From cb81b57e4cfe00ab4fe87994c762577fd0988d3d Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 20 Jul 2018 17:39:23 -0700
Subject: [PATCH] polymer refactoring, cleanup
---
.../structure/visual/polymer-trace-mesh.ts | 106 +-----------------
.../structure/visual/util/polymer.ts | 49 ++++++++
src/mol-math/linear-algebra/3d/mat4.ts | 9 ++
src/mol-math/linear-algebra/3d/vec3.ts | 16 ++-
4 files changed, 73 insertions(+), 107 deletions(-)
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 95292334e..a5d1d9b7e 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -23,57 +23,14 @@ import { Loci, EmptyLoci } from 'mol-model/loci';
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 { getPolymerElementCount, PolymerTraceIterator, interpolateNormals } from './util/polymer';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
-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) {
- Vec3.normalize(orthogonalizeTmpVec, Vec3.cross(orthogonalizeTmpVec, a, b))
- Vec3.normalize(out, Vec3.cross(out, orthogonalizeTmpVec, a))
- return out
-}
-
-function interpolateNormals(controlPoints: Helpers.NumberArray, tangentVectors: Helpers.NumberArray, normalVectors: Helpers.NumberArray, binormalVectors: Helpers.NumberArray, firstNormalVector: Vec3, lastNormalVector: Vec3) {
- const n = controlPoints.length / 3
-
- if (Vec3.dot(firstNormalVector, lastNormalVector) < 0) {
- Vec3.scale(lastNormalVector, lastNormalVector, -1)
- }
-
- Vec3.copy(prevNormal, firstNormalVector)
-
- for (let i = 0; i < n; ++i) {
- const t = i === 0 ? 0 : 1 / (n - i)
- Vec3.normalize(tmpNormal, Vec3.slerp(tmpNormal, prevNormal, lastNormalVector, t))
-
- Vec3.fromArray(tangentVec, tangentVectors, i * 3)
-
- orthogonalize(normalVec, tangentVec, tmpNormal)
- Vec3.toArray(normalVec, normalVectors, i * 3)
-
- Vec3.copy(prevNormal, normalVec)
-
- Vec3.normalize(binormalVec, Vec3.cross(binormalVec, tangentVec, normalVec))
- Vec3.toArray(binormalVec, binormalVectors, i * 3)
- }
-}
async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
@@ -91,8 +48,6 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
const tB = Vec3.zero()
const tangentVec = Vec3.zero()
- const tmp = Vec3.zero()
-
const pn = (linearSegments + 1) * 3
const controlPoints = new Float32Array(pn)
const tangentVectors = new Float32Array(pn)
@@ -128,63 +83,8 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
Vec3.toArray(tangentVec, tangentVectors, j * 3)
}
- const firstControlPoint = Vec3.zero()
- const lastControlPoint = Vec3.zero()
- const firstTangentVec = Vec3.zero()
- const lastTangentVec = Vec3.zero()
- const firstNormalVec = Vec3.zero()
- const lastNormalVec = Vec3.zero()
- const firstDirPoint = Vec3.zero()
- const lastDirPoint = Vec3.zero()
-
- Vec3.fromArray(firstControlPoint, controlPoints, 0)
- Vec3.fromArray(lastControlPoint, controlPoints, linearSegments * 3)
- Vec3.fromArray(firstTangentVec, tangentVectors, 0)
- Vec3.fromArray(lastTangentVec, tangentVectors, linearSegments * 3)
- Vec3.copy(firstDirPoint, v.d12)
- Vec3.copy(lastDirPoint, v.d23)
-
- Vec3.normalize(tmpNormal, Vec3.sub(tmp, firstControlPoint, firstDirPoint))
- orthogonalize(firstNormalVec, firstTangentVec, tmpNormal)
-
- Vec3.normalize(tmpNormal, Vec3.sub(tmp, lastControlPoint, lastDirPoint))
- orthogonalize(lastNormalVec, lastTangentVec, tmpNormal)
-
// console.log('ELEMENT', i)
- interpolateNormals(controlPoints, tangentVectors, normalVectors, binormalVectors, firstNormalVec, lastNormalVec)
-
- // const controlPoint = Vec3.zero()
- // for (let j = 0; j <= linearSegments; ++j) {
- // Vec3.fromArray(controlPoint, controlPoints, j * 3)
- // Vec3.fromArray(normalVec, normalVectors, j * 3)
- // Vec3.fromArray(binormalVec, binormalVectors, j * 3)
- // Vec3.fromArray(tangentVec, tangentVectors, j * 3)
- // builder.addIcosahedron(controlPoint, 0.25, 1)
- // builder.addCylinder(
- // controlPoint,
- // Vec3.add(tmp, controlPoint, normalVec),
- // 1.5,
- // { radiusTop: 0.07, radiusBottom: 0.07 }
- // )
- // builder.addCylinder(
- // controlPoint,
- // Vec3.add(tmp, controlPoint, binormalVec),
- // 0.8,
- // { radiusTop: 0.07, radiusBottom: 0.07 }
- // )
- // builder.addCylinder(
- // controlPoint,
- // Vec3.add(tmp, controlPoint, tangentVec),
- // j === 0 ? 2 : 1.5,
- // { radiusTop: 0.03, radiusBottom: 0.03 }
- // )
- // }
-
- // builder.addIcosahedron(v.t0, 0.25, 1)
- // builder.addIcosahedron(v.t1, 0.25, 1)
- // builder.addIcosahedron(v.t2, 0.25, 1)
- // builder.addIcosahedron(v.t3, 0.25, 1)
- // builder.addIcosahedron(v.t4, 0.25, 1)
+ interpolateNormals(controlPoints, tangentVectors, normalVectors, binormalVectors, v.d12, v.d23)
let width = 0.2, height = 0.2
@@ -213,7 +113,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
}
Mat4.targetTo(t, v.t3, v.t1, upVec)
- Mat4.mul(t, t, rotXY90)
+ Mat4.mul(t, t, Mat4.rotXY90)
Mat4.setTranslation(t, v.t2)
builder.addWedge(t, { width, height, depth })
}
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index 6b664c894..7918f8ccc 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -68,7 +68,56 @@ export function getPolymerGapCount(unit: Unit) {
return count
}
+const tmpNormal = Vec3.zero()
+const tangentVec = Vec3.zero()
+const normalVec = Vec3.zero()
+const binormalVec = Vec3.zero()
+const prevNormal = Vec3.zero()
+const firstControlPoint = Vec3.zero()
+const lastControlPoint = Vec3.zero()
+const firstTangentVec = Vec3.zero()
+const lastTangentVec = Vec3.zero()
+const firstNormalVec = Vec3.zero()
+const lastNormalVec = Vec3.zero()
+/**
+ * Populate normalVectors by interpolating from firstDirection to lastDirection with
+ * resulting vector perpendicular to tangentVectors and binormalVectors
+ */
+export function interpolateNormals(controlPoints: Helpers.NumberArray, tangentVectors: Helpers.NumberArray, normalVectors: Helpers.NumberArray, binormalVectors: Helpers.NumberArray, firstDirection: Vec3, lastDirection: Vec3) {
+ const n = controlPoints.length / 3
+
+ Vec3.fromArray(firstControlPoint, controlPoints, 0)
+ Vec3.fromArray(lastControlPoint, controlPoints, (n - 1) * 3)
+ Vec3.fromArray(firstTangentVec, tangentVectors, 0)
+ Vec3.fromArray(lastTangentVec, tangentVectors, (n - 1) * 3)
+
+ Vec3.normalize(tmpNormal, Vec3.sub(tmpNormal, firstControlPoint, firstDirection))
+ Vec3.orthogonalize(firstNormalVec, firstTangentVec, tmpNormal)
+
+ Vec3.normalize(tmpNormal, Vec3.sub(tmpNormal, lastControlPoint, lastDirection))
+ Vec3.orthogonalize(lastNormalVec, lastTangentVec, tmpNormal)
+
+ if (Vec3.dot(firstNormalVec, lastNormalVec) < 0) {
+ Vec3.scale(lastNormalVec, lastNormalVec, -1)
+ }
+ Vec3.copy(prevNormal, firstNormalVec)
+
+ for (let i = 0; i < n; ++i) {
+ const t = i === 0 ? 0 : 1 / (n - i)
+ Vec3.normalize(tmpNormal, Vec3.slerp(tmpNormal, prevNormal, lastNormalVec, t))
+
+ Vec3.fromArray(tangentVec, tangentVectors, i * 3)
+
+ Vec3.orthogonalize(normalVec, tangentVec, tmpNormal)
+ Vec3.toArray(normalVec, normalVectors, i * 3)
+
+ Vec3.copy(prevNormal, normalVec)
+
+ Vec3.normalize(binormalVec, Vec3.cross(binormalVec, tangentVec, normalVec))
+ Vec3.toArray(binormalVec, binormalVectors, i * 3)
+ }
+}
/** Iterates over consecutive pairs of residues/coarse elements in polymers */
export function PolymerBackboneIterator(unit: Unit): Iterator<PolymerBackbonePair> {
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index 603d486f6..92ae72e4c 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -20,8 +20,10 @@
import { EPSILON, equalEps } from './common'
import Vec3 from './vec3';
import Quat from './quat';
+import { degToRad } from '../../misc';
interface Mat4 extends Array<number> { [d: number]: number, '@type': 'mat4', length: 16 }
+interface ReadonlyMat4 extends Array<number> { readonly [d: number]: number, '@type': 'mat4', length: 16 }
function Mat4() {
return Mat4.zero();
@@ -830,6 +832,13 @@ namespace Mat4 {
}
return out;
}
+
+ /** Rotation matrix for 90deg rotation around x-axis */
+ export const rotX90: ReadonlyMat4 = Mat4.fromRotation(Mat4.identity(), degToRad(90), Vec3.create(1, 0, 0))
+ /** Rotation matrix for 90deg rotation around y-axis */
+ export const rotY90: ReadonlyMat4 = Mat4.fromRotation(Mat4.identity(), degToRad(90), Vec3.create(0, 1, 0))
+ /** Rotation matrix for 90deg rotation around first x-axis and then y-axis */
+ export const rotXY90: ReadonlyMat4 = Mat4.mul(Mat4.identity(), rotX90, rotY90)
}
export default Mat4
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index d95ab25e5..4b8efbb13 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -415,14 +415,22 @@ namespace Vec3 {
}
export function isZero(v: Vec3) {
- return v[0] === 0 && v[1] === 0 && v[2] === 0
+ return v[0] === 0 && v[1] === 0 && v[2] === 0;
}
export function projectPointOnVector(out: Vec3, point: Vec3, vector: Vec3, origin: Vec3) {
// point.sub(origin).projectOnVector(vector).add(origin)
- Vec3.sub(out, Vec3.copy(out, point), origin)
- const scalar = Vec3.dot(vector, out) / Vec3.squaredMagnitude(vector);
- return Vec3.add(out, Vec3.scale(out, Vec3.copy(out, vector), scalar), origin);
+ sub(out, copy(out, point), origin)
+ const scalar = dot(vector, out) / squaredMagnitude(vector);
+ return add(out, scale(out, copy(out, vector), scalar), origin);
+ }
+
+ const orthogonalizeTmp = zero();
+ /** Get a vector that is similar to b but orthogonal to a */
+ export function orthogonalize(out: Vec3, a: Vec3, b: Vec3) {
+ normalize(orthogonalizeTmp, cross(orthogonalizeTmp, a, b));
+ normalize(out, cross(out, orthogonalizeTmp, a));
+ return out;
}
export function toString(a: Vec3) {
--
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