fix/improve canRemap handling in IntraUnitBonds

CHANGELOG.md

@@ -18,6 +18,7 @@ Note that since we don't clearly distinguish between a public and private interf
     - Reuse unit boundary if sphere has not changed too much
     - Don't show 'inter-bond' and 'element-cross' visuals in line representations of polymerAndLigand preset
 - Fix additional mononucleotides detected as polymer components
+- Fix and improve ``canRemap`` handling in ``IntraUnitBonds``
 
 ## [v3.2.0] - 2022-02-17
 

src/mol-model/structure/structure/unit.ts

@@ -223,7 +223,12 @@ namespace Unit {
 
         remapModel(model: Model, dynamicBonds: boolean, props?: AtomicProperties) {
             if (!props) {
-                props = { ...this.props, bonds: dynamicBonds ? undefined : tryRemapBonds(this, this.props.bonds, model) };
+                props = {
+                    ...this.props,
+                    bonds: dynamicBonds && !this.props.bonds?.props?.canRemap
+                        ? undefined
+                        : tryRemapBonds(this, this.props.bonds, model, dynamicBonds)
+                };
                 if (!Unit.isSameConformation(this, model)) {
                     const b = props.boundary;
                     if (b) {
@@ -502,7 +507,7 @@ namespace Unit {
         return isSameConformation(a, b.model);
     }
 
-    function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model) {
+    function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model, dynamicBonds: boolean) {
         // TODO: should include additional checks?
 
         if (!old) return void 0;
@@ -516,7 +521,7 @@ namespace Unit {
             return void 0;
         }
 
-        if (old.props?.canRemap) {
+        if (old.props?.canRemap || !dynamicBonds) {
             return old;
         }
         return isSameConformation(a, model) ? old : void 0;

src/mol-model/structure/structure/unit/bonds/data.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -12,7 +12,13 @@ import { StructureElement } from '../../element';
 import { Bond } from '../bonds';
 import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
 
-type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, { readonly order: ArrayLike<number>, readonly flags: ArrayLike<BondType.Flag> }, { readonly canRemap?: boolean }>
+type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
+    readonly order: ArrayLike<number>,
+    readonly flags: ArrayLike<BondType.Flag>
+}, {
+    /** can remap even with dynamicBonds on, e.g., for water molecules */
+    readonly canRemap?: boolean
+}>
 
 namespace IntraUnitBonds {
     export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -141,7 +141,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
         const aI = atoms[_aI];
 
         const elemA = type_symbol.value(aI);
-        if (isWatery && (elemA !== 'H' || elemA !== 'O')) isWatery = false;
+        if (isWatery && (elemA !== 'H' && elemA !== 'O')) isWatery = false;
 
         const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
         let hasStructConn = false;