From 5d36a9253eaa0f4553a5c6e8b89b6dcc717b4aec Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 31 Jul 2018 20:34:40 -0700
Subject: [PATCH] wip, carbohydrate visual
---
src/mol-geo/primitive/polygon.ts | 2 +-
src/mol-geo/primitive/prism.ts | 16 ++++++++--------
.../visual/carbohydrate-symbol-mesh.ts | 17 +++++++++--------
src/mol-math/linear-algebra/3d/mat4.ts | 6 ++++++
src/mol-view/stage.ts | 4 ++--
5 files changed, 26 insertions(+), 19 deletions(-)
diff --git a/src/mol-geo/primitive/polygon.ts b/src/mol-geo/primitive/polygon.ts
index 83ff7c8c0..b7db9972e 100644
--- a/src/mol-geo/primitive/polygon.ts
+++ b/src/mol-geo/primitive/polygon.ts
@@ -12,7 +12,7 @@ export function polygon(sideCount: number, shift: boolean) {
const points = new Float32Array(sideCount * 2)
const radius = sideCount <= 4 ? Math.sqrt(2) / 2 : 0.6
- const offset = shift ? 0 : 1
+ const offset = shift ? 1 : 0
for (let i = 0, il = 2 * sideCount; i < il; i += 2) {
const c = (i + offset) / sideCount * Math.PI
diff --git a/src/mol-geo/primitive/prism.ts b/src/mol-geo/primitive/prism.ts
index 445ceed90..728d18404 100644
--- a/src/mol-geo/primitive/prism.ts
+++ b/src/mol-geo/primitive/prism.ts
@@ -78,7 +78,7 @@ export function Wedge() {
let box: Primitive
export function Box() {
- if (!box) box = Prism(polygon(4, false))
+ if (!box) box = Prism(polygon(4, true))
return box
}
@@ -88,14 +88,14 @@ export function DiamondPrism() {
return diamond
}
-let hexagonalPrism: Primitive
-export function HexagonalPrism() {
- if (!hexagonalPrism) hexagonalPrism = Prism(polygon(5, false))
- return hexagonalPrism
-}
-
let pentagonalPrism: Primitive
export function PentagonalPrism() {
- if (!pentagonalPrism) pentagonalPrism = Prism(polygon(6, true))
+ if (!pentagonalPrism) pentagonalPrism = Prism(polygon(5, false))
return pentagonalPrism
+}
+
+let hexagonalPrism: Primitive
+export function HexagonalPrism() {
+ if (!hexagonalPrism) hexagonalPrism = Prism(polygon(6, true))
+ return hexagonalPrism
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
index 265e32e78..70f363b02 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -83,44 +83,45 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
break
case SaccharideShapes.FlatBox:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
+ Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
builder.addBox(t)
break
case SaccharideShapes.FilledStar:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
+ Mat4.mul(t, t, Mat4.rotZY90)
builder.addStar(t, { outerRadius: side, innerRadius: side / 2, thickness: side / 2, pointCount: 5 })
break
case SaccharideShapes.FilledDiamond:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
+ Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addOctahedron(t)
break
case SaccharideShapes.DividedDiamond:
// TODO split
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
+ Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addOctahedron(t)
break
case SaccharideShapes.FlatDiamond:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
+ Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2))
builder.addDiamondPrism(t)
+ break
case SaccharideShapes.Pentagon:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
+ Mat4.mul(t, t, Mat4.rotZY90)
Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
builder.addPentagonalPrism(t)
break
case SaccharideShapes.FlatHexagon:
default:
centerAlign(cGeo.center, cGeo.normal, cGeo.direction)
- Mat4.mul(t, t, Mat4.rotY90)
- Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2))
+ Mat4.mul(t, t, Mat4.rotZYZ90)
+ Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side , side / 2))
builder.addHexagonalPrism(t)
break
}
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index dd56c80e6..ddd7eaafd 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -877,8 +877,14 @@ namespace Mat4 {
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 z-axis */
+ export const rotZ90: ReadonlyMat4 = Mat4.fromRotation(Mat4.identity(), degToRad(90), Vec3.create(0, 0, 1))
/** Rotation matrix for 90deg rotation around first x-axis and then y-axis */
export const rotXY90: ReadonlyMat4 = Mat4.mul(Mat4.identity(), rotX90, rotY90)
+ /** Rotation matrix for 90deg rotation around first z-axis and then y-axis */
+ export const rotZY90: ReadonlyMat4 = Mat4.mul(Mat4.identity(), rotZ90, rotY90)
+ /** Rotation matrix for 90deg rotation around first z-axis and then y-axis and then z-axis */
+ export const rotZYZ90: ReadonlyMat4 = Mat4.mul(Mat4.identity(), rotZY90, rotZ90)
}
export default Mat4
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index b806d5407..5ebbbb2db 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -98,14 +98,14 @@ export class Stage {
// this.loadPdbid('3sn6') // discontinuous chains
// this.loadPdbid('2zex') // contains carbohydrate polymer
// this.loadPdbid('3sgj') // contains carbohydrate polymer
- this.loadPdbid('3ina') // contains GlcN and IdoA
+ // this.loadPdbid('3ina') // contains GlcN and IdoA
// this.loadPdbid('1umz') // contains Xyl (Xyloglucan)
// this.loadPdbid('1mfb') // contains Abe
// this.loadPdbid('2gdu') // contains sucrose
// this.loadPdbid('2fnc') // contains maltotriose
// this.loadPdbid('4zs9') // contains raffinose
// this.loadPdbid('2yft') // contains kestose
- // this.loadPdbid('2b5t') // contains large carbohydrate polymer
+ this.loadPdbid('2b5t') // contains large carbohydrate polymer
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.cif`)
// this.loadMmcifUrl(`../../examples/1crn.cif`)
--
GitLab