diff --git a/src/mol-geo/primitive/box.ts b/src/mol-geo/primitive/box.ts
index 45a35ebea43fef38f413f23132372e8b7bac3eef..9ba23149f07dfba0daea75f5656101119a272145 100644
--- a/src/mol-geo/primitive/box.ts
+++ b/src/mol-geo/primitive/box.ts
@@ -17,7 +17,7 @@ export type BoxProps = Partial<typeof DefaultBoxProps>
const tmpVector = Vec3.zero();
-export default function Box(props?: BoxProps) {
+export function Box(props?: BoxProps) {
const { width, height, depth } = { ...DefaultBoxProps, ...props }
// buffers
diff --git a/src/mol-geo/primitive/cylinder.ts b/src/mol-geo/primitive/cylinder.ts
index cb49550f6478b8db8b8667aac6b448f3f46352a3..a17cc3ff8d68539e0f19c4365b82ab6d967f7acf 100644
--- a/src/mol-geo/primitive/cylinder.ts
+++ b/src/mol-geo/primitive/cylinder.ts
@@ -21,7 +21,7 @@ export const DefaultCylinderProps = {
}
export type CylinderProps = Partial<typeof DefaultCylinderProps>
-export default function Cylinder(props?: CylinderProps) {
+export function Cylinder(props?: CylinderProps) {
const { radiusTop, radiusBottom, height, radialSegments, heightSegments, topCap, bottomCap, thetaStart, thetaLength } = { ...DefaultCylinderProps, ...props };
// buffers
diff --git a/src/mol-geo/primitive/icosahedron.ts b/src/mol-geo/primitive/icosahedron.ts
index 07e544e07fcfdd7cddb36940173f2841c58da169..d9383aa0fe1dc119ec344dc351b1d80e098c6ea6 100644
--- a/src/mol-geo/primitive/icosahedron.ts
+++ b/src/mol-geo/primitive/icosahedron.ts
@@ -6,7 +6,7 @@
// adapted from three.js, MIT License Copyright 2010-2018 three.js authors
-import Polyhedron from './polyhedron'
+import { Polyhedron } from './polyhedron'
const t = ( 1 + Math.sqrt( 5 ) ) / 2;
@@ -33,6 +33,6 @@ export const DefaultIcosahedronProps = {
}
export type IcosahedronProps = Partial<typeof DefaultIcosahedronProps>
-export default function Icosahedron(props?: IcosahedronProps) {
+export function Icosahedron(props?: IcosahedronProps) {
return Polyhedron(vertices, indices, { ...DefaultIcosahedronProps, ...props })
}
\ No newline at end of file
diff --git a/src/mol-geo/primitive/plane.ts b/src/mol-geo/primitive/plane.ts
new file mode 100644
index 0000000000000000000000000000000000000000..c6e02744074056da32d3627050132a0e9d1c9267
--- /dev/null
+++ b/src/mol-geo/primitive/plane.ts
@@ -0,0 +1,34 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export const DefaultPlaneProps = {
+ width: 1,
+ height: 1
+}
+export type PlaneProps = Partial<typeof DefaultPlaneProps>
+
+export function Plane(props?: PlaneProps) {
+ const { width, height } = { ...DefaultPlaneProps, ...props }
+
+ return {
+ vertices: new Float32Array([
+ -width / 2, height / 2, 0,
+ width / 2, height / 2, 0,
+ -width / 2, -height / 2, 0,
+ width / 2, -height / 2, 0
+ ]),
+ normals: new Float32Array([
+ 0, 0, 1,
+ 0, 0, 1,
+ 0, 0, 1,
+ 0, 0, 1
+ ]),
+ indices: new Uint32Array([
+ 0, 2, 1,
+ 1, 2, 3
+ ])
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/primitive/polyhedron.ts b/src/mol-geo/primitive/polyhedron.ts
index 558cce08d59c2e61618855a2bfb5697e386e0eea..d5818b6a77ff30a2f9ae72d2e416cec4dc112655 100644
--- a/src/mol-geo/primitive/polyhedron.ts
+++ b/src/mol-geo/primitive/polyhedron.ts
@@ -15,7 +15,7 @@ export const DefaultPolyhedronProps = {
}
export type PolyhedronProps = Partial<typeof DefaultPolyhedronProps>
-export default function Polyhedron(_vertices: Helpers.NumberArray, _indices: Helpers.NumberArray, props?: PolyhedronProps) {
+export function Polyhedron(_vertices: Helpers.NumberArray, _indices: Helpers.NumberArray, props?: PolyhedronProps) {
const { radius, detail } = { ...DefaultPolyhedronProps, ...props }
const builder = createBuilder()
const { vertices, indices } = builder
diff --git a/src/mol-geo/primitive/wedge.ts b/src/mol-geo/primitive/wedge.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f15642e1e428e824d8efed00e51c7599112e5224
--- /dev/null
+++ b/src/mol-geo/primitive/wedge.ts
@@ -0,0 +1,121 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec3 } from 'mol-math/linear-algebra'
+
+export const DefaultWedgeProps = {
+ width: 1,
+ height: 1,
+ depth: 1
+}
+export type WedgeProps = Partial<typeof DefaultWedgeProps>
+
+const _a = Vec3.create(0, 0.5, 0.5)
+const _b = Vec3.create(0.5, -0.5, 0.5)
+const _c = Vec3.create(-0.5, -0.5, 0.5)
+const _d = Vec3.create(0, 0.5, -0.5)
+const _e = Vec3.create(0.5, -0.5, -0.5)
+const _f = Vec3.create(-0.5, -0.5, -0.5)
+
+const a = Vec3.zero(), b = Vec3.zero(), c = Vec3.zero()
+const d = Vec3.zero(), e = Vec3.zero(), f = Vec3.zero()
+
+const nabc = Vec3.create(0, 0, 1)
+const ndef = Vec3.create(0, 0, -1)
+const nabde = Vec3.zero()
+const nbcef = Vec3.create(0, -1, 0)
+const nacdf = Vec3.zero()
+
+const s = Vec3.zero()
+
+export function Wedge(props?: WedgeProps) {
+ const { width, height, depth } = { ...DefaultWedgeProps, ...props }
+
+ const vertices = new Float32Array(54)
+ const normals = new Float32Array(54)
+ const indices = new Uint32Array(24)
+
+ Vec3.set(s, width, height, depth)
+ Vec3.mul(a, _a, s); Vec3.mul(b, _b, s); Vec3.mul(c, _c, s)
+ Vec3.mul(d, _d, s); Vec3.mul(e, _e, s); Vec3.mul(f, _f, s)
+
+ Vec3.sub(nabde, b, a)
+ Vec3.normalize(nabde, Vec3.set(nabde, -nabde[1], nabde[0], 0))
+ Vec3.sub(nacdf, c, a)
+ Vec3.normalize(nacdf, Vec3.set(nacdf, nacdf[1], -nacdf[0], 0))
+
+ let vc = 0
+ let ic = 0
+
+ // abc
+ Vec3.toArray(a, vertices, vc + 0)
+ Vec3.toArray(c, vertices, vc + 3)
+ Vec3.toArray(b, vertices, vc + 6)
+ for (let i = 0; i < 3; ++i) Vec3.toArray(nabc, normals, vc + i * 3)
+ indices[ic + 0] = vc / 3 + 0
+ indices[ic + 1] = vc / 3 + 1
+ indices[ic + 2] = vc / 3 + 2
+ vc += 9
+ ic += 3
+
+ // def
+ Vec3.toArray(d, vertices, vc + 0)
+ Vec3.toArray(e, vertices, vc + 3)
+ Vec3.toArray(f, vertices, vc + 6)
+ for (let i = 0; i < 3; ++i) Vec3.toArray(ndef, normals, vc + i * 3)
+ indices[ic + 0] = vc / 3 + 0
+ indices[ic + 1] = vc / 3 + 1
+ indices[ic + 2] = vc / 3 + 2
+ vc += 9
+ ic += 3
+
+ // abde
+ Vec3.toArray(a, vertices, vc + 0)
+ Vec3.toArray(d, vertices, vc + 3)
+ Vec3.toArray(e, vertices, vc + 6)
+ Vec3.toArray(b, vertices, vc + 9)
+ for (let i = 0; i < 4; ++i) Vec3.toArray(nabde, normals, vc + i * 3)
+ indices[ic + 0] = vc / 3 + 2
+ indices[ic + 1] = vc / 3 + 1
+ indices[ic + 2] = vc / 3 + 0
+ indices[ic + 3] = vc / 3 + 0
+ indices[ic + 4] = vc / 3 + 3
+ indices[ic + 5] = vc / 3 + 2
+ vc += 12
+ ic += 6
+
+ // acdf
+ Vec3.toArray(d, vertices, vc + 0)
+ Vec3.toArray(a, vertices, vc + 3)
+ Vec3.toArray(c, vertices, vc + 6)
+ Vec3.toArray(f, vertices, vc + 9)
+ for (let i = 0; i < 4; ++i) Vec3.toArray(nacdf, normals, vc + i * 3)
+ indices[ic + 0] = vc / 3 + 2
+ indices[ic + 1] = vc / 3 + 1
+ indices[ic + 2] = vc / 3 + 0
+ indices[ic + 3] = vc / 3 + 0
+ indices[ic + 4] = vc / 3 + 3
+ indices[ic + 5] = vc / 3 + 2
+ vc += 12
+ ic += 6
+
+ // bcef
+ Vec3.toArray(e, vertices, vc + 0)
+ Vec3.toArray(f, vertices, vc + 3)
+ Vec3.toArray(c, vertices, vc + 6)
+ Vec3.toArray(b, vertices, vc + 9)
+ for (let i = 0; i < 4; ++i) Vec3.toArray(nbcef, normals, vc + i * 3)
+ indices[ic + 0] = vc / 3 + 2
+ indices[ic + 1] = vc / 3 + 1
+ indices[ic + 2] = vc / 3 + 0
+ indices[ic + 3] = vc / 3 + 0
+ indices[ic + 4] = vc / 3 + 3
+ indices[ic + 5] = vc / 3 + 2
+ vc += 12
+ ic += 6
+
+ return { vertices, normals, indices }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
index 271782dbcc2ef96c39780c838e5af20c33691a6c..95292334e241d173939257de1e73a4624607591a 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -24,17 +24,24 @@ import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerTraceIterator } from './util/polymer';
-import { Vec3 } from 'mol-math/linear-algebra';
+import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
-// import { radToDeg } from 'mol-math/misc';
+import { degToRad } from 'mol-math/misc';
+
+// TODO handle polymer ends properly
+// TODO avoid allocating Vec3, use global temp vars
const tmpNormal = Vec3.zero()
const tangentVec = Vec3.zero()
const normalVec = Vec3.zero()
const binormalVec = Vec3.zero()
-
const prevNormal = Vec3.zero()
+const t = Mat4.identity()
+const rotX90 = Mat4.fromRotation(Mat4.identity(), degToRad(90), Vec3.create(1, 0, 0))
+const rotY90 = Mat4.fromRotation(Mat4.identity(), degToRad(90), Vec3.create(0, 1, 0))
+const rotXY90 = Mat4.mul(Mat4.identity(), rotX90, rotY90)
+
const orthogonalizeTmpVec = Vec3.zero()
/** Get a vector that is similar to b but orthogonal to a */
function orthogonalize(out: Vec3, a: Vec3, b: Vec3) {
@@ -45,13 +52,9 @@ function orthogonalize(out: Vec3, a: Vec3, b: Vec3) {
function interpolateNormals(controlPoints: Helpers.NumberArray, tangentVectors: Helpers.NumberArray, normalVectors: Helpers.NumberArray, binormalVectors: Helpers.NumberArray, firstNormalVector: Vec3, lastNormalVector: Vec3) {
const n = controlPoints.length / 3
- // const n1 = n - 1
- // const angle = radToDeg(Math.acos(Vec3.dot(firstNormalVector, lastNormalVector)))
- // console.log('angle', angle)
if (Vec3.dot(firstNormalVector, lastNormalVector) < 0) {
Vec3.scale(lastNormalVector, lastNormalVector, -1)
- // console.log('flipped last normal vector')
}
Vec3.copy(prevNormal, firstNormalVector)
@@ -65,13 +68,6 @@ function interpolateNormals(controlPoints: Helpers.NumberArray, tangentVectors:
orthogonalize(normalVec, tangentVec, tmpNormal)
Vec3.toArray(normalVec, normalVectors, i * 3)
- // const deltaAngle = radToDeg(Math.acos(Vec3.dot(prevNormal, normalVec)))
- // if (deltaAngle > (angle / n1) * 5 && deltaAngle > 20) {
- // console.warn(i, 'large delta angle', deltaAngle)
- // }
- // if (Vec3.dot(normalVec, prevNormal) < 0) {
- // console.warn(i, 'flip compared to prev', radToDeg(Math.acos(Vec3.dot(prevNormal, normalVec))))
- // }
Vec3.copy(prevNormal, normalVec)
Vec3.normalize(binormalVec, Vec3.cross(binormalVec, tangentVec, normalVec))
@@ -107,11 +103,11 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- // builder.setId(elements[v.center.element])
builder.setId(v.center.element)
const isNucleic = v.moleculeType === MoleculeType.DNA || v.moleculeType === MoleculeType.RNA
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
+ const isHelix = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix)
const tension = (isNucleic || isSheet) ? 0.5 : 0.9
for (let j = 0; j <= linearSegments; ++j) {
@@ -198,7 +194,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
const arrowHeight = v.secStrucChange ? 1.7 : 0
builder.addSheet(controlPoints, normalVectors, binormalVectors, linearSegments, width, height, arrowHeight, true, true)
} else {
- if (SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix)) {
+ if (isHelix) {
width = 0.2; height = 1.0
} else if (isNucleic) {
width = 1.5; height = 0.3
@@ -206,6 +202,22 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
builder.addTube(controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, width, height, 1, true, true)
}
+ if ((isSheet && !v.secStrucChange) || !isSheet) {
+ const upVec = Vec3.zero()
+ let width = 0.5, height = 1.2, depth = 0.6
+ if (isNucleic) {
+ Vec3.fromArray(upVec, binormalVectors, Math.round(linearSegments / 2) * 3)
+ depth = 0.9
+ } else {
+ Vec3.fromArray(upVec, normalVectors, Math.round(linearSegments / 2) * 3)
+ }
+
+ Mat4.targetTo(t, v.t3, v.t1, upVec)
+ Mat4.mul(t, t, rotXY90)
+ Mat4.setTranslation(t, v.t2)
+ builder.addWedge(t, { width, height, depth })
+ }
+
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Polymer trace mesh', current: i, max: polymerElementCount });
}
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/shape/mesh-builder.ts
index 306670182c020c003780b71cc021b0b3ed7d6bf3..42f5383b828a1d55647c0b18986a84c8f529bb11 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/shape/mesh-builder.ts
@@ -8,9 +8,11 @@ import { ValueCell } from 'mol-util/value-cell'
import { Vec3, Mat4, Mat3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
-import Box, { BoxProps } from '../primitive/box';
-import Cylinder, { CylinderProps } from '../primitive/cylinder';
-import Icosahedron, { IcosahedronProps } from '../primitive/icosahedron';
+import { Box, BoxProps } from '../primitive/box';
+import { Plane, PlaneProps } from '../primitive/plane';
+import { Wedge, WedgeProps } from '../primitive/wedge';
+import { Cylinder, CylinderProps } from '../primitive/cylinder';
+import { Icosahedron, IcosahedronProps } from '../primitive/icosahedron';
import { Mesh } from './mesh';
import { getNormalMatrix } from '../util';
import { addSheet } from '../primitive/sheet';
@@ -31,6 +33,8 @@ export interface MeshBuilderState {
export interface MeshBuilder {
add(t: Mat4, _vertices: Float32Array, _normals: Float32Array, _indices?: Uint32Array): void
addBox(t: Mat4, props?: BoxProps): void
+ addPlane(t: Mat4, props?: PlaneProps): void
+ addWedge(t: Mat4, props?: WedgeProps): 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
@@ -128,8 +132,16 @@ export namespace MeshBuilder {
return {
add,
addBox: (t: Mat4, props?: BoxProps) => {
- const box = Box(props)
- add(t, box.vertices, box.normals, box.indices)
+ const { vertices, normals, indices } = Box(props)
+ add(t, vertices, normals, indices)
+ },
+ addPlane: (t: Mat4, props?: PlaneProps) => {
+ const { vertices, normals, indices } = Plane(props)
+ add(t, vertices, normals, indices)
+ },
+ addWedge: (t: Mat4, props?: WedgeProps) => {
+ const { vertices, normals, indices } = Wedge(props)
+ add(t, vertices, normals, indices)
},
addCylinder: (start: Vec3, end: Vec3, lengthScale: number, props: CylinderProps) => {
const d = Vec3.distance(start, end) * lengthScale
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 3f7e29c69e5b2ce52d280c52fdacb7870e4cfeef..ddd499c4b2d34ae291c606beacb9f196791a6b25 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -81,9 +81,9 @@ export class Stage {
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
// this.loadPdbid('2np2') // dna
- this.loadPdbid('1d66') // dna
+ // this.loadPdbid('1d66') // dna
// this.loadPdbid('9dna') // A form dna
- // this.loadPdbid('1bna') // B form dna
+ this.loadPdbid('1bna') // B form dna
// this.loadPdbid('199d') // C form dna
// this.loadPdbid('4lb6') // Z form dna
// this.loadPdbid('1egk') // 4-way dna-rna junction