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Commit 15782111 authored by Alexander Rose's avatar Alexander Rose
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add helix profile option to cartoon repr

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CHANGELOG.md
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View file @ 15782111
...@@ -9,6 +9,7 @@ Note that since we don't clearly distinguish between a public and private interf ...@@ -9,6 +9,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Added ``ViewerOptions.collapseRightPanel`` - Added ``ViewerOptions.collapseRightPanel``
- Added ``Viewer.loadTrajectory`` to support loading "composed" trajectories (e.g. from gro + xtc) - Added ``Viewer.loadTrajectory`` to support loading "composed" trajectories (e.g. from gro + xtc)
- Fix: handle parent in Structure.remapModel - Fix: handle parent in Structure.remapModel
- Add ``rounded`` and ``square`` helix profile options to Cartoon representation (in addition to the default ``elliptical``)
## [v2.3.6] - 2021-11-8 ## [v2.3.6] - 2021-11-8
......
src/mol-geo/geometry/mesh/builder/sheet.ts
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/** /**
* 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> * @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com> * @author David Sehnal <david.sehnal@gmail.com>
...@@ -40,7 +40,7 @@ const v3set = Vec3.set; ...@@ -40,7 +40,7 @@ const v3set = Vec3.set;
const caAdd3 = ChunkedArray.add3; const caAdd3 = ChunkedArray.add3;
const caAdd = ChunkedArray.add; const caAdd = ChunkedArray.add;
function addCap(offset: number, state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, width: number, leftHeight: number, rightHeight: number) { function addCap(offset: number, state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, width: number, leftHeight: number, rightHeight: number, flip: boolean) {
const { vertices, normals, indices } = state; const { vertices, normals, indices } = state;
const vertexCount = vertices.elementCount; const vertexCount = vertices.elementCount;
...@@ -74,11 +74,19 @@ function addCap(offset: number, state: MeshBuilder.State, controlPoints: ArrayLi ...@@ -74,11 +74,19 @@ function addCap(offset: number, state: MeshBuilder.State, controlPoints: ArrayLi
v3copy(verticalVector, verticalLeftVector); v3copy(verticalVector, verticalLeftVector);
} }
for (let i = 0; i < 4; ++i) { if (flip) {
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]); for (let i = 0; i < 4; ++i) {
caAdd3(normals, -normalVector[0], -normalVector[1], -normalVector[2]);
}
caAdd3(indices, vertexCount, vertexCount + 1, vertexCount + 2);
caAdd3(indices, vertexCount + 2, vertexCount + 3, vertexCount);
} else {
for (let i = 0; i < 4; ++i) {
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
}
caAdd3(indices, vertexCount + 2, vertexCount + 1, vertexCount);
caAdd3(indices, vertexCount, vertexCount + 3, vertexCount + 2);
} }
caAdd3(indices, vertexCount + 2, vertexCount + 1, vertexCount);
caAdd3(indices, vertexCount, vertexCount + 3, vertexCount + 2);
} }
/** set arrowHeight = 0 for no arrow */ /** set arrowHeight = 0 for no arrow */
...@@ -193,19 +201,18 @@ export function addSheet(state: MeshBuilder.State, controlPoints: ArrayLike<numb ...@@ -193,19 +201,18 @@ export function addSheet(state: MeshBuilder.State, controlPoints: ArrayLike<numb
const width = widthValues[0]; const width = widthValues[0];
const height = heightValues[0]; const height = heightValues[0];
const h = arrowHeight === 0 ? height : arrowHeight; const h = arrowHeight === 0 ? height : arrowHeight;
addCap(0, state, controlPoints, normalVectors, binormalVectors, width, h, h); addCap(0, state, controlPoints, normalVectors, binormalVectors, width, h, h, false);
} else if (arrowHeight > 0) { } else if (arrowHeight > 0) {
const width = widthValues[0]; const width = widthValues[0];
const height = heightValues[0]; const height = heightValues[0];
addCap(0, state, controlPoints, normalVectors, binormalVectors, width, arrowHeight, -height); addCap(0, state, controlPoints, normalVectors, binormalVectors, width, arrowHeight, -height, false);
addCap(0, state, controlPoints, normalVectors, binormalVectors, width, -arrowHeight, height); addCap(0, state, controlPoints, normalVectors, binormalVectors, width, -arrowHeight, height, false);
} }
if (endCap && arrowHeight === 0) { if (endCap && arrowHeight === 0) {
const width = widthValues[linearSegments]; const width = widthValues[linearSegments];
const height = heightValues[linearSegments]; const height = heightValues[linearSegments];
// use negative height to flip the direction the cap's triangles are facing addCap(linearSegments * 3, state, controlPoints, normalVectors, binormalVectors, width, height, height, true);
addCap(linearSegments * 3, state, controlPoints, normalVectors, binormalVectors, width, -height, -height);
} }
const addedVertexCount = (linearSegments + 1) * 8 + const addedVertexCount = (linearSegments + 1) * 8 +
......
src/mol-geo/geometry/mesh/builder/tube.ts
+ 60
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View file @ 15782111
/** /**
* 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> * @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com> * @author David Sehnal <david.sehnal@gmail.com>
...@@ -30,9 +30,10 @@ function add3AndScale2(out: Vec3, a: Vec3, b: Vec3, c: Vec3, sa: number, sb: num ...@@ -30,9 +30,10 @@ function add3AndScale2(out: Vec3, a: Vec3, b: Vec3, c: Vec3, sa: number, sb: num
// avoiding namespace lookup improved performance in Chrome (Aug 2020) // avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3fromArray = Vec3.fromArray; const v3fromArray = Vec3.fromArray;
const v3normalize = Vec3.normalize; const v3normalize = Vec3.normalize;
const v3negate = Vec3.negate; const v3scaleAndAdd = Vec3.scaleAndAdd;
const v3copy = Vec3.copy;
const v3cross = Vec3.cross; const v3cross = Vec3.cross;
const v3dot = Vec3.dot;
const v3unitX = Vec3.unitX;
const caAdd3 = ChunkedArray.add3; const caAdd3 = ChunkedArray.add3;
const CosSinCache = new Map<number, { cos: number[], sin: number[] }>(); const CosSinCache = new Map<number, { cos: number[], sin: number[] }>();
...@@ -50,13 +51,16 @@ function getCosSin(radialSegments: number) { ...@@ -50,13 +51,16 @@ function getCosSin(radialSegments: number) {
return CosSinCache.get(radialSegments)!; return CosSinCache.get(radialSegments)!;
} }
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>, 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>, startCap: boolean, endCap: boolean, crossSection: 'elliptical' | 'rounded') {
const { currentGroup, vertices, normals, indices, groups } = state; const { currentGroup, vertices, normals, indices, groups } = state;
let vertexCount = vertices.elementCount; let vertexCount = vertices.elementCount;
const { cos, sin } = getCosSin(radialSegments); const { cos, sin } = getCosSin(radialSegments);
const q1 = radialSegments / 4;
const q3 = q1 * 3;
for (let i = 0; i <= linearSegments; ++i) { for (let i = 0; i <= linearSegments; ++i) {
const i3 = i * 3; const i3 = i * 3;
v3fromArray(u, normalVectors, i3); v3fromArray(u, normalVectors, i3);
...@@ -65,14 +69,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe ...@@ -65,14 +69,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
const width = widthValues[i]; const width = widthValues[i];
const height = heightValues[i]; const height = heightValues[i];
const rounded = crossSection === 'rounded' && height > width;
for (let j = 0; j < radialSegments; ++j) { for (let j = 0; j < radialSegments; ++j) {
add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]); if (rounded) {
if (radialSegments === 2) { add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[j], width * sin[j]);
v3copy(normalVector, v); const h = v3dot(v, v3unitX) < 0
v3normalize(normalVector, normalVector); ? (j < q1 || j >= q3) ? height - width : -height + width
if (j !== 0 || i % 2 === 0) v3negate(normalVector, normalVector); : (j >= q1 && j < q3) ? -height + width : height - width;
v3scaleAndAdd(surfacePoint, surfacePoint, u, h);
add2AndScale2(normalVector, u, v, cos[j], sin[j]);
} else { } else {
add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);
add2AndScale2(normalVector, u, v, width * cos[j], height * sin[j]); add2AndScale2(normalVector, u, v, width * cos[j], height * sin[j]);
} }
v3normalize(normalVector, normalVector); v3normalize(normalVector, normalVector);
...@@ -82,19 +90,37 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe ...@@ -82,19 +90,37 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
} }
} }
const radialSegmentsHalf = Math.round(radialSegments / 2);
for (let i = 0; i < linearSegments; ++i) { for (let i = 0; i < linearSegments; ++i) {
for (let j = 0; j < radialSegments; ++j) { // the triangles are arranged such that opposing triangles of the sheet align
// which prevents triangle intersection within tight curves
for (let j = 0; j < radialSegmentsHalf; ++j) {
caAdd3(
indices,
vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
vertexCount + i * radialSegments + j // b
);
caAdd3(
indices,
vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
vertexCount + (i + 1) * radialSegments + j, // d
vertexCount + i * radialSegments + j // b
);
}
for (let j = radialSegmentsHalf; j < radialSegments; ++j) {
caAdd3( caAdd3(
indices, indices,
vertexCount + i * radialSegments + (j + 1) % radialSegments, vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, vertexCount + (i + 1) * radialSegments + j, // d
vertexCount + i * radialSegments + j vertexCount + i * radialSegments + j // b
); );
caAdd3( caAdd3(
indices, indices,
vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
vertexCount + (i + 1) * radialSegments + j, vertexCount + (i + 1) * radialSegments + j, // d
vertexCount + i * radialSegments + j vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
); );
} }
} }
...@@ -111,11 +137,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe ...@@ -111,11 +137,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]); caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
const width = widthValues[0]; const width = widthValues[0];
const height = heightValues[0]; let height = heightValues[0];
const rounded = crossSection === 'rounded' && height > width;
if (rounded) height -= width;
vertexCount = vertices.elementCount; vertexCount = vertices.elementCount;
for (let i = 0; i < radialSegments; ++i) { for (let i = 0; i < radialSegments; ++i) {
add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]); if (rounded) {
add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[i], width * sin[i]);
v3scaleAndAdd(surfacePoint, surfacePoint, u, (i < q1 || i >= q3) ? height : -height);
} else {
add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]);
}
caAdd3(vertices, surfacePoint[0], surfacePoint[1], surfacePoint[2]); caAdd3(vertices, surfacePoint[0], surfacePoint[1], surfacePoint[2]);
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]); caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
...@@ -141,11 +174,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe ...@@ -141,11 +174,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]); caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
const width = widthValues[linearSegments]; const width = widthValues[linearSegments];
const height = heightValues[linearSegments]; let height = heightValues[linearSegments];
const rounded = crossSection === 'rounded' && height > width;
if (rounded) height -= width;
vertexCount = vertices.elementCount; vertexCount = vertices.elementCount;
for (let i = 0; i < radialSegments; ++i) { for (let i = 0; i < radialSegments; ++i) {
add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]); if (rounded) {
add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[i], width * sin[i]);
v3scaleAndAdd(surfacePoint, surfacePoint, u, (i < q1 || i >= q3) ? height : -height);
} else {
add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]);
}
caAdd3(vertices, surfacePoint[0], surfacePoint[1], surfacePoint[2]); caAdd3(vertices, surfacePoint[0], surfacePoint[1], surfacePoint[2]);
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]); caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
......
src/mol-repr/structure/visual/polymer-trace-mesh.ts
+ 20
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...@@ -27,8 +27,9 @@ import { StructureGroup } from './util/common'; ...@@ -27,8 +27,9 @@ import { StructureGroup } from './util/common';
export const PolymerTraceMeshParams = { export const PolymerTraceMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }), aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }), arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }),
tubularHelices: PD.Boolean(false), tubularHelices: PD.Boolean(false, { description: 'Draw alpha helices as tubes' }),
helixProfile: PD.Select('elliptical', PD.arrayToOptions(['elliptical', 'rounded', 'square'] as const), { description: 'Protein and nucleic helix trace profile' }),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, BaseGeometry.CustomQualityParamInfo), linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, BaseGeometry.CustomQualityParamInfo),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo) radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo)
...@@ -42,7 +43,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc ...@@ -42,7 +43,7 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
const polymerElementCount = unit.polymerElements.length; const polymerElementCount = unit.polymerElements.length;
if (!polymerElementCount) return Mesh.createEmpty(mesh); if (!polymerElementCount) return Mesh.createEmpty(mesh);
const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor, tubularHelices } = props; const { sizeFactor, detail, linearSegments, radialSegments, aspectRatio, arrowFactor, tubularHelices, helixProfile } = props;
const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2; const vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2;
const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh); const builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
...@@ -131,9 +132,6 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc ...@@ -131,9 +132,6 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
h0 = w0 * aspectRatio; h0 = w0 * aspectRatio;
h1 = w1 * aspectRatio; h1 = w1 * aspectRatio;
h2 = w2 * aspectRatio; h2 = w2 * aspectRatio;
[w0, h0] = [h0, w0];
[w1, h1] = [h1, w1];
[w2, h2] = [h2, w2];
} else { } else {
h0 = w0; h0 = w0;
h1 = w1; h1 = w1;
...@@ -142,18 +140,26 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc ...@@ -142,18 +140,26 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift); interpolateSizes(state, w0, w1, w2, h0, h1, h2, shift);
const [normals, binormals] = isNucleicType && !v.isCoarseBackbone ? [binormalVectors, normalVectors] : [normalVectors, binormalVectors];
if (isNucleicType && !v.isCoarseBackbone) {
// TODO: find a cleaner way to swap normal and binormal for nucleic types
for (let i = 0, il = normals.length; i < il; i++) normals[i] *= -1;
}
if (radialSegments === 2) { if (radialSegments === 2) {
if (isNucleicType && !v.isCoarseBackbone) { if (isNucleicType && !v.isCoarseBackbone) {
// TODO find a cleaner way to swap normal and binormal for nucleic types addRibbon(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0);
for (let i = 0, il = binormalVectors.length; i < il; i++) binormalVectors[i] *= -1;
addRibbon(builderState, curvePoints, binormalVectors, normalVectors, segmentCount, heightValues, widthValues, 0);
} else { } else {
addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0); addRibbon(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0);
} }
} else if (radialSegments === 4) { } else if (radialSegments === 4) {
addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap); addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
} else if (h1 === w1) {
addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
} else if (helixProfile === 'square') {
addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
} else { } else {
addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap); addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, helixProfile);
} }
} }
...@@ -189,7 +195,8 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace ...@@ -189,7 +195,8 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace
newProps.linearSegments !== currentProps.linearSegments || newProps.linearSegments !== currentProps.linearSegments ||
newProps.radialSegments !== currentProps.radialSegments || newProps.radialSegments !== currentProps.radialSegments ||
newProps.aspectRatio !== currentProps.aspectRatio || newProps.aspectRatio !== currentProps.aspectRatio ||
newProps.arrowFactor !== currentProps.arrowFactor newProps.arrowFactor !== currentProps.arrowFactor ||
newProps.helixProfile !== currentProps.helixProfile
); );
const secondaryStructureHash = SecondaryStructureProvider.get(newStructureGroup.structure).version; const secondaryStructureHash = SecondaryStructureProvider.get(newStructureGroup.structure).version;
......
src/mol-repr/structure/visual/polymer-tube-mesh.ts
+ 1
− 1
View file @ 15782111
...@@ -93,7 +93,7 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct ...@@ -93,7 +93,7 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
} else if (radialSegments === 4) { } else if (radialSegments === 4) {
addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap); addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
} else { } else {
addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap); addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
} }
++i; ++i;
......
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