fix bond atoms not added in selection manager

CHANGELOG.md

@@ -7,7 +7,7 @@ Note that since we don't clearly distinguish between a public and private interf
 ## [Unreleased]
 
 - Add Charmm saccharide names
-- Treat missing occupancy column as occupany of 1
+- Treat missing occupancy column as occupancy of 1
 - Fix line shader not accounting for aspect ratio
 - [Breaking] Fix point repr & shader
     - Was unusable with ``wboit``
@@ -16,6 +16,7 @@ Note that since we don't clearly distinguish between a public and private interf
     - Set ``sizeTheme`` to ``uniform`` by default
 - Fix pickScale not taken into account in line/point shader
 - Add pixel-scale & pick-scale GET params to Viewer app
+- Fix selecting bonds not adding their atoms in selection manager
 
 ## [v2.3.0] - 2021-09-06
 

src/mol-model/loci.ts

@@ -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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -283,8 +283,8 @@ namespace Loci {
      * Converts structure related loci to StructureElement.Loci and applies
      * granularity if given
      */
-    export function normalize(loci: Loci, granularity?: Granularity) {
-        if (granularity !== 'element' && Bond.isLoci(loci)) {
+    export function normalize(loci: Loci, granularity?: Granularity, alwaysConvertBonds = false) {
+        if ((granularity !== 'element' || alwaysConvertBonds) && Bond.isLoci(loci)) {
             // convert Bond.Loci to a StructureElement.Loci so granularity can be applied
             loci = Bond.toStructureElementLoci(loci);
         }

src/mol-plugin-state/manager/interactivity.ts

@@ -101,10 +101,10 @@ namespace InteractivityManager {
             // TODO clear, then re-apply remaining providers
         }
 
-        protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity = true) {
+        protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity: boolean, alwaysConvertBonds = false) {
             const { loci, repr } = reprLoci;
             const granularity = applyGranularity ? this.props.granularity : undefined;
-            return { loci: Loci.normalize(loci, granularity), repr };
+            return { loci: Loci.normalize(loci, granularity, alwaysConvertBonds), repr };
         }
 
         protected mark(current: Representation.Loci, action: MarkerAction, noRender = false) {
@@ -187,7 +187,8 @@ namespace InteractivityManager {
         toggle(current: Representation.Loci, applyGranularity = true) {
             if (Loci.isEmpty(current.loci)) return;
 
-            const normalized = this.normalizedLoci(current, applyGranularity);
+            const normalized = this.normalizedLoci(current, applyGranularity, true);
+
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.toggleSel(normalized);
             } else {
@@ -198,7 +199,7 @@ namespace InteractivityManager {
         toggleExtend(current: Representation.Loci, applyGranularity = true) {
             if (Loci.isEmpty(current.loci)) return;
 
-            const normalized = this.normalizedLoci(current, applyGranularity);
+            const normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 const loci = this.sel.tryGetRange(normalized.loci) || normalized.loci;
                 this.toggleSel({ loci, repr: normalized.repr });
@@ -206,7 +207,7 @@ namespace InteractivityManager {
         }
 
         select(current: Representation.Loci, applyGranularity = true) {
-            const normalized = this.normalizedLoci(current, applyGranularity);
+            const normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('add', normalized.loci);
             }
@@ -214,7 +215,7 @@ namespace InteractivityManager {
         }
 
         selectJoin(current: Representation.Loci, applyGranularity = true) {
-            const normalized = this.normalizedLoci(current, applyGranularity);
+            const normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('intersect', normalized.loci);
             }
@@ -222,7 +223,7 @@ namespace InteractivityManager {
         }
 
         selectOnly(current: Representation.Loci, applyGranularity = true) {
-            const normalized = this.normalizedLoci(current, applyGranularity);
+            const normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 // only deselect for the structure of the given loci
                 this.deselect({ loci: Structure.toStructureElementLoci(normalized.loci.structure), repr: normalized.repr }, false);
@@ -232,7 +233,7 @@ namespace InteractivityManager {
         }
 
         deselect(current: Representation.Loci, applyGranularity = true) {
-            const normalized = this.normalizedLoci(current, applyGranularity);
+            const normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('remove', normalized.loci);
             }
@@ -255,8 +256,9 @@ namespace InteractivityManager {
                     // do a full deselect/select for the current structure so visuals that are
                     // marked with granularity unequal to 'element' and join/intersect operations
                     // are handled properly
-                    super.mark({ loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, true);
-                    super.mark({ loci: this.sel.getLoci(loci.structure) }, MarkerAction.Select);
+                    const selLoci = this.sel.getLoci(loci.structure);
+                    super.mark({ loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, !Loci.isEmpty(selLoci));
+                    super.mark({ loci: selLoci }, MarkerAction.Select);
                 } else {
                     super.mark(current, action);
                 }