remap loci per repr not per visual

src/mol-repr/structure/complex-representation.ts

@@ -8,7 +8,7 @@
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { StructureParams, ComplexVisual, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationState } from './representation';
 import { RepresentationContext, RepresentationParamsGetter } from '../representation';
-import { Structure } from '../../mol-model/structure';
+import { Structure, StructureElement, Link } from '../../mol-model/structure';
 import { Subject } from 'rxjs';
 import { getNextMaterialId, GraphicsRenderObject } from '../../mol-gl/render-object';
 import { createEmptyTheme, Theme } from '../../mol-theme/theme';
@@ -55,6 +55,14 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
     }
 
     function mark(loci: Loci, action: MarkerAction) {
+        if (!_structure) return false
+        if (!StructureElement.isLoci(loci) && !Link.isLoci(loci)) return false
+        if (!Structure.areParentsEquivalent(loci.structure, _structure)) return false
+        if (StructureElement.isLoci(loci)) {
+            loci = StructureElement.Loci.remap(loci, _structure)
+        } else if (Link.isLoci(loci)) {
+            loci = Link.remapLoci(loci, _structure)
+        }
         return visual ? visual.mark(loci, action) : false
     }
 

src/mol-repr/structure/units-representation.ts

@@ -11,7 +11,7 @@ import { UnitKind, UnitKindOptions } from './visual/util/common';
 import { Visual } from '../visual';
 import { StructureGroup } from './units-visual';
 import { RepresentationContext, RepresentationParamsGetter } from '../representation';
-import { Structure, Unit } from '../../mol-model/structure';
+import { Structure, Unit, StructureElement, Link } from '../../mol-model/structure';
 import { Subject } from 'rxjs';
 import { getNextMaterialId, GraphicsRenderObject } from '../../mol-gl/render-object';
 import { createEmptyTheme, Theme } from '../../mol-theme/theme';
@@ -164,6 +164,14 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
 
     function mark(loci: Loci, action: MarkerAction) {
         let changed = false
+        if (!_structure) return false
+        if (!StructureElement.isLoci(loci) && !Link.isLoci(loci)) return false
+        if (!Structure.areParentsEquivalent(loci.structure, _structure)) return false
+        if (StructureElement.isLoci(loci)) {
+            loci = StructureElement.Loci.remap(loci, _structure)
+        } else if (Link.isLoci(loci)) {
+            loci = Link.remapLoci(loci, _structure)
+        }
         visuals.forEach(({ visual }) => {
             changed = visual.mark(loci, action) || changed
         })

src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts

@@ -119,8 +119,7 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
 function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
     let changed = false
     if (Link.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = Link.remapLoci(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         const { getLinkIndex } = structure.carbohydrates
         for (const l of loci.links) {
             const idx = getLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
@@ -129,8 +128,7 @@ function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval
             }
         }
     } else if (StructureElement.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = StructureElement.Loci.remap(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         // TODO mark link only when both of the link elements are in a StructureElement.Loci
         const { getElementIndex, getLinkIndices, elements } = structure.carbohydrates
         for (const e of loci.elements) {

src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts

@@ -196,8 +196,7 @@ function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: In
     const { getElementIndex, getAnomericCarbons } = structure.carbohydrates
     let changed = false
     if (!StructureElement.isLoci(loci)) return false
-    if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-    loci = StructureElement.Loci.remap(loci, structure)
+    if (!Structure.areEquivalent(loci.structure, structure)) return false
     for (const e of loci.elements) {
         // TODO make more efficient by handling/grouping `e.indices` by residue index
         // TODO only call apply when the full alt-residue of the unit is part of `e`

src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts

@@ -133,8 +133,7 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
     const { getTerminalLinkIndex } = structure.carbohydrates
     let changed = false
     if (Link.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = Link.remapLoci(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         for (const l of loci.links) {
             const idx = getTerminalLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
             if (idx !== undefined) {
@@ -142,8 +141,7 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
             }
         }
     } else if (StructureElement.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = StructureElement.Loci.remap(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         // TODO mark link only when both of the link elements are in a StructureElement.Loci
         const { getElementIndex, getTerminalLinkIndices, elements } = structure.carbohydrates
         for (const e of loci.elements) {

src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts

@@ -107,8 +107,7 @@ function eachCrossLink(loci: Loci, structure: Structure, apply: (interval: Inter
     const crossLinks = structure.crossLinkRestraints
     let changed = false
     if (Link.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = Link.remapLoci(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         for (const b of loci.links) {
             const indices = crossLinks.getPairIndices(b.aIndex, b.aUnit, b.bIndex, b.bUnit)
             if (indices) {

src/mol-repr/structure/visual/inter-unit-link-cylinder.ts

@@ -97,8 +97,7 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
 function eachLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
     let changed = false
     if (Link.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = Link.remapLoci(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         for (const b of loci.links) {
             const idx = structure.links.getBondIndex(b.aIndex, b.aUnit, b.bIndex, b.bUnit)
             if (idx !== -1) {
@@ -106,8 +105,7 @@ function eachLink(loci: Loci, structure: Structure, apply: (interval: Interval)
             }
         }
     } else if (StructureElement.isLoci(loci)) {
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = StructureElement.Loci.remap(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         // TODO mark link only when both of the link elements are in a StructureElement.Loci
         for (const e of loci.elements) {
             OrderedSet.forEach(e.indices, v => {

src/mol-repr/structure/visual/intra-unit-link-cylinder.ts

@@ -121,8 +121,7 @@ function eachLink(loci: Loci, structureGroup: StructureGroup, apply: (interval:
     let changed = false
     if (Link.isLoci(loci)) {
         const { structure, group } = structureGroup
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = Link.remapLoci(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         const unit = group.units[0]
         if (!Unit.isAtomic(unit)) return false
         const groupCount = unit.links.edgeCount * 2
@@ -137,8 +136,7 @@ function eachLink(loci: Loci, structureGroup: StructureGroup, apply: (interval:
         }
     } else if (StructureElement.isLoci(loci)) {
         const { structure, group } = structureGroup
-        if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-        loci = StructureElement.Loci.remap(loci, structure)
+        if (!Structure.areEquivalent(loci.structure, structure)) return false
         const unit = group.units[0]
         if (!Unit.isAtomic(unit)) return false
         const groupCount = unit.links.edgeCount * 2

src/mol-repr/structure/visual/util/element.ts

@@ -72,8 +72,7 @@ export function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (
     let changed = false
     if (!StructureElement.isLoci(loci)) return false
     const { structure, group } = structureGroup
-    if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-    loci = StructureElement.Loci.remap(loci, structure)
+    if (!Structure.areEquivalent(loci.structure, structure)) return false
     const elementCount = group.elements.length
     for (const e of loci.elements) {
         const unitIdx = group.unitIndexMap.get(e.unit.id)

src/mol-repr/structure/visual/util/nucleotide.ts

@@ -45,8 +45,7 @@ export function eachNucleotideElement(loci: Loci, structureGroup: StructureGroup
     let changed = false
     if (!StructureElement.isLoci(loci)) return false
     const { structure, group } = structureGroup
-    if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-    loci = StructureElement.Loci.remap(loci, structure)
+    if (!Structure.areEquivalent(loci.structure, structure)) return false
     const unit = group.units[0]
     if (!Unit.isAtomic(unit)) return false
     const { nucleotideElements, model, elements } = unit

src/mol-repr/structure/visual/util/polymer.ts

@@ -95,8 +95,7 @@ export function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, a
     let changed = false
     if (!StructureElement.isLoci(loci)) return false
     const { structure, group } = structureGroup
-    if (!Structure.areParentsEquivalent(loci.structure, structure)) return false
-    loci = StructureElement.Loci.remap(loci, structure)
+    if (!Structure.areEquivalent(loci.structure, structure)) return false
     const { polymerElements, model, elements } = group.units[0]
     const { index, offsets } = model.atomicHierarchy.residueAtomSegments
     const { traceElementIndex } = model.atomicHierarchy.derived.residue