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 b1852e23a216c80e5eac7ca424898f61ee63bc48..fa76a9e30682fb81d21be816edc22eb1c5f830ea 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
@@ -31,25 +31,20 @@ async function createInterUnitLinkCylinderMesh(ctx: RuntimeContext, structure: S
if (!bondCount) return Mesh.createEmpty(mesh)
- function referencePosition(edgeIndex: number): Vec3 | null {
- // TODO
- return null
- }
-
- 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 order(edgeIndex: number): number {
- return bonds[edgeIndex].order
+ const builderProps = {
+ linkCount: bondCount,
+ referencePosition: (edgeIndex: number) => null, // TODO
+ position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+ 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)
+ },
+ order: (edgeIndex: number) => bonds[edgeIndex].order,
+ flags: (edgeIndex: number) => bonds[edgeIndex].flag
}
- const linkBuilder = { linkCount: bondCount, referencePosition, position, order }
-
- return createLinkCylinderMesh(ctx, linkBuilder, props, mesh)
+ return createLinkCylinderMesh(ctx, builderProps, props, mesh)
}
export const DefaultInterUnitLinkProps = {
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 8d8b2f199b875a85dce6845ce3483654d075a632..15564c2cf637ee2879c72bb557fa48e7bd8fcab7 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
@@ -32,38 +32,35 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
const elements = unit.elements;
const links = unit.links
const { edgeCount, a, b, edgeProps, offset } = links
- const { order: _order } = edgeProps
+ const { order: _order, flags: _flags } = edgeProps
if (!edgeCount) return Mesh.createEmpty(mesh)
const vRef = Vec3.zero()
-
const pos = unit.conformation.invariantPosition
- 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)
- }
- for (let i = offset[bI], il = offset[bI + 1]; i < il; ++i) {
- if (a[i] !== aI) return pos(elements[a[i]], vRef)
- }
- return null
- }
-
- function position(posA: Vec3, posB: Vec3, edgeIndex: number): void {
- pos(elements[a[edgeIndex]], posA)
- pos(elements[b[edgeIndex]], posB)
- }
-
- function order(edgeIndex: number): number {
- return _order[edgeIndex]
+ const builderProps = {
+ linkCount: edgeCount * 2,
+ referencePosition: (edgeIndex: number) => {
+ 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)
+ }
+ for (let i = offset[bI], il = offset[bI + 1]; i < il; ++i) {
+ if (a[i] !== aI) return pos(elements[a[i]], vRef)
+ }
+ return null
+ },
+ position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+ pos(elements[a[edgeIndex]], posA)
+ pos(elements[b[edgeIndex]], posB)
+ },
+ order: (edgeIndex: number) => _order[edgeIndex],
+ flags: (edgeIndex: number) => _flags[edgeIndex]
}
- const builder = { linkCount: edgeCount * 2, referencePosition, position, order }
-
- return createLinkCylinderMesh(ctx, builder, props, mesh)
+ return createLinkCylinderMesh(ctx, builderProps, props, mesh)
}
export const DefaultIntraUnitLinkProps = {
diff --git a/src/mol-geo/representation/structure/visual/util/link.ts b/src/mol-geo/representation/structure/visual/util/link.ts
index 52079675792df5de3f4f06a971e963d7e08e2523..4d23190b207f3cea2ca31bd5df6256758d01f6c3 100644
--- a/src/mol-geo/representation/structure/visual/util/link.ts
+++ b/src/mol-geo/representation/structure/visual/util/link.ts
@@ -8,6 +8,7 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { RuntimeContext } from 'mol-task';
import { Mesh } from '../../../../shape/mesh';
import { MeshBuilder } from '../../../../shape/mesh-builder';
+import { LinkType } from 'mol-model/structure/model/types';
export const DefaultLinkCylinderProps = {
linkScale: 0.4,
@@ -52,6 +53,7 @@ export interface LinkCylinderMeshBuilderProps {
referencePosition(edgeIndex: number): Vec3 | null
position(posA: Vec3, posB: Vec3, edgeIndex: number): void
order(edgeIndex: number): number
+ flags(edgeIndex: number): LinkType.Flag
}
/**
@@ -59,12 +61,13 @@ export interface LinkCylinderMeshBuilderProps {
* the half closer to the first vertex, i.e. vertex a.
*/
export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: LinkCylinderMeshBuilderProps, props: LinkCylinderProps, mesh?: Mesh) {
- const { linkCount, referencePosition, position, order } = linkBuilder
+ const { linkCount, referencePosition, position, order, flags } = linkBuilder
if (!linkCount) return Mesh.createEmpty(mesh)
- // approximate vertextCount, exact calculation would need to take link orders into account
- const vertexCount = 32 * linkCount
+ // approximate vertextCount (* 2), exact calculation would need to take
+ // multiple cylinders for bond orders and metall coordinations into account
+ const vertexCount = props.radialSegments * 2 * linkCount * 2
const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
const va = Vec3.zero()
@@ -84,9 +87,15 @@ export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: L
position(va, vb, edgeIndex)
const o = order(edgeIndex)
+ const f = flags(edgeIndex) as any as LinkType // TODO
meshBuilder.setId(edgeIndex)
- if (o === 2 || o === 3) {
+ if (LinkType.is(f, LinkType.Flag.MetallicCoordination)) {
+ // show metall coordinations with dashed cylinders
+ cylinderParams.radiusTop = cylinderParams.radiusBottom = linkRadius / 3
+ meshBuilder.addFixedCountDashedCylinder(va, vb, 0.5, 7, cylinderParams)
+ } else if (o === 2 || o === 3) {
+ // show bonds with order 2 or 3 using 2 or 3 parallel cylinders
const multiRadius = linkRadius * (linkScale / (0.5 * o))
const absOffset = (linkRadius - multiRadius) * linkSpacing
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/shape/mesh-builder.ts
index cb72406c13ab18e2a5607c40ac055d72a97c5cfa..6eed0f441cc4772eb606763c1f731e67880c964c 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/shape/mesh-builder.ts
@@ -21,12 +21,12 @@ type Primitive = {
}
export interface MeshBuilder {
- add(t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices?: Uint32Array): number
- addBox(t: Mat4, props?: BoxProps): 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
+ add(t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices?: Uint32Array): void
+ addBox(t: Mat4, props?: BoxProps): void
+ addCylinder(start: Vec3, end: Vec3, lengthScale: number, props: CylinderProps): void
+ addDoubleCylinder(start: Vec3, end: Vec3, lengthScale: number, shift: Vec3, props: CylinderProps): void
+ addFixedCountDashedCylinder(start: Vec3, end: Vec3, lengthScale: number, segmentCount: number, props: CylinderProps): void
+ addIcosahedron(center: Vec3, radius: number, detail: number): void
setId(id: number): void
getMesh(): Mesh
}
@@ -43,7 +43,7 @@ const tmpCylinderMatDir = Vec3.zero()
const tmpCylinderCenter = Vec3.zero()
const tmpCylinderMat = Mat4.zero()
// const tmpCylinderMatTrans = Mat4.zero()
-const tmpShiftedCylinderStart = Vec3.zero()
+const tmpCylinderStart = Vec3.zero()
function setCylinderMat(m: Mat4, start: Vec3, dir: Vec3, length: number) {
Vec3.setMagnitude(tmpCylinderMatDir, dir, length / 2)
@@ -99,7 +99,7 @@ export namespace MeshBuilder {
let currentId = -1
function add(t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices: Uint32Array) {
- const { elementCount, elementSize } = vertices
+ const { elementCount } = vertices
const n = getNormalMatrix(tmpMat3, t)
for (let i = 0, il = _vertices.length; i < il; i += 3) {
// position
@@ -116,41 +116,64 @@ export namespace MeshBuilder {
for (let i = 0, il = _indices.length; i < il; i += 3) {
ChunkedArray.add3(indices, _indices[i] + elementCount, _indices[i + 1] + elementCount, _indices[i + 2] + elementCount);
}
- return elementCount * elementSize
}
return {
add,
addBox: (t: Mat4, props?: BoxProps) => {
const box = Box(props)
- return add(t, box.vertices, box.normals, box.indices)
+ add(t, box.vertices, box.normals, box.indices)
},
- addCylinder: (start: Vec3, end: Vec3, scale: number, props: CylinderProps) => {
- const d = Vec3.distance(start, end) * scale
+ addCylinder: (start: Vec3, end: Vec3, lengthScale: number, props: CylinderProps) => {
+ const d = Vec3.distance(start, end) * lengthScale
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)
+ add(tmpCylinderMat, vertices, normals, indices)
},
- addDoubleCylinder: (start: Vec3, end: Vec3, scale: number, shift: Vec3, props: CylinderProps) => {
- const d = Vec3.distance(start, end) * scale
+ addDoubleCylinder: (start: Vec3, end: Vec3, lengthScale: number, shift: Vec3, props: CylinderProps) => {
+ const d = Vec3.distance(start, end) * lengthScale
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)
+ Vec3.add(tmpCylinderStart, start, shift)
+ setCylinderMat(tmpCylinderMat, tmpCylinderStart, 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)
+ Vec3.sub(tmpCylinderStart, start, shift)
+ setCylinderMat(tmpCylinderMat, tmpCylinderStart, tmpCylinderDir, d)
+ add(tmpCylinderMat, vertices, normals, indices)
+ },
+ addFixedCountDashedCylinder: (start: Vec3, end: Vec3, lengthScale: number, segmentCount: number, props: CylinderProps) => {
+ const s = Math.floor(segmentCount / 2)
+ const step = 1 / segmentCount
+
+ // automatically adjust length so links/bonds that are rendered as two half cylinders
+ // have evenly spaced dashed cylinders
+ if (lengthScale < 1) {
+ const bias = lengthScale / 2 / segmentCount
+ lengthScale += segmentCount % 2 === 1 ? bias : -bias
+ }
+
+ const d = Vec3.distance(start, end) * lengthScale
+ props.height = d * step
+ const { vertices, normals, indices } = getCylinder(props)
+ Vec3.sub(tmpCylinderDir, end, start)
+
+ for (let j = 0; j < s; ++j) {
+ const f = step * (j * 2 + 1)
+ Vec3.setMagnitude(tmpCylinderDir, tmpCylinderDir, d * f)
+ Vec3.add(tmpCylinderStart, start, tmpCylinderDir)
+ setCylinderMat(tmpCylinderMat, tmpCylinderStart, tmpCylinderDir, d * step)
+ 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)
+ add(tmpIcosahedronMat, vertices, normals, indices)
},
setId: (id: number) => {
if (currentId !== id) {
diff --git a/src/mol-util/bit-flags.ts b/src/mol-util/bit-flags.ts
index 8143eb160bcbc0a1268cb3ddb9ef56d094d2d6e8..7f0bb8870771381b93be9e199f14e8bd52a4394e 100644
--- a/src/mol-util/bit-flags.ts
+++ b/src/mol-util/bit-flags.ts
@@ -10,7 +10,7 @@ namespace BitFlags {
export function create<F>(flags: F): BitFlags<F> { return flags as any; }
export function has<F>(flags: BitFlags<F>, flag: F) { return ((flags as any) & (flag as any)) !== 0; }
- // toCheck must be non-zero
+ /** toCheck must be non-zero */
export function hasAll<F>(flags: BitFlags<F>, toCheck: BitFlags<F>) { return !!toCheck && ((flags as any) & (toCheck as any)) === (toCheck as any); }
}
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 25d2ae1914a12d0de4d450ac7a5029380ff3c546..b9afd01aaf4d647893092389258bbd3b35f3dc75 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -42,9 +42,10 @@ export class Stage {
// this.loadPdbid('1jj2')
// this.loadPdbid('4umt') // ligand has bond with order 3
- // this.loadPdbid('1crn')
- this.loadPdbid('3pqr')
- // this.loadPdbid('4v5a')
+ // this.loadPdbid('1crn') // small
+ this.loadPdbid('1blu') // metal coordination
+ // this.loadPdbid('3pqr') // inter unit bonds
+ // this.loadPdbid('4v5a') // ribosome
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
}