,OAAO,KAAK,CAAC;IACpF,IAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;IAC3D,IAAM,aAAa,GAAG,SAAS,CAAC,SAAS,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC;IAChE,IAAM,aAAa,GAAG,SAAS,CAAC,cAAc,IAAI,CAAC,CAAC,CAAC,yCAAyC;IAC9F,OAAO,CAAE,MAAc,CAAC,QAAQ,IAAI,CAAC,KAAK,IAAI,CAAC,aAAa,IAAI,aAAa,CAAC,CAAC,CAAC;AACpF,CAAC;AAED,MAAM,CAAC,IAAM,YAAY,GAAG;IACxB,IAAI,MAAA;IACJ,OAAO,EAAE;QACL,eAAe,EAAE,IAAI,CAAC,+BAA+B,EAAE,GAAG,CAAC;QAC3D,mBAAmB,EAAE,IAAI,CAAC,oCAAoC,EAAE,KAAK,CAAC;QACtE,4BAA4B,EAAE,IAAI,CAAC,+CAA+C,EAAE,KAAK,CAAC;QAC1F,UAAU,EAAE,IAAI,CAAC,2BAA2B,EAAE,CAAC,CAAC;QAChD,SAAS,EAAE,IAAI,CAAC,0BAA0B,EAAE,IAAI,CAAC;QACjD,WAAW,EAAE,IAAI,CAAC,4BAA4B,EAAE,CAAC,CAAC;QAClD,WAAW,EAAE,IAAI,CAAC,4BAA4B,EAAE,IAAI,CAAC;QACrD,oDAAoD;QACpD,yDAAyD;QACzD,YAAY,EAAE,IAAI,CAAC,6BAA6B,EAAE,MAAM,EAAE,CAAC;KAC9D;IACD,KAAK,EAAE;QACH,aAAa,EAAE,IAAI,CAAC,qBAAqB,EAAE,4CAA4C,CAAC;QACxF,aAAa,EAAE,IAAI,CAAC,qBAAqB,EAAE,4CAA4C,CAAC;QACxF,eAAe,EAAE,IAAI,CAAC,yBAAyB,EAAE,CAAC,CAAC;KACtD;IACD,eAAe,EAAE;QACb,OAAO,EAAE,IAAI,CAAC,0BAA0B,EAAE,IAAI,CAAC;QAC/C,aAAa,EAAE,IAAI,CAAC,yBAAyB,EAAE,wBAAwB,CAAC;QACxE,SAAS,EAAE,IAAI,CAAC,6BAA6B,EAAE,UAAC,CAAY,EAAE,MAAqB;YAC/E,OAAO,CAAC,CAAC,MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;QAC7E,CAAC,CAAC;QACF,gBAAgB,EAAE,IAAI,CAAC,qCAAqC,EAAE,2CAA2C,CAAC;KAC7G;IACD,QAAQ,EAAE;QACN,UAAU,EAAE,IAAI,CAAC,2BAA2B,EAAE,IAAI,CAAC;QACnD,YAAY,EAAE,IAAI,CAAC,6BAA6B,EAAE,IAAI,CAAC;QACvD,YAAY,EAAE,IAAI,CAAC,6BAA6B,EAAE,IAAI,CAAC;QACvD,iBAAiB,EAAE,IAAI,CAAC,oCAAoC,EAAE,IAAI,CAAC;QACnE,aAAa,EAAE,IAAI,CAAC,8BAA8B,EAAE,IAAI,CAAC;KAC5D;IACD,QAAQ,EAAE;QACN,kBAAkB,EAAE,IAAI,CAAsB,+BAA+B,EAAE,MAAM,CAAC;QACtF,mBAAmB,EAAE,IAAI,CAAuB,gCAAgC,EAAE,MAAM,CAAC;KAC5F;IACD,SAAS,EAAE;QACP,cAAc,EAAE,IAAI,CAAC,2BAA2B,EAAE,SAAS,CAAC,qBAAqB,CAAC;QAClF,iCAAiC,EAAE,IAAI,CAAqD,gDAAgD,EAAE,EAAG,CAAC;KACrJ;CACJ,CAAC;AAEF;IAgBI,6BAAY,OAAuC;QAAnD,iBAGC;QAlBO,YAAO,GAAG,IAAI,GAAG,EAAkC,CAAC;QAgBxD,IAAI,CAAC,OAAO;YAAE,OAAO;QACrB,OAAO,CAAC,OAAO,CAAC,UAAC,EAAM;gBAAL,CAAC,QAAA,EAAE,CAAC,QAAA;YAAM,OAAA,KAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;QAAtB,CAAsB,CAAC,CAAC;IACxD,CAAC;IAhBD,iCAAG,GAAH,UAAO,GAAwB;QAC3B,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC;YAAE,OAAO,GAAG,CAAC,YAAY,CAAC;QACpD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAM,CAAC;IACtC,CAAC;IAED,iCAAG,GAAH,UAAO,GAAwB,EAAE,KAAQ;QACrC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IACjC,CAAC;IAED,oCAAM,GAAN,UAAU,GAAwB;QAC9B,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IAC7B,CAAC;IAML,0BAAC;AAAD,CAAC,AApBD,IAoBC"}

package/lib/mol-plugin/context.js

@@ -185,7 +185,7 @@ var PluginContext = /** @class */ (function () {
     };
     PluginContext.prototype.initViewer = function (canvas, container, canvas3dContext) {
         var _this = this;
-        var _a, _b, _c, _d, _e;
+        var _a, _b, _c, _d, _e, _f;
         try {
             this.layout.setRoot(container);
             if (this.spec.layout && this.spec.layout.initial)
@@ -198,19 +198,21 @@ var PluginContext = /** @class */ (function () {
                 var preserveDrawingBuffer = !((_b = this.config.get(PluginConfig.General.DisablePreserveDrawingBuffer)) !== null && _b !== void 0 ? _b : false);
                 var pixelScale = this.config.get(PluginConfig.General.PixelScale) || 1;
                 var pickScale = this.config.get(PluginConfig.General.PickScale) || 0.25;
+                var pickPadding = (_c = this.config.get(PluginConfig.General.PickPadding)) !== null && _c !== void 0 ? _c : 1;
                 var enableWboit = this.config.get(PluginConfig.General.EnableWboit) || false;
                 var preferWebGl1 = this.config.get(PluginConfig.General.PreferWebGl1) || false;
                 this.canvas3dContext = Canvas3DContext.fromCanvas(canvas, { antialias: antialias, preserveDrawingBuffer: preserveDrawingBuffer, pixelScale: pixelScale, pickScale: pickScale, enableWboit: enableWboit, preferWebGl1: preferWebGl1 });
+                this.canvas3dContext = Canvas3DContext.fromCanvas(canvas, { antialias: antialias, preserveDrawingBuffer: preserveDrawingBuffer, pixelScale: pixelScale, pickScale: pickScale, pickPadding: pickPadding, enableWboit: enableWboit });
             }
             this.canvas3d = Canvas3D.create(this.canvas3dContext);
             this.canvas3dInit.next(true);
             var props = this.spec.canvas3d;
             var backgroundColor_1 = Color(0xFCFBF9);
             if (!props) {
-                (_c = this.canvas3d) === null || _c === void 0 ? void 0 : _c.setProps({ renderer: { backgroundColor: backgroundColor_1 } });
+                (_d = this.canvas3d) === null || _d === void 0 ? void 0 : _d.setProps({ renderer: { backgroundColor: backgroundColor_1 } });
             }
             else {
-                if (((_d = props.renderer) === null || _d === void 0 ? void 0 : _d.backgroundColor) === void 0) {
+                if (((_e = props.renderer) === null || _e === void 0 ? void 0 : _e.backgroundColor) === void 0) {
                     props = produce(props, function (p) {
                         if (p.renderer)
                             p.renderer.backgroundColor = backgroundColor_1;
@@ -218,7 +220,7 @@ var PluginContext = /** @class */ (function () {
                             p.renderer = { backgroundColor: backgroundColor_1 };
                     });
                 }
-                (_e = this.canvas3d) === null || _e === void 0 ? void 0 : _e.setProps(props);
+                (_f = this.canvas3d) === null || _f === void 0 ? void 0 : _f.setProps(props);
             }
             this.animationLoop.start();
             this.helpers.viewportScreenshot = new ViewportScreenshotHelper(this);