diff --git a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
index 2416ef089851893f697d471c8f200e9df4bb5662..b6eaf79647a2004288a76212be17ce0f6090618a 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -16,6 +16,7 @@ import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/
import { StructureElementIterator } from './util/location-iterator';
import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
+import { OrderedSet } from 'mol-data/int';
const t = Mat4.identity()
const sVec = Vec3.zero()
@@ -48,7 +49,7 @@ async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit,
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setId(v.center.element)
+ builder.setId(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
const isNucleic = v.moleculeType === MoleculeType.DNA || v.moleculeType === MoleculeType.RNA
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
diff --git a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
index 86ee412bf4c70f4ec68f00c75b8e429cea4cb553..da04a008c769a1214ee024875f64ee4dbe317e84 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -15,6 +15,7 @@ import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/
import { StructureElementIterator } from './util/location-iterator';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
+import { OrderedSet } from 'mol-data/int';
export interface PolymerTraceMeshProps {
sizeTheme: SizeThemeProps
@@ -43,7 +44,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, props: Po
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setId(v.center.element)
+ builder.setId(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
const isNucleic = v.moleculeType === MoleculeType.DNA || v.moleculeType === MoleculeType.RNA
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
diff --git a/src/mol-geo/representation/structure/visual/util/location-iterator.ts b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
index 79e58062934db58cf38f5e31a5ae0faf913d73ec..aad0da64abdedce9ec3d4221379b91f56e256255 100644
--- a/src/mol-geo/representation/structure/visual/util/location-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
@@ -103,7 +103,7 @@ export namespace StructureElementIterator {
const elementCount = group.elements.length
const instanceCount = group.units.length
const location = StructureElement.create(unit)
- const getLocation = (elementIndex: number, instanceIndex: number) => {
+ const getLocation = (elementIndex: number) => {
location.element = unit.elements[elementIndex]
return location
}
@@ -117,7 +117,7 @@ export namespace LinkIterator {
const elementCount = Unit.isAtomic(unit) ? unit.links.edgeCount * 2 : 0
const instanceCount = group.units.length
const location = StructureElement.create(unit)
- const getLocation = (elementIndex: number, instanceIndex: number) => {
+ const getLocation = (elementIndex: number) => {
location.element = unit.elements[(unit as Unit.Atomic).links.a[elementIndex]]
return location
}
@@ -128,7 +128,7 @@ export namespace LinkIterator {
const elementCount = structure.links.bondCount
const instanceCount = 1
const location = Link.Location()
- const getLocation = (elementIndex: number, instanceIndex: number) => {
+ const getLocation = (elementIndex: number) => {
const bond = structure.links.bonds[elementIndex]
location.aUnit = bond.unitA
location.aIndex = bond.indexA as StructureElement.UnitIndex
diff --git a/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts b/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
index e304208088159359912777b228740c80288d120c..df4cfabc5ae57639e16fed87086ab7af9f5f78ec 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
@@ -5,7 +5,7 @@
*/
import { Unit, StructureElement, ElementIndex, ResidueIndex } from 'mol-model/structure';
-import { Segmentation, SortedArray } from 'mol-data/int';
+import { Segmentation } from 'mol-data/int';
import { MoleculeType, SecondaryStructureType, AtomRole } from 'mol-model/structure/model/types';
import Iterator from 'mol-data/iterator';
import { Vec3 } from 'mol-math/linear-algebra';
@@ -94,7 +94,6 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (residueIndex < this.residueSegmentMin) {
const cyclicIndex = cyclicPolymerMap.get(this.residueSegmentMin)
if (cyclicIndex !== undefined) {
-
residueIndex = cyclicIndex - (this.residueSegmentMin - residueIndex - 1) as ResidueIndex
} else {
residueIndex = this.residueSegmentMin
@@ -107,17 +106,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
residueIndex = this.residueSegmentMax
}
}
- return getElementIndexForAtomRole(this.unit.model, residueIndex as ResidueIndex, atomRole)
- }
-
- private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
- const index = this.getAtomIndex(residueIndex, atomRole)
- // TODO handle case when it returns -1
- const elementIndex = SortedArray.indexOf(this.unit.elements, index) as ElementIndex
- if (elementIndex === -1) {
- console.log('-1', residueIndex, atomRole, index)
- }
- return elementIndex === -1 ? 0 as ElementIndex : elementIndex
+ return getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
}
private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
@@ -146,7 +135,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (this.state === AtomicPolymerTraceIteratorState.nextResidue) {
const { index: residueIndex } = residueIt.move();
- value.center.element = this.getElementIndex(residueIndex, 'trace')
+ value.center.element = this.getAtomIndex(residueIndex, 'trace')
this.pos(this.p0, this.getAtomIndex(residueIndex - 3 as ResidueIndex, 'trace'))
this.pos(this.p1, this.getAtomIndex(residueIndex - 2 as ResidueIndex, 'trace'))
diff --git a/src/mol-geo/util/color-data.ts b/src/mol-geo/util/color-data.ts
index 5b89a4a07850aec6adc35bf89e90c90430352911..47e7eaf1d2383bdcc81eebf46a45d6864b1fb913 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -77,8 +77,8 @@ export function createInstanceColor(locationIt: LocationIterator, colorFn: Locat
const { instanceCount} = locationIt
const colors = colorData && colorData.tColor.ref.value.array.length >= instanceCount * 3 ? colorData.tColor.ref.value : createTextureImage(instanceCount, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const v = locationIt.move()
- Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.instanceIndex * 3)
+ const { location, isSecondary, instanceIndex } = locationIt.move()
+ Color.toArray(colorFn(location, isSecondary), colors.array, instanceIndex * 3)
locationIt.skipInstance()
}
return createTextureColor(colors, 'instance', colorData)
@@ -89,9 +89,8 @@ export function createElementColor(locationIt: LocationIterator, colorFn: Locati
const { elementCount } = locationIt
const colors = colorData && colorData.tColor.ref.value.array.length >= elementCount * 3 ? colorData.tColor.ref.value : createTextureImage(elementCount, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const v = locationIt.move()
- // console.log(v)
- Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.elementIndex * 3)
+ const { location, isSecondary, elementIndex } = locationIt.move()
+ Color.toArray(colorFn(location, isSecondary), colors.array, elementIndex * 3)
}
return createTextureColor(colors, 'element', colorData)
}
@@ -102,8 +101,8 @@ export function createElementInstanceColor(locationIt: LocationIterator, colorFn
const count = instanceCount * elementCount
const colors = colorData && colorData.tColor.ref.value.array.length >= count * 3 ? colorData.tColor.ref.value : createTextureImage(count, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const v = locationIt.move()
- Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.index * 3)
+ const { location, isSecondary, index } = locationIt.move()
+ Color.toArray(colorFn(location, isSecondary), colors.array, index * 3)
}
return createTextureColor(colors, 'elementInstance', colorData)
}
\ No newline at end of file