diff --git a/src/mol-geo/primitive/cylinder.ts b/src/mol-geo/primitive/cylinder.ts
index f1782fb3bcd5d1b81742ef2673a996e6e27b7bb7..cb49550f6478b8db8b8667aac6b448f3f46352a3 100644
--- a/src/mol-geo/primitive/cylinder.ts
+++ b/src/mol-geo/primitive/cylinder.ts
@@ -14,14 +14,15 @@ export const DefaultCylinderProps = {
height: 1,
radialSegments: 8,
heightSegments: 1,
- openEnded: false,
+ topCap: false,
+ bottomCap: false,
thetaStart: 0.0,
thetaLength: Math.PI * 2
}
export type CylinderProps = Partial<typeof DefaultCylinderProps>
export default function Cylinder(props?: CylinderProps) {
- const { radiusTop, radiusBottom, height, radialSegments, heightSegments, openEnded, thetaStart, thetaLength } = { ...DefaultCylinderProps, ...props };
+ const { radiusTop, radiusBottom, height, radialSegments, heightSegments, topCap, bottomCap, thetaStart, thetaLength } = { ...DefaultCylinderProps, ...props };
// buffers
const indices: number[] = [];
@@ -36,10 +37,8 @@ export default function Cylinder(props?: CylinderProps) {
// generate geometry
generateTorso();
- if (openEnded === false) {
- if (radiusTop > 0) generateCap(true);
- if (radiusBottom > 0) generateCap(false);
- }
+ if (topCap && radiusTop > 0) generateCap(true);
+ if (bottomCap && radiusBottom > 0) generateCap(false);
return {
vertices: new Float32Array(vertices),
diff --git a/src/mol-geo/representation/structure/ball-and-stick.ts b/src/mol-geo/representation/structure/ball-and-stick.ts
index 6038d6b5691feab7c2e9e29c27807860e137774f..c5a4755ef2fb157c3e9514af94b80418b13d4aef 100644
--- a/src/mol-geo/representation/structure/ball-and-stick.ts
+++ b/src/mol-geo/representation/structure/ball-and-stick.ts
@@ -29,6 +29,7 @@ export function BallAndStickRepresentation(): StructureRepresentation<BallAndSti
return {
get renderObjects() {
+ // return linkRepr.renderObjects
return [ ...elmementRepr.renderObjects, ...linkRepr.renderObjects ]
},
create: (structure: Structure, props: BallAndStickProps = {} as BallAndStickProps) => {
diff --git a/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
index 569ae8c83edc9f4ebef72f6cb1eaafa30d1ca2de..b1852e23a216c80e5eac7ca424898f61ee63bc48 100644
--- a/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
@@ -31,34 +31,23 @@ async function createInterUnitLinkCylinderMesh(ctx: RuntimeContext, structure: S
if (!bondCount) return Mesh.createEmpty(mesh)
- async function eachLink(ctx: RuntimeContext, cb: (edgeIndex: number, aI: number, bI: number) => void) {
- for (let edgeIndex = 0, il = bondCount; edgeIndex < il; ++edgeIndex) {
- const b = bonds[edgeIndex]
- const aI = b.indexA, bI = b.indexB;
- cb(edgeIndex, aI, bI)
- if (edgeIndex % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Cylinder mesh', current: edgeIndex, max: bondCount });
- }
- }
- }
-
- function getRefPos(aI: number, bI: number): Vec3 | null {
+ function referencePosition(edgeIndex: number): Vec3 | null {
// TODO
return null
}
- function setPositions(posA: Vec3, posB: Vec3, edgeIndex: number): void {
+ function position(posA: Vec3, posB: Vec3, edgeIndex: number): void {
const b = bonds[edgeIndex]
const uA = b.unitA, uB = b.unitB
uA.conformation.position(uA.elements[b.indexA], posA)
uB.conformation.position(uB.elements[b.indexB], posB)
}
- function getOrder(edgeIndex: number): number {
+ function order(edgeIndex: number): number {
return bonds[edgeIndex].order
}
- const linkBuilder = { linkCount: bondCount, eachLink, getRefPos, setPositions, getOrder }
+ const linkBuilder = { linkCount: bondCount, referencePosition, position, order }
return createLinkCylinderMesh(ctx, linkBuilder, props, mesh)
}
diff --git a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
index 4449969d209350a83ca7ba85ac7464fdba3ad426..8d8b2f199b875a85dce6845ce3483654d075a632 100644
--- a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
@@ -32,7 +32,7 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
const elements = unit.elements;
const links = unit.links
const { edgeCount, a, b, edgeProps, offset } = links
- const { order } = edgeProps
+ const { order: _order } = edgeProps
if (!edgeCount) return Mesh.createEmpty(mesh)
@@ -40,17 +40,9 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
const pos = unit.conformation.invariantPosition
- async function eachLink(ctx: RuntimeContext, cb: (edgeIndex: number, aI: number, bI: number) => void) {
- for (let edgeIndex = 0, _eI = edgeCount * 2; edgeIndex < _eI; ++edgeIndex) {
- const aI = a[edgeIndex], bI = b[edgeIndex];
- cb(edgeIndex, aI, bI)
- if (edgeIndex % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Cylinder mesh', current: edgeIndex, max: edgeCount });
- }
- }
- }
-
- function getRefPos(aI: number, bI: number): Vec3 | null {
+ function referencePosition(edgeIndex: number): Vec3 | null {
+ let aI = a[edgeIndex], bI = b[edgeIndex];
+ if (aI > bI) [aI, bI] = [bI, aI]
for (let i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
if (b[i] !== bI) return pos(elements[b[i]], vRef)
}
@@ -60,16 +52,16 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
return null
}
- function setPositions(posA: Vec3, posB: Vec3, edgeIndex: number): void {
+ function position(posA: Vec3, posB: Vec3, edgeIndex: number): void {
pos(elements[a[edgeIndex]], posA)
pos(elements[b[edgeIndex]], posB)
}
- function getOrder(edgeIndex: number): number {
- return order[edgeIndex]
+ function order(edgeIndex: number): number {
+ return _order[edgeIndex]
}
- const builder = { linkCount: edgeCount, eachLink, getRefPos, setPositions, getOrder }
+ const builder = { linkCount: edgeCount * 2, referencePosition, position, order }
return createLinkCylinderMesh(ctx, builder, props, mesh)
}
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index c34a3d3d2d3db58e74b2ec5cdf1200c734719aa2..396b24996ac023859f221a7678d016238d388658 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Vec3, Mat4 } from 'mol-math/linear-algebra';
+import { Vec3 } from 'mol-math/linear-algebra';
import { Unit, Element } from 'mol-model/structure';
import { SizeTheme } from '../../../../theme';
import { RuntimeContext } from 'mol-task';
@@ -36,8 +36,6 @@ export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, r
const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
const v = Vec3.zero()
- const m = Mat4.identity()
-
const pos = unit.conformation.invariantPosition
const l = Element.Location()
l.unit = unit
@@ -45,10 +43,9 @@ export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, r
for (let i = 0; i < elementCount; i++) {
l.element = elements[i]
pos(elements[i], v)
- Mat4.setTranslation(m, v)
meshBuilder.setId(i)
- meshBuilder.addIcosahedron(m, { radius: radius(l), detail })
+ meshBuilder.addIcosahedron(v, radius(l), detail)
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Sphere mesh', current: i, max: elementCount });
diff --git a/src/mol-geo/representation/structure/visual/util/link.ts b/src/mol-geo/representation/structure/visual/util/link.ts
index a38d9983724df8153d9cf7b12795a49d2a8556f3..52079675792df5de3f4f06a971e963d7e08e2523 100644
--- a/src/mol-geo/representation/structure/visual/util/link.ts
+++ b/src/mol-geo/representation/structure/visual/util/link.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Vec3, Mat4 } from 'mol-math/linear-algebra';
+import { Vec3 } from 'mol-math/linear-algebra';
import { RuntimeContext } from 'mol-task';
import { Mesh } from '../../../../shape/mesh';
import { MeshBuilder } from '../../../../shape/mesh-builder';
@@ -22,7 +22,7 @@ const tmpShiftV13 = Vec3.zero()
/** Calculate 'shift' direction that is perpendiculat to v1 - v2 and goes through v3 */
export function calculateShiftDir (out: Vec3, v1: Vec3, v2: Vec3, v3: Vec3 | null) {
- Vec3.sub(tmpShiftV12, v1, v2)
+ Vec3.normalize(tmpShiftV12, Vec3.sub(tmpShiftV12, v1, v2))
if (v3 !== null) {
Vec3.sub(tmpShiftV13, v1, v3)
@@ -47,21 +47,19 @@ export function calculateShiftDir (out: Vec3, v1: Vec3, v2: Vec3, v3: Vec3 | nul
return Vec3.normalize(out, tmpShiftV13)
}
-export interface LinkCylinderMeshBuilder {
+export interface LinkCylinderMeshBuilderProps {
linkCount: number
- eachLink(ctx: RuntimeContext, cb: (edgeIndex: number, aI: number, bI: number) => void): Promise<void>
- // assumes aI < bI
- getRefPos(aI: number, bI: number): Vec3 | null
- setPositions(posA: Vec3, posB: Vec3, edgeIndex: number): void
- getOrder(edgeIndex: number): number
+ referencePosition(edgeIndex: number): Vec3 | null
+ position(posA: Vec3, posB: Vec3, edgeIndex: number): void
+ order(edgeIndex: number): number
}
/**
* Each edge is included twice to allow for coloring/picking
* the half closer to the first vertex, i.e. vertex a.
*/
-export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: LinkCylinderMeshBuilder, props: LinkCylinderProps, mesh?: Mesh) {
- const { linkCount, eachLink, getRefPos, setPositions, getOrder } = linkBuilder
+export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: LinkCylinderMeshBuilderProps, props: LinkCylinderProps, mesh?: Mesh) {
+ const { linkCount, referencePosition, position, order } = linkBuilder
if (!linkCount) return Mesh.createEmpty(mesh)
@@ -71,13 +69,7 @@ export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: L
const va = Vec3.zero()
const vb = Vec3.zero()
- const vd = Vec3.zero()
- const vc = Vec3.zero()
- const m = Mat4.identity()
- const mt = Mat4.identity()
-
const vShift = Vec3.zero()
- const vCenter = Vec3.zero()
const { linkScale, linkSpacing, linkRadius, radialSegments } = props
@@ -85,65 +77,35 @@ export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: L
height: 1,
radiusTop: linkRadius,
radiusBottom: linkRadius,
- radialSegments,
- openEnded: true
+ radialSegments
}
- // for (let edgeIndex = 0, _eI = edgeCount * 2; edgeIndex < _eI; ++edgeIndex) {
- await eachLink(ctx, (edgeIndex, aI, bI) => {
- // const aI = a[edgeIndex], bI = b[edgeIndex];
-
- setPositions(va, vb, edgeIndex)
- const d = Vec3.distance(va, vb)
+ for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
+ position(va, vb, edgeIndex)
- Vec3.sub(vd, vb, va)
- Vec3.scale(vd, Vec3.normalize(vd, vd), d / 4)
- Vec3.add(vc, va, vd)
- // ensure both edge halfs are pointing in the the same direction so the triangles align
- if (aI > bI) Vec3.scale(vd, vd, -1)
- Vec3.makeRotation(m, Vec3.create(0, 1, 0), vd)
-
- const order = getOrder(edgeIndex)
+ const o = order(edgeIndex)
meshBuilder.setId(edgeIndex)
- cylinderParams.height = d / 2
- if (order === 2 || order === 3) {
- const multiRadius = linkRadius * (linkScale / (0.5 * order))
+ if (o === 2 || o === 3) {
+ const multiRadius = linkRadius * (linkScale / (0.5 * o))
const absOffset = (linkRadius - multiRadius) * linkSpacing
- if (aI < bI) {
- calculateShiftDir(vShift, va, vb, getRefPos(aI, bI))
- } else {
- calculateShiftDir(vShift, vb, va, getRefPos(bI, aI))
- }
+ calculateShiftDir(vShift, va, vb, referencePosition(edgeIndex))
Vec3.setMagnitude(vShift, vShift, absOffset)
- cylinderParams.radiusTop = multiRadius
- cylinderParams.radiusBottom = multiRadius
-
- if (order === 3) {
- Mat4.fromTranslation(mt, vc)
- Mat4.mul(mt, mt, m)
- meshBuilder.addCylinder(mt, cylinderParams)
- }
+ cylinderParams.radiusTop = cylinderParams.radiusBottom = multiRadius
- Vec3.add(vCenter, vc, vShift)
- Mat4.fromTranslation(mt, vCenter)
- Mat4.mul(mt, mt, m)
- meshBuilder.addCylinder(mt, cylinderParams)
-
- Vec3.sub(vCenter, vc, vShift)
- Mat4.fromTranslation(mt, vCenter)
- Mat4.mul(mt, mt, m)
- meshBuilder.addCylinder(mt, cylinderParams)
+ if (o === 3) meshBuilder.addCylinder(va, vb, 0.5, cylinderParams)
+ meshBuilder.addDoubleCylinder(va, vb, 0.5, vShift, cylinderParams)
} else {
- cylinderParams.radiusTop = linkRadius
- cylinderParams.radiusBottom = linkRadius
+ cylinderParams.radiusTop = cylinderParams.radiusBottom = linkRadius
+ meshBuilder.addCylinder(va, vb, 0.5, cylinderParams)
+ }
- Mat4.setTranslation(m, vc)
- meshBuilder.addCylinder(m, cylinderParams)
+ if (edgeIndex % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Cylinder mesh', current: edgeIndex, max: linkCount });
}
- })
+ }
return meshBuilder.getMesh()
}
\ No newline at end of file
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/shape/mesh-builder.ts
index 5efda4e2a1514e8f8eeb12b87a11eb871cb5dc06..cb72406c13ab18e2a5607c40ac055d72a97c5cfa 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/shape/mesh-builder.ts
@@ -23,15 +23,68 @@ type Primitive = {
export interface MeshBuilder {
add(t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices?: Uint32Array): number
addBox(t: Mat4, props?: BoxProps): number
- addCylinder(t: Mat4, props?: CylinderProps): number
- addIcosahedron(t: Mat4, props?: IcosahedronProps): number
+ addCylinder(start: Vec3, end: Vec3, scale: number, props: CylinderProps): number
+ addDoubleCylinder(start: Vec3, end: Vec3, scale: number, shift: Vec3, props: CylinderProps): number
+ // addFixedCountDashedCylinder(t: Mat4, props?: CylinderProps): number
+ addIcosahedron(center: Vec3, radius: number, detail: number): number
setId(id: number): void
getMesh(): Mesh
}
+const cylinderMap = new Map<string, Primitive>()
+const icosahedronMap = new Map<string, Primitive>()
+
+const up = Vec3.create(0, 1, 0)
const tmpV = Vec3.zero()
const tmpMat3 = Mat3.zero()
+const tmpCylinderDir = Vec3.zero()
+const tmpCylinderMatDir = Vec3.zero()
+const tmpCylinderCenter = Vec3.zero()
+const tmpCylinderMat = Mat4.zero()
+// const tmpCylinderMatTrans = Mat4.zero()
+const tmpShiftedCylinderStart = Vec3.zero()
+
+function setCylinderMat(m: Mat4, start: Vec3, dir: Vec3, length: number) {
+ Vec3.setMagnitude(tmpCylinderMatDir, dir, length / 2)
+ Vec3.add(tmpCylinderCenter, start, tmpCylinderMatDir)
+ // ensure the direction use to create the rotation is always pointing in the same
+ // direction so the triangles of adjacent cylinder will line up
+ if (Vec3.dot(tmpCylinderMatDir, up) < 0) Vec3.scale(tmpCylinderMatDir, tmpCylinderMatDir, -1)
+ Vec3.makeRotation(m, up, tmpCylinderMatDir)
+ // Mat4.fromTranslation(tmpCylinderMatTrans, tmpCylinderCenter)
+ // Mat4.mul(m, tmpCylinderMatTrans, m)
+ Mat4.setTranslation(m, tmpCylinderCenter)
+ return m
+}
+
+function getCylinder(props: CylinderProps) {
+ const key = JSON.stringify(props)
+ let cylinder = cylinderMap.get(key)
+ if (cylinder === undefined) {
+ cylinder = Cylinder(props)
+ cylinderMap.set(key, cylinder)
+ }
+ return cylinder
+}
+
+const tmpIcosahedronMat = Mat4.identity()
+
+function setIcosahedronMat(m: Mat4, center: Vec3) {
+ Mat4.setTranslation(m, center)
+ return m
+}
+
+function getIcosahedron(props: IcosahedronProps) {
+ const key = JSON.stringify(props)
+ let icosahedron = icosahedronMap.get(key)
+ if (icosahedron === undefined) {
+ icosahedron = Icosahedron(props)
+ icosahedronMap.set(key, icosahedron)
+ }
+ return icosahedron
+}
+
// TODO cache primitives based on props
export namespace MeshBuilder {
@@ -45,10 +98,7 @@ export namespace MeshBuilder {
let currentId = -1
- const cylinderMap = new Map<string, Primitive>()
- const icosahedronMap = new Map<string, Primitive>()
-
- const add = (t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices: Uint32Array) => {
+ function add(t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices: Uint32Array) {
const { elementCount, elementSize } = vertices
const n = getNormalMatrix(tmpMat3, t)
for (let i = 0, il = _vertices.length; i < il; i += 3) {
@@ -60,7 +110,7 @@ export namespace MeshBuilder {
Vec3.fromArray(tmpV, _normals, i)
Vec3.transformMat3(tmpV, tmpV, n)
ChunkedArray.add3(normals, tmpV[0], tmpV[1], tmpV[2]);
-
+ // id
ChunkedArray.add(ids, currentId);
}
for (let i = 0, il = _indices.length; i < il; i += 3) {
@@ -75,23 +125,32 @@ export namespace MeshBuilder {
const box = Box(props)
return add(t, box.vertices, box.normals, box.indices)
},
- addCylinder: (t: Mat4, props?: CylinderProps) => {
- const key = JSON.stringify(props)
- let cylinder = cylinderMap.get(key)
- if (cylinder === undefined) {
- cylinder = Cylinder(props)
- cylinderMap.set(key, cylinder)
- }
- return add(t, cylinder.vertices, cylinder.normals, cylinder.indices)
+ addCylinder: (start: Vec3, end: Vec3, scale: number, props: CylinderProps) => {
+ const d = Vec3.distance(start, end) * scale
+ props.height = d
+ const { vertices, normals, indices } = getCylinder(props)
+ Vec3.sub(tmpCylinderDir, end, start)
+ setCylinderMat(tmpCylinderMat, start, tmpCylinderDir, d)
+ return add(tmpCylinderMat, vertices, normals, indices)
},
- addIcosahedron: (t: Mat4, props: IcosahedronProps) => {
- const key = JSON.stringify(props)
- let icosahedron = icosahedronMap.get(key)
- if (icosahedron === undefined) {
- icosahedron = Icosahedron(props)
- icosahedronMap.set(key, icosahedron)
- }
- return add(t, icosahedron.vertices, icosahedron.normals, icosahedron.indices)
+ addDoubleCylinder: (start: Vec3, end: Vec3, scale: number, shift: Vec3, props: CylinderProps) => {
+ const d = Vec3.distance(start, end) * scale
+ props.height = d
+ const { vertices, normals, indices } = getCylinder(props)
+ Vec3.sub(tmpCylinderDir, end, start)
+ // positivly shifted cylinder
+ Vec3.add(tmpShiftedCylinderStart, start, shift)
+ setCylinderMat(tmpCylinderMat, tmpShiftedCylinderStart, tmpCylinderDir, d)
+ add(tmpCylinderMat, vertices, normals, indices)
+ // negativly shifted cylinder
+ Vec3.sub(tmpShiftedCylinderStart, start, shift)
+ setCylinderMat(tmpCylinderMat, tmpShiftedCylinderStart, tmpCylinderDir, d)
+ return add(tmpCylinderMat, vertices, normals, indices)
+ },
+ addIcosahedron: (center: Vec3, radius: number, detail: number) => {
+ const { vertices, normals, indices } = getIcosahedron({ radius, detail })
+ setIcosahedronMat(tmpIcosahedronMat, center)
+ return add(tmpIcosahedronMat, vertices, normals, indices)
},
setId: (id: number) => {
if (currentId !== id) {