diff --git a/src/mol-geo/geometry/mesh/builder/tube.ts b/src/mol-geo/geometry/mesh/builder/tube.ts
index d60dd528dae400f318347d87753903715b48f367..693bc69d8cd9d0a90ed6f3160f1dab7db7170a56 100644
--- a/src/mol-geo/geometry/mesh/builder/tube.ts
+++ b/src/mol-geo/geometry/mesh/builder/tube.ts
@@ -27,7 +27,7 @@ function add3AndScale2(out: Vec3, a: Vec3, b: Vec3, c: Vec3, sa: number, sb: num
out[2] = (a[2] * sa) + (b[2] * sb) + c[2];
}
-export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, linearSegments: number, radialSegments: number, width: number, height: number, waveFactor: number, startCap: boolean, endCap: boolean) {
+export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, linearSegments: number, radialSegments: number, widthValues: ArrayLike<number>, heightValues: ArrayLike<number>, waveFactor: number, startCap: boolean, endCap: boolean) {
const { currentGroup, vertices, normals, indices, groups } = state
let vertexCount = vertices.elementCount
@@ -39,6 +39,9 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
Vec3.fromArray(v, binormalVectors, i3)
Vec3.fromArray(controlPoint, controlPoints, i3)
+ const width = widthValues[i]
+ const height = heightValues[i]
+
const tt = di * i - 0.5;
const ff = 1 + (waveFactor - 1) * (Math.cos(2 * Math.PI * tt) + 1);
const w = ff * width, h = ff * height;
@@ -83,6 +86,9 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
ChunkedArray.add3(vertices, controlPoint[0], controlPoint[1], controlPoint[2]);
ChunkedArray.add3(normals, normalVector[0], normalVector[1], normalVector[2]);
+ const width = widthValues[0]
+ const height = heightValues[0]
+
vertexCount = vertices.elementCount
for (let i = 0; i < radialSegments; ++i) {
const t = 2 * Math.PI * i / radialSegments;
@@ -112,6 +118,9 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
ChunkedArray.add3(vertices, controlPoint[0], controlPoint[1], controlPoint[2]);
ChunkedArray.add3(normals, normalVector[0], normalVector[1], normalVector[2]);
+ const width = widthValues[linearSegments]
+ const height = heightValues[linearSegments]
+
vertexCount = vertices.elementCount
for (let i = 0; i < radialSegments; ++i) {
const t = 2 * Math.PI * i / radialSegments
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index deb5042742b2b45d282c1fedbbca8d1285f26f95..1da10764176ca24e053608db0e38aa325d3be4db 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -7,7 +7,7 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement } from './util/polymer';
+import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement, interpolateSizes } from './util/polymer';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
import { ParamDefinition as PD } from 'mol-util/param-definition';
@@ -41,7 +41,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
const isCoarse = Unit.isCoarse(unit)
const state = createCurveSegmentState(linearSegments)
- const { curvePoints, normalVectors, binormalVectors } = state
+ const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state
let i = 0
const polymerTraceIt = PolymerTraceIterator(unit)
@@ -57,24 +57,39 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
interpolateCurveSegment(state, v, tension, shift)
- let width = theme.size.size(v.center) * sizeFactor
- if (isCoarse) width *= aspectRatio / 2
+ let w0 = theme.size.size(v.centerPrev) * sizeFactor
+ let w1 = theme.size.size(v.center) * sizeFactor
+ let w2 = theme.size.size(v.centerNext) * sizeFactor
+ if (isCoarse) {
+ w0 *= aspectRatio / 2
+ w1 *= aspectRatio / 2
+ w2 *= aspectRatio / 2
+ }
if (isSheet) {
- const height = width * aspectRatio
- const arrowHeight = v.secStrucLast ? height * arrowFactor : 0
- addSheet(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, width, height, arrowHeight, v.secStrucFirst, v.secStrucLast)
+ const h1 = w1 * aspectRatio
+ const arrowHeight = v.secStrucLast ? h1 * arrowFactor : 0
+ addSheet(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, w1, h1, arrowHeight, v.secStrucFirst, v.secStrucLast)
} else {
- let height: number
+ let h0: number, h1: number, h2: number
if (isHelix) {
- height = width * aspectRatio
+ h0 = w0 * aspectRatio
+ h1 = w1 * aspectRatio
+ h2 = w2 * aspectRatio
} else if (isNucleicType) {
- height = width * aspectRatio;
- [width, height] = [height, width]
+ h0 = w0 * aspectRatio;
+ [w0, h0] = [h0, w0]
+ h1 = w1 * aspectRatio;
+ [w1, h1] = [h1, w1]
+ h2 = w2 * aspectRatio;
+ [w2, h2] = [h2, w2]
} else {
- height = width
+ h0 = w0
+ h1 = w1
+ h2 = w2
}
- addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, width, height, 1, v.secStrucFirst, v.secStrucLast)
+ interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift)
+ addTube(builderState, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, 1, v.secStrucFirst, v.secStrucLast)
}
++i
diff --git a/src/mol-repr/structure/visual/util/polymer/curve-segment.ts b/src/mol-repr/structure/visual/util/polymer/curve-segment.ts
index 1231c6bb0f9e160f9ed62b36cae038b867f9c2f8..07ebb90f650415900756038b8a3d779e3df85a9a 100644
--- a/src/mol-repr/structure/visual/util/polymer/curve-segment.ts
+++ b/src/mol-repr/structure/visual/util/polymer/curve-segment.ts
@@ -6,12 +6,15 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { NumberArray } from 'mol-util/type-helpers';
+import { lerp } from 'mol-math/interpolate';
export interface CurveSegmentState {
curvePoints: NumberArray,
tangentVectors: NumberArray,
normalVectors: NumberArray,
binormalVectors: NumberArray,
+ widthValues: NumberArray,
+ heightValues: NumberArray,
linearSegments: number
}
@@ -21,12 +24,15 @@ export interface CurveSegmentControls {
}
export function createCurveSegmentState(linearSegments: number): CurveSegmentState {
- const pn = (linearSegments + 1) * 3
+ const n = linearSegments + 1
+ const pn = n * 3
return {
curvePoints: new Float32Array(pn),
tangentVectors: new Float32Array(pn),
normalVectors: new Float32Array(pn),
binormalVectors: new Float32Array(pn),
+ widthValues: new Float32Array(n),
+ heightValues: new Float32Array(n),
linearSegments
}
}
@@ -112,4 +118,21 @@ export function interpolateNormals(state: CurveSegmentState, controls: CurveSegm
Vec3.normalize(binormalVec, Vec3.cross(binormalVec, tangentVec, normalVec))
Vec3.toArray(binormalVec, binormalVectors, i * 3)
}
+}
+
+export function interpolateSizes(state: CurveSegmentState, w0: number, w1: number, w2: number, h0: number, h1: number, h2: number, shift: number) {
+ const { widthValues, heightValues, linearSegments } = state
+
+ const shift1 = 1 - shift
+
+ for (let i = 0; i <= linearSegments; ++i) {
+ const t = i * 1.0 / linearSegments;
+ if (t < shift1) {
+ widthValues[i] = lerp(w0, w1, t + shift)
+ heightValues[i] = lerp(h0, h1, t + shift)
+ } else {
+ widthValues[i] = lerp(w1, w2, t - shift1)
+ heightValues[i] = lerp(h1, h2, t - shift1)
+ }
+ }
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index fa3d7555572402e4978bbbb5ad81c5e46a48340f..5332a697035c9b1f42f7ed175fb709af5280caa0 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -29,6 +29,8 @@ export function PolymerTraceIterator(unit: Unit): Iterator<PolymerTraceElement>
interface PolymerTraceElement {
center: StructureElement
+ centerPrev: StructureElement
+ centerNext: StructureElement
first: boolean, last: boolean
secStrucFirst: boolean, secStrucLast: boolean
secStrucType: SecondaryStructureType
@@ -43,6 +45,8 @@ const SecStrucTypeNA = SecondaryStructureType.create(SecondaryStructureType.Flag
function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
return {
center: StructureElement.create(unit),
+ centerPrev: StructureElement.create(unit),
+ centerNext: StructureElement.create(unit),
first: false, last: false,
secStrucFirst: false, secStrucLast: false,
secStrucType: SecStrucTypeNA,
@@ -154,23 +158,35 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
this.nextSecStrucType = residueIt.hasNext ? this.secondaryStructureType[residueIndex + 1] : SecStrucTypeNA
value.secStrucType = this.currSecStrucType
- value.center.element = this.traceElementIndex[residueIndex]
value.first = residueIndex === this.residueSegmentMin
value.last = residueIndex === this.residueSegmentMax
value.secStrucFirst = this.prevSecStrucType !== this.currSecStrucType
value.secStrucLast = this.currSecStrucType !== this.nextSecStrucType
value.moleculeType = this.moleculeType[residueIndex]
+ const residueIndexPrev3 = this.getResidueIndex(residueIndex - 3)
+ const residueIndexPrev2 = this.getResidueIndex(residueIndex - 2)
+ const residueIndexPrev1 = this.getResidueIndex(residueIndex - 1)
+ const residueIndexNext1 = this.getResidueIndex(residueIndex + 1)
+ const residueIndexNext2 = this.getResidueIndex(residueIndex + 2)
+ const residueIndexNext3 = this.getResidueIndex(residueIndex + 3)
+
if (value.first) {
- this.pos(this.p0, this.traceElementIndex[this.getResidueIndex(residueIndex - 3)])
- this.pos(this.p1, this.traceElementIndex[this.getResidueIndex(residueIndex - 2)])
- this.pos(this.p2, this.traceElementIndex[this.getResidueIndex(residueIndex - 1)])
- this.pos(this.p3, value.center.element)
- this.pos(this.p4, this.traceElementIndex[this.getResidueIndex(residueIndex + 1)])
- this.pos(this.p5, this.traceElementIndex[this.getResidueIndex(residueIndex + 2)])
-
- this.pos(this.v12, this.directionElementIndex[this.getResidueIndex(residueIndex - 1)])
+ value.centerPrev.element = this.traceElementIndex[residueIndexPrev1]
+ value.center.element = this.traceElementIndex[residueIndex]
+
+ this.pos(this.p0, this.traceElementIndex[residueIndexPrev3])
+ this.pos(this.p1, this.traceElementIndex[residueIndexPrev2])
+ this.pos(this.p2, this.traceElementIndex[residueIndexPrev1])
+ this.pos(this.p3, this.traceElementIndex[residueIndex])
+ this.pos(this.p4, this.traceElementIndex[residueIndexNext1])
+ this.pos(this.p5, this.traceElementIndex[residueIndexNext2])
+
+ this.pos(this.v12, this.directionElementIndex[residueIndexPrev1])
} else {
+ value.centerPrev.element = value.center.element
+ value.center.element = value.centerNext.element
+
Vec3.copy(this.p0, this.p1)
Vec3.copy(this.p1, this.p2)
Vec3.copy(this.p2, this.p3)
@@ -180,14 +196,15 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
Vec3.copy(this.v12, this.v23)
}
- this.pos(this.p6, this.traceElementIndex[this.getResidueIndex(residueIndex + 3 as ResidueIndex)])
+ value.centerNext.element = this.traceElementIndex[residueIndexNext1]
+ this.pos(this.p6, this.traceElementIndex[residueIndexNext3])
this.pos(this.v23, this.directionElementIndex[residueIndex])
- this.setControlPoint(value.p0, this.p0, this.p1, this.p2, residueIndex - 2 as ResidueIndex)
- this.setControlPoint(value.p1, this.p1, this.p2, this.p3, residueIndex - 1 as ResidueIndex)
+ this.setControlPoint(value.p0, this.p0, this.p1, this.p2, residueIndexPrev2)
+ this.setControlPoint(value.p1, this.p1, this.p2, this.p3, residueIndexPrev1)
this.setControlPoint(value.p2, this.p2, this.p3, this.p4, residueIndex)
- this.setControlPoint(value.p3, this.p3, this.p4, this.p5, residueIndex + 1 as ResidueIndex)
- this.setControlPoint(value.p4, this.p4, this.p5, this.p6, residueIndex + 2 as ResidueIndex)
+ this.setControlPoint(value.p3, this.p3, this.p4, this.p5, residueIndexNext1)
+ this.setControlPoint(value.p4, this.p4, this.p5, this.p6, residueIndexNext2)
Vec3.copy(value.d12, this.v12)
Vec3.copy(value.d23, this.v23)
@@ -228,8 +245,11 @@ export class CoarsePolymerTraceIterator implements Iterator<PolymerTraceElement>
private elementIndex: number
hasNext: boolean = false;
+ private getElementIndex(elementIndex: number) {
+ return Math.min(Math.max(this.polymerSegment.start, elementIndex), this.polymerSegment.end - 1) as ElementIndex
+ }
+
private pos(target: Vec3, elementIndex: number) {
- elementIndex = Math.min(Math.max(this.polymerSegment.start, elementIndex), this.polymerSegment.end - 1)
const index = this.unit.elements[elementIndex]
target[0] = this.conformation.x[index]
target[1] = this.conformation.y[index]
@@ -251,13 +271,21 @@ export class CoarsePolymerTraceIterator implements Iterator<PolymerTraceElement>
if (this.state === CoarsePolymerTraceIteratorState.nextElement) {
this.elementIndex += 1
+
+ const elementIndexPrev2 = this.getElementIndex(this.elementIndex - 2)
+ const elementIndexPrev1 = this.getElementIndex(this.elementIndex - 1)
+ const elementIndexNext1 = this.getElementIndex(this.elementIndex + 1)
+ const elementIndexNext2 = this.getElementIndex(this.elementIndex + 2)
+
+ this.value.centerPrev.element = this.value.center.unit.elements[elementIndexPrev1]
this.value.center.element = this.value.center.unit.elements[this.elementIndex]
+ this.value.centerNext.element = this.value.center.unit.elements[elementIndexNext1]
- this.pos(this.value.p0, this.elementIndex - 2)
- this.pos(this.value.p1, this.elementIndex - 1)
+ this.pos(this.value.p0, elementIndexPrev2)
+ this.pos(this.value.p1, elementIndexPrev1)
this.pos(this.value.p2, this.elementIndex)
- this.pos(this.value.p3, this.elementIndex + 1)
- this.pos(this.value.p4, this.elementIndex + 2)
+ this.pos(this.value.p3, elementIndexNext1)
+ this.pos(this.value.p4, elementIndexNext2)
this.value.first = this.elementIndex === this.polymerSegment.start
this.value.last = this.elementIndex === this.polymerSegment.end - 1