diff --git a/CHANGELOG.md b/CHANGELOG.md
index 720111904f159b51468e4ebf2855ce260059735a..5c7347791352acfc7676256c61fa412bab87d7a9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Added ``ViewerOptions.collapseRightPanel``
- Added ``Viewer.loadTrajectory`` to support loading "composed" trajectories (e.g. from gro + xtc)
- 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
diff --git a/src/mol-geo/geometry/mesh/builder/sheet.ts b/src/mol-geo/geometry/mesh/builder/sheet.ts
index 0140d94ce00dcbe16ed0489faed6971f1e8345de..1a8cbfd91cec0ec5782581af80fd6c1a29a96d53 100644
--- a/src/mol-geo/geometry/mesh/builder/sheet.ts
+++ b/src/mol-geo/geometry/mesh/builder/sheet.ts
@@ -1,5 +1,5 @@
/**
- * 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 David Sehnal <david.sehnal@gmail.com>
@@ -40,7 +40,7 @@ const v3set = Vec3.set;
const caAdd3 = ChunkedArray.add3;
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 vertexCount = vertices.elementCount;
@@ -74,11 +74,19 @@ function addCap(offset: number, state: MeshBuilder.State, controlPoints: ArrayLi
v3copy(verticalVector, verticalLeftVector);
}
- for (let i = 0; i < 4; ++i) {
- caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
+ if (flip) {
+ 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 */
@@ -193,19 +201,18 @@ export function addSheet(state: MeshBuilder.State, controlPoints: ArrayLike<numb
const width = widthValues[0];
const height = heightValues[0];
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) {
const width = widthValues[0];
const height = heightValues[0];
- addCap(0, state, controlPoints, normalVectors, binormalVectors, width, arrowHeight, -height);
- 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, false);
}
if (endCap && arrowHeight === 0) {
const width = widthValues[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);
+ addCap(linearSegments * 3, state, controlPoints, normalVectors, binormalVectors, width, height, height, true);
}
const addedVertexCount = (linearSegments + 1) * 8 +
diff --git a/src/mol-geo/geometry/mesh/builder/tube.ts b/src/mol-geo/geometry/mesh/builder/tube.ts
index ad4f1aa1068dd5e5f72df37b08a585760b310195..68a3189770d4b3664389da2bb633b7debfe779ee 100644
--- a/src/mol-geo/geometry/mesh/builder/tube.ts
+++ b/src/mol-geo/geometry/mesh/builder/tube.ts
@@ -1,5 +1,5 @@
/**
- * 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 David Sehnal <david.sehnal@gmail.com>
@@ -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)
const v3fromArray = Vec3.fromArray;
const v3normalize = Vec3.normalize;
-const v3negate = Vec3.negate;
-const v3copy = Vec3.copy;
+const v3scaleAndAdd = Vec3.scaleAndAdd;
const v3cross = Vec3.cross;
+const v3dot = Vec3.dot;
+const v3unitX = Vec3.unitX;
const caAdd3 = ChunkedArray.add3;
const CosSinCache = new Map<number, { cos: number[], sin: number[] }>();
@@ -50,13 +51,16 @@ function getCosSin(radialSegments: number) {
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;
let vertexCount = vertices.elementCount;
const { cos, sin } = getCosSin(radialSegments);
+ const q1 = radialSegments / 4;
+ const q3 = q1 * 3;
+
for (let i = 0; i <= linearSegments; ++i) {
const i3 = i * 3;
v3fromArray(u, normalVectors, i3);
@@ -65,14 +69,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
const width = widthValues[i];
const height = heightValues[i];
+ const rounded = crossSection === 'rounded' && height > width;
for (let j = 0; j < radialSegments; ++j) {
- add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);
- if (radialSegments === 2) {
- v3copy(normalVector, v);
- v3normalize(normalVector, normalVector);
- if (j !== 0 || i % 2 === 0) v3negate(normalVector, normalVector);
+ if (rounded) {
+ add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[j], width * sin[j]);
+ const h = v3dot(v, v3unitX) < 0
+ ? (j < q1 || j >= q3) ? height - width : -height + width
+ : (j >= q1 && j < q3) ? -height + width : height - width;
+ v3scaleAndAdd(surfacePoint, surfacePoint, u, h);
+ add2AndScale2(normalVector, u, v, cos[j], sin[j]);
} else {
+ add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);
add2AndScale2(normalVector, u, v, width * cos[j], height * sin[j]);
}
v3normalize(normalVector, normalVector);
@@ -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 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(
indices,
- vertexCount + i * radialSegments + (j + 1) % radialSegments,
- vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments,
- vertexCount + i * radialSegments + j
+ vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
+ vertexCount + (i + 1) * radialSegments + j, // d
+ vertexCount + i * radialSegments + j // b
);
caAdd3(
indices,
- vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments,
- vertexCount + (i + 1) * radialSegments + j,
- vertexCount + i * radialSegments + j
+ vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
+ vertexCount + (i + 1) * radialSegments + j, // d
+ vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
);
}
}
@@ -111,11 +137,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
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;
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(normals, normalVector[0], normalVector[1], normalVector[2]);
@@ -141,11 +174,18 @@ export function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<numbe
caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
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;
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(normals, normalVector[0], normalVector[1], normalVector[2]);
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 416c3f4be26f0565965219b8213de7c75ec544ce..b407f980c199c131ab27634565761e6b34195bb5 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -27,8 +27,9 @@ import { StructureGroup } from './util/common';
export const PolymerTraceMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
- arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }),
- tubularHelices: PD.Boolean(false),
+ arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }),
+ 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),
linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, 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
const polymerElementCount = unit.polymerElements.length;
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 builderState = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
@@ -131,9 +132,6 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
h0 = w0 * aspectRatio;
h1 = w1 * aspectRatio;
h2 = w2 * aspectRatio;
- [w0, h0] = [h0, w0];
- [w1, h1] = [h1, w1];
- [w2, h2] = [h2, w2];
} else {
h0 = w0;
h1 = w1;
@@ -142,18 +140,26 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
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 (isNucleicType && !v.isCoarseBackbone) {
- // TODO find a cleaner way to swap normal and binormal for nucleic types
- for (let i = 0, il = binormalVectors.length; i < il; i++) binormalVectors[i] *= -1;
- addRibbon(builderState, curvePoints, binormalVectors, normalVectors, segmentCount, heightValues, widthValues, 0);
+ addRibbon(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0);
} else {
- addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0);
+ addRibbon(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0);
}
} 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 {
- 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
newProps.linearSegments !== currentProps.linearSegments ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.aspectRatio !== currentProps.aspectRatio ||
- newProps.arrowFactor !== currentProps.arrowFactor
+ newProps.arrowFactor !== currentProps.arrowFactor ||
+ newProps.helixProfile !== currentProps.helixProfile
);
const secondaryStructureHash = SecondaryStructureProvider.get(newStructureGroup.structure).version;
diff --git a/src/mol-repr/structure/visual/polymer-tube-mesh.ts b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
index 1aee4f505893892deb0ef9f77341b5ba62ef4cd0..af0e7837eee9ab1612d3754958b98f284c973a31 100644
--- a/src/mol-repr/structure/visual/polymer-tube-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-tube-mesh.ts
@@ -93,7 +93,7 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
} else if (radialSegments === 4) {
addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
} 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;