diff --git a/src/mol-app/ui/transform/backbone.tsx b/src/mol-app/ui/transform/backbone.tsx
index 76bb3475c7ed50883e426c557bff7f326500518f..3586f32082a2c0a7712bba2000880c4935116528 100644
--- a/src/mol-app/ui/transform/backbone.tsx
+++ b/src/mol-app/ui/transform/backbone.tsx
@@ -15,21 +15,12 @@ import { Toggle } from '../controls/common';
import { BackboneEntity } from 'mol-view/state/entity';
import { BackboneUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme } from 'mol-geo/theme';
+import { ColorTheme, SizeTheme, ColorThemeNames, ColorThemeName } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
-export const ColorThemeInfo = {
- 'atom-index': {},
- 'chain-id': {},
- 'element-symbol': {},
- 'instance-index': {},
- 'uniform': {}
-}
-export type ColorThemeInfo = keyof typeof ColorThemeInfo
-
interface BackboneState {
doubleSided: boolean
flipSided: boolean
@@ -86,7 +77,7 @@ export class Backbone extends View<Controller<any>, BackboneState, { transform:
return <option key={value} value={value}>{value.toString()}</option>
})
- const colorThemeOptions = Object.keys(ColorThemeInfo).map((name, idx) => {
+ const colorThemeOptions = ColorThemeNames.map((name, idx) => {
return <option key={name} value={name}>{name}</option>
})
@@ -137,19 +128,12 @@ export class Backbone extends View<Controller<any>, BackboneState, { transform:
className='molstar-form-control'
value={this.state.colorTheme.name}
onChange={(e) => {
- const colorThemeName = e.target.value as ColorThemeInfo
- if (colorThemeName === 'uniform') {
- this.update({
- colorTheme: {
- name: colorThemeName,
- value: this.state.colorValue
- }
- })
- } else {
- this.update({
- colorTheme: { name: colorThemeName }
- })
- }
+ this.update({
+ colorTheme: {
+ name: e.target.value as ColorThemeName,
+ value: this.state.colorValue
+ }
+ })
}}
>
{colorThemeOptions}
diff --git a/src/mol-app/ui/transform/ball-and-stick.tsx b/src/mol-app/ui/transform/ball-and-stick.tsx
index 9ed5c5e35c133e5193d4e33c0e821cbce760a607..9ccf4be39ee89a4ca40215df6071936c0b05894d 100644
--- a/src/mol-app/ui/transform/ball-and-stick.tsx
+++ b/src/mol-app/ui/transform/ball-and-stick.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { DistanceRestraintEntity } from 'mol-view/state/entity';
import { DistanceRestraintUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme } from 'mol-geo/theme';
+import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -23,6 +23,7 @@ import { Unit } from 'mol-model/structure';
export const ColorThemeInfo = {
'atom-index': {},
+ 'carbohydrate-symbol': {},
'chain-id': {},
'element-symbol': {},
'instance-index': {},
@@ -89,7 +90,7 @@ export class BallAndStick extends View<Controller<any>, BallAndStickState, { tra
return <option key={name} value={name}>{name}</option>
})
- const colorThemeOptions = Object.keys(ColorThemeInfo).map((name, idx) => {
+ const colorThemeOptions = ColorThemeNames.map((name, idx) => {
return <option key={name} value={name}>{name}</option>
})
@@ -128,19 +129,12 @@ export class BallAndStick extends View<Controller<any>, BallAndStickState, { tra
className='molstar-form-control'
value={this.state.colorTheme.name}
onChange={(e) => {
- const colorThemeName = e.target.value as ColorThemeInfo
- if (colorThemeName === 'uniform') {
- this.update({
- colorTheme: {
- name: colorThemeName,
- value: this.state.colorValue
- }
- })
- } else {
- this.update({
- colorTheme: { name: colorThemeName }
- })
- }
+ this.update({
+ colorTheme: {
+ name: e.target.value as ColorThemeName,
+ value: this.state.colorValue
+ }
+ })
}}
>
{colorThemeOptions}
diff --git a/src/mol-app/ui/transform/cartoon.tsx b/src/mol-app/ui/transform/cartoon.tsx
index da5da45e7f27e5feb50f7ef2932637e82d3eb35d..eb8f356b580ab58ef91292a75a1c345701c503aa 100644
--- a/src/mol-app/ui/transform/cartoon.tsx
+++ b/src/mol-app/ui/transform/cartoon.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { CartoonEntity } from 'mol-view/state/entity';
import { CartoonUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme } from 'mol-geo/theme';
+import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -23,6 +23,7 @@ import { Unit } from 'mol-model/structure';
export const ColorThemeInfo = {
'atom-index': {},
+ 'carbohydrate-symbol': {},
'chain-id': {},
'element-symbol': {},
'instance-index': {},
@@ -86,7 +87,7 @@ export class Cartoon extends View<Controller<any>, CartoonState, { transform: Ca
return <option key={value} value={value}>{value.toString()}</option>
})
- const colorThemeOptions = Object.keys(ColorThemeInfo).map((name, idx) => {
+ const colorThemeOptions = ColorThemeNames.map((name, idx) => {
return <option key={name} value={name}>{name}</option>
})
@@ -137,19 +138,12 @@ export class Cartoon extends View<Controller<any>, CartoonState, { transform: Ca
className='molstar-form-control'
value={this.state.colorTheme.name}
onChange={(e) => {
- const colorThemeName = e.target.value as ColorThemeInfo
- if (colorThemeName === 'uniform') {
- this.update({
- colorTheme: {
- name: colorThemeName,
- value: this.state.colorValue
- }
- })
- } else {
- this.update({
- colorTheme: { name: colorThemeName }
- })
- }
+ this.update({
+ colorTheme: {
+ name: e.target.value as ColorThemeName,
+ value: this.state.colorValue
+ }
+ })
}}
>
{colorThemeOptions}
diff --git a/src/mol-app/ui/transform/distance-restraint.tsx b/src/mol-app/ui/transform/distance-restraint.tsx
index cf74c3992c5b83c9c9fc57b21b1dc3743c69019f..a032eeaf2a37d6f41ee36575a841f7537167befa 100644
--- a/src/mol-app/ui/transform/distance-restraint.tsx
+++ b/src/mol-app/ui/transform/distance-restraint.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { DistanceRestraintEntity } from 'mol-view/state/entity';
import { DistanceRestraintUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme } from 'mol-geo/theme';
+import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -23,6 +23,7 @@ import { Unit } from 'mol-model/structure';
export const ColorThemeInfo = {
'atom-index': {},
+ 'carbohydrate-symbol': {},
'chain-id': {},
'element-symbol': {},
'instance-index': {},
@@ -89,7 +90,7 @@ export class DistanceRestraint extends View<Controller<any>, DistanceRestraintSt
return <option key={name} value={name}>{name}</option>
})
- const colorThemeOptions = Object.keys(ColorThemeInfo).map((name, idx) => {
+ const colorThemeOptions = ColorThemeNames.map((name, idx) => {
return <option key={name} value={name}>{name}</option>
})
@@ -128,19 +129,12 @@ export class DistanceRestraint extends View<Controller<any>, DistanceRestraintSt
className='molstar-form-control'
value={this.state.colorTheme.name}
onChange={(e) => {
- const colorThemeName = e.target.value as ColorThemeInfo
- if (colorThemeName === 'uniform') {
- this.update({
- colorTheme: {
- name: colorThemeName,
- value: this.state.colorValue
- }
- })
- } else {
- this.update({
- colorTheme: { name: colorThemeName }
- })
- }
+ this.update({
+ colorTheme: {
+ name: e.target.value as ColorThemeName,
+ value: this.state.colorValue
+ }
+ })
}}
>
{colorThemeOptions}
diff --git a/src/mol-app/ui/transform/spacefill.tsx b/src/mol-app/ui/transform/spacefill.tsx
index 55377180ac8c6eaa6b29cc678649e40c47e76530..42719bd63ffca7cd02ad3bda4edff290f610fd8d 100644
--- a/src/mol-app/ui/transform/spacefill.tsx
+++ b/src/mol-app/ui/transform/spacefill.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { SpacefillEntity } from 'mol-view/state/entity';
import { SpacefillUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorTheme, SizeTheme } from 'mol-geo/theme';
+import { ColorTheme, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -23,6 +23,7 @@ import { Unit } from 'mol-model/structure';
export const ColorThemeInfo = {
'atom-index': {},
+ 'carbohydrate-symbol': {},
'chain-id': {},
'element-symbol': {},
'instance-index': {},
@@ -86,7 +87,7 @@ export class Spacefill extends View<Controller<any>, SpacefillState, { transform
return <option key={value} value={value}>{value.toString()}</option>
})
- const colorThemeOptions = Object.keys(ColorThemeInfo).map((name, idx) => {
+ const colorThemeOptions = ColorThemeNames.map((name, idx) => {
return <option key={name} value={name}>{name}</option>
})
@@ -137,19 +138,12 @@ export class Spacefill extends View<Controller<any>, SpacefillState, { transform
className='molstar-form-control'
value={this.state.colorTheme.name}
onChange={(e) => {
- const colorThemeName = e.target.value as ColorThemeInfo
- if (colorThemeName === 'uniform') {
- this.update({
- colorTheme: {
- name: colorThemeName,
- value: this.state.colorValue
- }
- })
- } else {
- this.update({
- colorTheme: { name: colorThemeName }
- })
- }
+ this.update({
+ colorTheme: {
+ name: e.target.value as ColorThemeName,
+ value: this.state.colorValue
+ }
+ })
}}
>
{colorThemeOptions}
diff --git a/src/mol-geo/primitive/box.ts b/src/mol-geo/primitive/box.ts
index ee7e5b906485c4546c6a9bfb29e07c11b627e35c..990730641206701eda7102ee6e4fb8441398dd95 100644
--- a/src/mol-geo/primitive/box.ts
+++ b/src/mol-geo/primitive/box.ts
@@ -4,72 +4,55 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-// adapted from three.js, MIT License Copyright 2010-2018 three.js authors
-
import { Vec3 } from 'mol-math/linear-algebra'
-import { Primitive } from './primitive';
-
-export const DefaultBoxProps = {
- width: 1,
- height: 1,
- depth: 1
-}
-export type BoxProps = Partial<typeof DefaultBoxProps>
-
-const tmpVector = Vec3.zero();
-
-export function Box(props?: BoxProps): Primitive {
- const { width, height, depth } = { ...DefaultBoxProps, ...props }
-
- // buffers
- const vertices = new Float32Array(72);
- const normals = new Float32Array(72);
- const indices = new Uint32Array(36);
-
- // helper variables
- let vertexCount = 0;
-
- // build each side of the box geometry
- buildPlane(2, 1, 0, -1, -1, depth, height, width); // px
- buildPlane(2, 1, 0, 1, -1, depth, height, -width); // nx
- buildPlane(0, 2, 1, 1, 1, width, depth, height); // py
- buildPlane(0, 2, 1, 1, -1, width, depth, -height); // ny
- buildPlane(0, 1, 2, 1, -1, width, height, depth); // pz
- buildPlane(0, 1, 2, -1, -1, width, height, -depth); // nz
+import { Primitive, PrimitiveBuilder } from './primitive';
+import { polygon } from './polygon'
- return { vertices, normals, indices }
+const a = Vec3.zero(), b = Vec3.zero(), c = Vec3.zero(), d = Vec3.zero()
+const points = polygon(4, true)
- function buildPlane(u: number, v: number, w: number, udir: number, vdir: number, width: number, height: number, depth: number) {
- // generate vertices and normals
- for (let iy = 0; iy < 2; ++iy) {
- const y = iy * height - height / 2;
- for (let ix = 0; ix < 2; ++ix) {
- const x = ix * width - width / 2;
-
- // set values to correct vector component and add to vertex buffer
- tmpVector[u] = x * udir;
- tmpVector[v] = y * vdir;
- tmpVector[w] = depth / 2;
- Vec3.toArray(tmpVector, vertices, vertexCount * 3);
+/**
+ * Create a box
+ */
+function createBox(perforated: boolean): Primitive {
+ const builder = PrimitiveBuilder(12)
+
+ // create sides
+ for (let i = 0; i < 4; ++i) {
+ const ni = (i + 1) % 4
+ Vec3.set(a, points[i * 2], points[i * 2 + 1], -0.5)
+ Vec3.set(b, points[ni * 2], points[ni * 2 + 1], -0.5)
+ Vec3.set(c, points[ni * 2], points[ni * 2 + 1], 0.5)
+ Vec3.set(d, points[i * 2], points[i * 2 + 1], 0.5)
+ builder.add(a, b, c)
+ if (!perforated) builder.add(c, d, a)
+ }
- // set values to correct vector component and add to normal buffer
- tmpVector[u] = 0;
- tmpVector[v] = 0;
- tmpVector[w] = depth > 0 ? 1 : -1;
- Vec3.toArray(tmpVector, normals, vertexCount * 3);
+ // create bases
+ Vec3.set(a, points[0], points[1], -0.5)
+ Vec3.set(b, points[2], points[3], -0.5)
+ Vec3.set(c, points[4], points[5], -0.5)
+ Vec3.set(d, points[6], points[7], -0.5)
+ builder.add(a, b, c)
+ if (!perforated) builder.add(c, d, a)
+ Vec3.set(a, points[0], points[1], 0.5)
+ Vec3.set(b, points[2], points[3], 0.5)
+ Vec3.set(c, points[4], points[5], 0.5)
+ Vec3.set(d, points[6], points[7], 0.5)
+ builder.add(a, b, c)
+ if (!perforated) builder.add(c, d, a)
+
+ return builder.getPrimitive()
+}
- ++vertexCount;
- }
- }
+let box: Primitive
+export function Box() {
+ if (!box) box = createBox(false)
+ return box
+}
- // faces
- const vc = vertexCount - 4
- const iidx = (vc / 2) * 3
- indices[iidx] = vc
- indices[iidx + 1] = vc + 2
- indices[iidx + 2] = vc + 1
- indices[iidx + 3] = vc + 2
- indices[iidx + 4] = vc + 3
- indices[iidx + 5] = vc + 1
- }
+let perforatedBox: Primitive
+export function PerforatedBox() {
+ if (!perforatedBox) perforatedBox = createBox(true)
+ return perforatedBox
}
\ No newline at end of file
diff --git a/src/mol-geo/primitive/octahedron.ts b/src/mol-geo/primitive/octahedron.ts
index 3375145fa02c4984f6121038392c6b6cd90b696b..cb23691c9cb84b24b83677026009649e1a462453 100644
--- a/src/mol-geo/primitive/octahedron.ts
+++ b/src/mol-geo/primitive/octahedron.ts
@@ -10,13 +10,20 @@ export const octahedronVertices: ReadonlyArray<number> = [
0.5, 0, 0, -0.5, 0, 0, 0, 0.5, 0,
0, -0.5, 0, 0, 0, 0.5, 0, 0, -0.5
];
-
export const octahedronIndices: ReadonlyArray<number> = [
0, 2, 4, 0, 4, 3, 0, 3, 5,
0, 5, 2, 1, 2, 5, 1, 5, 3,
1, 3, 4, 1, 4, 2
];
+export const perforatedOctahedronIndices: ReadonlyArray<number> = [
+ 0, 2, 4, 0, 4, 3,
+ // 0, 3, 5, 0, 5, 2,
+ 1, 2, 5, 1, 5, 3,
+ // 1, 3, 4, 1, 4, 2
+];
const octahedron = createPrimitive(octahedronVertices, octahedronIndices)
+const perforatedOctahedron = createPrimitive(octahedronVertices, perforatedOctahedronIndices)
-export function Octahedron(): Primitive { return octahedron }
\ No newline at end of file
+export function Octahedron(): Primitive { return octahedron }
+export function PerforatedOctahedron(): Primitive { return perforatedOctahedron }
\ No newline at end of file
diff --git a/src/mol-geo/primitive/prism.ts b/src/mol-geo/primitive/prism.ts
index 681bb3260cffacfa9e4f48d50bd0aafbfe54594e..d7ad601033b04cd4429ae07d725dc2ba57e5beef 100644
--- a/src/mol-geo/primitive/prism.ts
+++ b/src/mol-geo/primitive/prism.ts
@@ -12,12 +12,13 @@ const on = Vec3.create(0, 0, -0.5), op = Vec3.create(0, 0, 0.5)
const a = Vec3.zero(), b = Vec3.zero(), c = Vec3.zero(), d = Vec3.zero()
/**
- * Create a prism with a poligonal base
+ * Create a prism with a poligonal base of 5 or more points
*/
export function Prism(points: ArrayLike<number>): Primitive {
const sideCount = points.length / 2
- const baseCount = sideCount === 3 ? 1 : sideCount === 4 ? 2 : sideCount
- const count = 2 * baseCount + 2 * sideCount
+ if (sideCount < 5) throw new Error('need at least 5 points to build a prism')
+
+ const count = 4 * sideCount
const builder = PrimitiveBuilder(count)
// create sides
@@ -32,55 +33,19 @@ export function Prism(points: ArrayLike<number>): Primitive {
}
// create bases
- if (sideCount === 3) {
- Vec3.set(a, points[0], points[1], -0.5)
- Vec3.set(b, points[2], points[3], -0.5)
- Vec3.set(c, points[4], points[5], -0.5)
- builder.add(a, b, c)
- Vec3.set(a, points[0], points[1], 0.5)
- Vec3.set(b, points[2], points[3], 0.5)
- Vec3.set(c, points[4], points[5], 0.5)
- builder.add(c, b, a)
- } else if (sideCount === 4) {
- Vec3.set(a, points[0], points[1], -0.5)
- Vec3.set(b, points[2], points[3], -0.5)
- Vec3.set(c, points[4], points[5], -0.5)
- Vec3.set(d, points[6], points[7], -0.5)
- builder.add(a, b, c)
- builder.add(c, d, a)
- Vec3.set(a, points[0], points[1], 0.5)
- Vec3.set(b, points[2], points[3], 0.5)
- Vec3.set(c, points[4], points[5], 0.5)
- Vec3.set(d, points[6], points[7], 0.5)
- builder.add(a, b, c)
- builder.add(c, d, a)
- } else {
- for (let i = 0; i < sideCount; ++i) {
- const ni = (i + 1) % sideCount
- Vec3.set(a, points[i * 2], points[i * 2 + 1], -0.5)
- Vec3.set(b, points[ni * 2], points[ni * 2 + 1], -0.5)
- builder.add(a, b, on)
- Vec3.set(a, points[i * 2], points[i * 2 + 1], 0.5)
- Vec3.set(b, points[ni * 2], points[ni * 2 + 1], 0.5)
- builder.add(op, b, a)
- }
+ for (let i = 0; i < sideCount; ++i) {
+ const ni = (i + 1) % sideCount
+ Vec3.set(a, points[i * 2], points[i * 2 + 1], -0.5)
+ Vec3.set(b, points[ni * 2], points[ni * 2 + 1], -0.5)
+ builder.add(a, b, on)
+ Vec3.set(a, points[i * 2], points[i * 2 + 1], 0.5)
+ Vec3.set(b, points[ni * 2], points[ni * 2 + 1], 0.5)
+ builder.add(op, b, a)
}
return builder.getPrimitive()
}
-let wedge: Primitive
-export function Wedge() {
- if (!wedge) wedge = Prism(polygon(3, false))
- return wedge
-}
-
-let box: Primitive
-export function Box() {
- if (!box) box = Prism(polygon(4, true))
- return box
-}
-
let diamond: Primitive
export function DiamondPrism() {
if (!diamond) diamond = Prism(polygon(4, false))
diff --git a/src/mol-geo/primitive/pyramid.ts b/src/mol-geo/primitive/pyramid.ts
index a188f7232fbd1a2ae5dff1edc04fcdef6e0c3b6a..1a0fb1ae9bf801d9eb575f1c0e67950be5288d70 100644
--- a/src/mol-geo/primitive/pyramid.ts
+++ b/src/mol-geo/primitive/pyramid.ts
@@ -5,7 +5,7 @@
*/
import { Vec3 } from 'mol-math/linear-algebra'
-import { Primitive, PrimitiveBuilder } from './primitive';
+import { Primitive, PrimitiveBuilder, createPrimitive } from './primitive';
import { polygon } from './polygon'
const on = Vec3.create(0, 0, -0.5), op = Vec3.create(0, 0, 0.5)
@@ -57,4 +57,31 @@ let octagonalPyramide: Primitive
export function OctagonalPyramide() {
if (!octagonalPyramide) octagonalPyramide = Pyramide(polygon(8, true))
return octagonalPyramide
+}
+
+//
+
+let perforatedOctagonalPyramide: Primitive
+export function PerforatedOctagonalPyramide() {
+ if (!perforatedOctagonalPyramide) {
+ const points = polygon(8, true)
+ const vertices = new Float32Array(8 * 3 + 6)
+ for (let i = 0; i < 8; ++i) {
+ vertices[i * 3] = points[i * 2]
+ vertices[i * 3 + 1] = points[i * 2 + 1]
+ vertices[i * 3 + 2] = -0.5
+ }
+ vertices[8 * 3] = 0
+ vertices[8 * 3 + 1] = 0
+ vertices[8 * 3 + 2] = -0.5
+ vertices[8 * 3 + 3] = 0
+ vertices[8 * 3 + 4] = 0
+ vertices[8 * 3 + 5] = 0.5
+ const indices: ReadonlyArray<number> = [
+ 0, 1, 8, 1, 2, 8, 4, 5, 8, 5, 6, 8,
+ 2, 3, 9, 3, 4, 9, 6, 7, 9, 7, 0, 9
+ ];
+ perforatedOctagonalPyramide = createPrimitive(vertices, indices)
+ }
+ return perforatedOctagonalPyramide
}
\ No newline at end of file
diff --git a/src/mol-geo/primitive/wedge.ts b/src/mol-geo/primitive/wedge.ts
index 1b00533691b83741e101278050762b9c8db19dd9..3b2d317b9e3575e1aaf527e3697638692179c648 100644
--- a/src/mol-geo/primitive/wedge.ts
+++ b/src/mol-geo/primitive/wedge.ts
@@ -5,118 +5,44 @@
*/
import { Vec3 } from 'mol-math/linear-algebra'
-import { Primitive } from './primitive';
+import { Primitive, PrimitiveBuilder } from './primitive';
+import { polygon } from './polygon'
-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): Primitive {
- 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))
+const a = Vec3.zero(), b = Vec3.zero(), c = Vec3.zero(), d = Vec3.zero()
+const points = polygon(3, false)
- 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
+/**
+ * Create a prism with a poligonal base
+ */
+export function createWedge(): Primitive {
+ const builder = PrimitiveBuilder(8)
+
+ // create sides
+ for (let i = 0; i < 3; ++i) {
+ const ni = (i + 1) % 3
+ Vec3.set(a, points[i * 2], points[i * 2 + 1], -0.5)
+ Vec3.set(b, points[ni * 2], points[ni * 2 + 1], -0.5)
+ Vec3.set(c, points[ni * 2], points[ni * 2 + 1], 0.5)
+ Vec3.set(d, points[i * 2], points[i * 2 + 1], 0.5)
+ builder.add(a, b, c)
+ builder.add(c, d, a)
+ }
+
+ // create bases
+ Vec3.set(a, points[0], points[1], -0.5)
+ Vec3.set(b, points[2], points[3], -0.5)
+ Vec3.set(c, points[4], points[5], -0.5)
+ builder.add(a, b, c)
+ Vec3.set(a, points[0], points[1], 0.5)
+ Vec3.set(b, points[2], points[3], 0.5)
+ Vec3.set(c, points[4], points[5], 0.5)
+ builder.add(c, b, a)
+
+ return builder.getPrimitive()
+}
- return { vertices, normals, indices }
+let wedge: Primitive
+export function Wedge() {
+ if (!wedge) wedge = createWedge()
+ return wedge
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index bc6c343baadbcbfa74b75a8759fa680a9fedfb03..7b95c2c54e9f71eb35e7fc66fe9d3a6868c9cce0 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -35,6 +35,7 @@ export function StructureRepresentation<P extends StructureProps>(visualCtor: ()
function create(structure: Structure, props: P = {} as P) {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, structure))
+ _props.colorTheme!.structure = structure
return Task.create('Creating StructureRepresentation', async ctx => {
if (!_structure) {
@@ -56,6 +57,7 @@ export function StructureRepresentation<P extends StructureProps>(visualCtor: ()
function update(props: P) {
return Task.create('Updating StructureRepresentation', async ctx => {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, _structure))
+ _props.colorTheme!.structure = _structure
if (!await visual.update(ctx, _props)) {
await visual.create(ctx, _structure, _props)
@@ -98,6 +100,7 @@ export function StructureUnitsRepresentation<P extends StructureProps>(visualCto
function create(structure: Structure, props: P = {} as P) {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, structure))
+ _props.colorTheme!.structure = structure
return Task.create('Creating StructureRepresentation', async ctx => {
if (!_structure) {
@@ -151,6 +154,7 @@ export function StructureUnitsRepresentation<P extends StructureProps>(visualCto
function update(props: P) {
return Task.create('Updating StructureRepresentation', async ctx => {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, _structure))
+ _props.colorTheme!.structure = _structure
visuals.forEach(async ({ visual, group }) => {
if (!await visual.update(ctx, _props)) {
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
index 49676477f3217edfaf6f8897a03f80e2927481a0..0bebb4471114e9413bbce503881f0c0f89db3fe5 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -78,14 +78,13 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
currentStructure = structure
const { colorTheme } = { ...DefaultCarbohydrateLinkProps, ...props }
+ const elementCount = structure.carbohydrates.links.length
const instanceCount = 1
- const elementCount = currentStructure.elementCount
mesh = await createCarbohydrateLinkCylinderMesh(ctx, currentStructure, currentProps, mesh)
- // console.log(mesh)
const transforms = createIdentityTransform()
- const color = createColors(createCarbohydrateLinkIterator(structure), colorTheme)
+ const color = createColors(CarbohydrateLinkIterator(structure), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -114,7 +113,7 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
}
if (updateColor) {
- createColors(createCarbohydrateLinkIterator(currentStructure), newProps.colorTheme, renderObject.values)
+ createColors(CarbohydrateLinkIterator(currentStructure), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
@@ -135,7 +134,7 @@ export function CarbohydrateLinkVisual(): StructureVisual<CarbohydrateLinkProps>
}
}
-function createCarbohydrateLinkIterator(structure: Structure): LocationIterator {
+function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
const { elements, links } = structure.carbohydrates
const elementCount = links.length
const instanceCount = 1
@@ -178,7 +177,7 @@ function markLink(loci: Loci, action: MarkerAction, structure: Structure, values
const tMarker = values.tMarker
const { getLinkIndex } = structure.carbohydrates
- const elementCount = structure.carbohydrates.elements.length
+ const elementCount = structure.carbohydrates.links.length
let changed = false
const array = tMarker.ref.value.array
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 e51b2049c9b18dfa6a1c4092f0a8a40dc08e1850..806964cf9474783a013146c38fa45d00c9f8e8b7 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -47,7 +47,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
Mat4.targetTo(t, center, pd, normal)
Mat4.setTranslation(t, center)
- builder.setId(i)
+ builder.setId(i * 2)
switch (shapeType) {
case SaccharideShapes.FilledSphere:
@@ -58,18 +58,22 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
builder.addBox(t)
break;
case SaccharideShapes.CrossedCube:
- // TODO split
Mat4.scaleUniformly(t, t, side)
- builder.addBox(t)
+ builder.addPerforatedBox(t)
+ Mat4.mul(t, t, Mat4.rotZ90X180)
+ builder.setId(i * 2 + 1)
+ builder.addPerforatedBox(t)
break;
case SaccharideShapes.FilledCone:
Mat4.scaleUniformly(t, t, side * 1.2)
builder.addOctagonalPyramid(t)
break
case SaccharideShapes.DevidedCone:
- // TODO split
Mat4.scaleUniformly(t, t, side * 1.2)
- builder.addOctagonalPyramid(t)
+ builder.addPerforatedOctagonalPyramid(t)
+ Mat4.mul(t, t, Mat4.rotZ90)
+ builder.setId(i * 2 + 1)
+ builder.addPerforatedOctagonalPyramid(t)
break
case SaccharideShapes.FlatBox:
Mat4.mul(t, t, Mat4.rotZY90)
@@ -86,10 +90,12 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
builder.addOctahedron(t)
break
case SaccharideShapes.DividedDiamond:
- // TODO split
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)
+ builder.addPerforatedOctahedron(t)
+ Mat4.mul(t, t, Mat4.rotY90)
+ builder.setId(i * 2 + 1)
+ builder.addPerforatedOctahedron(t)
break
case SaccharideShapes.FlatDiamond:
Mat4.mul(t, t, Mat4.rotZY90)
@@ -141,7 +147,7 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh)
const transforms = createIdentityTransform()
- const color = createColors(createCarbohydrateElementIterator(structure), colorTheme)
+ const color = createColors(CarbohydrateElementIterator(structure), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -170,7 +176,7 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
}
if (updateColor) {
- createColors(createCarbohydrateElementIterator(currentStructure), newProps.colorTheme, renderObject.values)
+ createColors(CarbohydrateElementIterator(currentStructure), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
@@ -191,24 +197,27 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
}
}
-function createCarbohydrateElementIterator(structure: Structure): LocationIterator {
+function CarbohydrateElementIterator(structure: Structure): LocationIterator {
const carbElements = structure.carbohydrates.elements
- const elementCount = carbElements.length
+ const elementCount = carbElements.length * 2
const instanceCount = 1
const location = StructureElement.create()
- const getLocation = (elementIndex: number, instanceIndex: number) => {
- const carb = carbElements[elementIndex]
+ function getLocation (elementIndex: number, instanceIndex: number) {
+ const carb = carbElements[Math.floor(elementIndex / 2)]
location.unit = carb.unit
location.element = carb.anomericCarbon
return location
}
- return LocationIterator(elementCount, instanceCount, getLocation)
+ function isSecondary (elementIndex: number, instanceIndex: number) {
+ return (elementIndex % 2) === 1
+ }
+ return LocationIterator(elementCount, instanceCount, getLocation, isSecondary)
}
function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: number) {
const { objectId, elementId } = pickingId
if (id === objectId) {
- const carb = structure.carbohydrates.elements[elementId]
+ const carb = structure.carbohydrates.elements[Math.floor(elementId / 2)]
const { unit } = carb
const index = OrderedSet.findPredecessorIndex(unit.elements, carb.anomericCarbon)
const indices = OrderedSet.ofSingleton(index as StructureElement.UnitIndex)
@@ -221,7 +230,7 @@ function markCarbohydrate(loci: Loci, action: MarkerAction, structure: Structure
const tMarker = values.tMarker
const { getElementIndex } = structure.carbohydrates
- const elementCount = structure.carbohydrates.elements.length
+ const elementCount = structure.carbohydrates.elements.length * 2
let changed = false
const array = tMarker.ref.value.array
@@ -234,7 +243,7 @@ function markCarbohydrate(loci: Loci, action: MarkerAction, structure: Structure
OrderedSet.forEach(e.indices, index => {
const idx = getElementIndex(e.unit, e.unit.elements[index])
if (idx !== undefined) {
- if (applyMarkerAction(array, idx, idx + 1, action) && !changed) {
+ if (applyMarkerAction(array, idx * 2, idx * 2 + 2, action) && !changed) {
changed = true
}
}
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index 07bc94993cb11eafcf00208fd395fe0aed5175dd..d4264354fee2a72890d394307d57debcdd9aa364 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -39,7 +39,7 @@ export function createColors(locationIt: LocationIterator, props: ColorTheme, co
case 'atom-index':
return elementIndexColorData(locationIt, colorData)
case 'carbohydrate-symbol':
- return carbohydrateSymbolColorData(locationIt, colorData)
+ return carbohydrateSymbolColorData(locationIt, props, colorData)
case 'chain-id':
return chainIdColorData(locationIt, colorData)
case 'element-symbol':
@@ -47,7 +47,7 @@ export function createColors(locationIt: LocationIterator, props: ColorTheme, co
case 'instance-index':
return instanceIndexColorData(locationIt, colorData)
case 'uniform':
- return createUniformColor(locationIt, () => props.value, colorData)
+ return createUniformColor(locationIt, () => props.value || 0x000000, colorData)
}
}
diff --git a/src/mol-geo/representation/structure/visual/util/location-iterator.ts b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
index 5dc3d76ce9380de088e6119900ea4ec895edcc6c..2fc20e011ef88f779cac6fbaaec3e84f5fa465c6 100644
--- a/src/mol-geo/representation/structure/visual/util/location-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
@@ -13,13 +13,15 @@ export interface LocationValue {
index: number
elementIndex: number
instanceIndex: number
+ isSecondary: boolean
}
-export const NullLocationValue = {
+export const NullLocationValue: LocationValue = {
location: NullLocation,
index: 0,
elementIndex: 0,
- instanceIndex: 0
+ instanceIndex: 0,
+ isSecondary: false
}
export interface LocationIterator extends Iterator<LocationValue> {
@@ -32,13 +34,15 @@ export interface LocationIterator extends Iterator<LocationValue> {
}
type LocationGetter = (elementIndex: number, instanceIndex: number) => Location
+type IsSecondaryGetter = (elementIndex: number, instanceIndex: number) => boolean
-export function LocationIterator(elementCount: number, instanceCount: number, getLocation: LocationGetter): LocationIterator {
- const value = {
+export function LocationIterator(elementCount: number, instanceCount: number, getLocation: LocationGetter, isSecondary: IsSecondaryGetter = () => false): LocationIterator {
+ const value: LocationValue = {
location: NullLocation as Location,
index: 0,
elementIndex: 0,
- instanceIndex: 0
+ instanceIndex: 0,
+ isSecondary: false
}
let hasNext = value.elementIndex < elementCount
@@ -57,6 +61,7 @@ export function LocationIterator(elementCount: number, instanceCount: number, ge
value.instanceIndex = instanceIndex
value.index = instanceIndex * elementCount + elementIndex
value.location = getLocation(elementIndex, instanceIndex)
+ value.isSecondary = isSecondary(elementIndex, instanceIndex)
++elementIndex
if (elementIndex === elementCount) {
++instanceIndex
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/shape/mesh-builder.ts
index 8b8404c19794dc5be1bb54f3a214d6aedbdb7269..f3dafe8a41d33153039a6af87bb1dee4bfd44e81 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/shape/mesh-builder.ts
@@ -16,10 +16,12 @@ import { getNormalMatrix } from '../util';
import { addSheet } from '../primitive/sheet';
import { addTube } from '../primitive/tube';
import { StarProps, Star } from '../primitive/star';
-import { Octahedron } from '../primitive/octahedron';
+import { Octahedron, PerforatedOctahedron } from '../primitive/octahedron';
import { Primitive } from '../primitive/primitive';
-import { Wedge, Box, DiamondPrism, PentagonalPrism, HexagonalPrism } from '../primitive/prism';
-import { OctagonalPyramide } from '../primitive/pyramid';
+import { DiamondPrism, PentagonalPrism, HexagonalPrism } from '../primitive/prism';
+import { OctagonalPyramide, PerforatedOctagonalPyramide } from '../primitive/pyramid';
+import { PerforatedBox, Box } from '../primitive/box';
+import { Wedge } from '../primitive/wedge';
export interface MeshBuilderState {
vertices: ChunkedArray<number, 3>
@@ -30,14 +32,17 @@ export interface MeshBuilderState {
export interface MeshBuilder {
add(t: Mat4, _vertices: ArrayLike<number>, _normals: ArrayLike<number>, _indices?: ArrayLike<number>): void
addBox(t: Mat4): void
+ addPerforatedBox(t: Mat4): void
addPlane(t: Mat4, props?: PlaneProps): void
addWedge(t: Mat4): void
addDiamondPrism(t: Mat4): void
addPentagonalPrism(t: Mat4): void
addHexagonalPrism(t: Mat4): void
addOctagonalPyramid(t: Mat4): void
+ addPerforatedOctagonalPyramid(t: Mat4): void
addStar(t: Mat4, props?: StarProps): void
addOctahedron(t: Mat4): void
+ addPerforatedOctahedron(t: Mat4): 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
@@ -140,6 +145,10 @@ export namespace MeshBuilder {
const { vertices, normals, indices } = Box()
add(t, vertices, normals, indices)
},
+ addPerforatedBox: (t: Mat4) => {
+ const { vertices, normals, indices } = PerforatedBox()
+ add(t, vertices, normals, indices)
+ },
addPlane: (t: Mat4, props?: PlaneProps) => {
const { vertices, normals, indices } = Plane(props)
add(t, vertices, normals, indices)
@@ -164,6 +173,10 @@ export namespace MeshBuilder {
const { vertices, normals, indices } = OctagonalPyramide()
add(t, vertices, normals, indices)
},
+ addPerforatedOctagonalPyramid: (t: Mat4) => {
+ const { vertices, normals, indices } = PerforatedOctagonalPyramide()
+ add(t, vertices, normals, indices)
+ },
addStar: (t: Mat4, props?: StarProps) => {
const { vertices, normals, indices } = Star(props)
add(t, vertices, normals, indices)
@@ -172,6 +185,10 @@ export namespace MeshBuilder {
const { vertices, normals, indices } = Octahedron()
add(t, vertices, normals, indices)
},
+ addPerforatedOctahedron: (t: Mat4) => {
+ const { vertices, normals, indices } = PerforatedOctahedron()
+ add(t, vertices, normals, indices)
+ },
addCylinder: (start: Vec3, end: Vec3, lengthScale: number, props: CylinderProps) => {
const d = Vec3.distance(start, end) * lengthScale
props.height = d
diff --git a/src/mol-geo/theme/index.ts b/src/mol-geo/theme/index.ts
index d34cb26a6d101a9ff03d58d9d03b136337ce69d1..0e0ed1a9c73405bcc3a52371f0d7d17b346e85ef 100644
--- a/src/mol-geo/theme/index.ts
+++ b/src/mol-geo/theme/index.ts
@@ -5,22 +5,25 @@
*/
import { Color } from 'mol-util/color';
+import { Structure } from 'mol-model/structure';
-export interface UniformColorTheme {
- name: 'uniform'
- value: Color
-}
-
-export interface ScaleColorTheme {
- name: 'atom-index' | 'chain-id'| 'instance-index'
+export interface ColorTheme {
+ name: 'atom-index' | 'chain-id'| 'instance-index' | 'uniform' | 'carbohydrate-symbol' | 'element-symbol'
domain?: [number, number]
+ value?: Color
+ structure?: Structure
}
-export interface TableColorTheme {
- name: 'carbohydrate-symbol' | 'element-symbol'
+export const ColorThemeInfo = {
+ 'atom-index': {},
+ 'carbohydrate-symbol': {},
+ 'chain-id': {},
+ 'element-symbol': {},
+ 'instance-index': {},
+ 'uniform': {}
}
-
-export type ColorTheme = UniformColorTheme | ScaleColorTheme | TableColorTheme
+export type ColorThemeName = keyof typeof ColorThemeInfo
+export const ColorThemeNames = Object.keys(ColorThemeInfo)
export interface UniformSizeTheme {
name: 'uniform',
diff --git a/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts b/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
index e6f8065b436ea3260b77f9aea806b1f8dead892a..1417b4e39578e8776ac4ea0ab6e36e6fcb14f212 100644
--- a/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
+++ b/src/mol-geo/theme/structure/color/carbohydrate-symbol.ts
@@ -4,41 +4,47 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureProperties, StructureElement, Link } from 'mol-model/structure';
+import { StructureElement, Link, ElementIndex, Unit } from 'mol-model/structure';
import { ColorData, createElementColor } from '../../../util/color-data';
-import { ColorScale, Color } from 'mol-util/color';
+import { Color } from 'mol-util/color';
import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
+import { ColorTheme } from '../..';
+import { SaccharideColors } from 'mol-model/structure/structure/carbohydrates/constants';
-function getAsymId(unit: Unit): StructureElement.Property<string> {
- switch (unit.kind) {
- case Unit.Kind.Atomic:
- return StructureProperties.chain.label_asym_id
- case Unit.Kind.Spheres:
- case Unit.Kind.Gaussians:
- return StructureProperties.coarse.asym_id
- }
-}
-
-export function carbohydrateSymbolColorData(locationIt: LocationIterator, colorData?: ColorData) {
- const l = StructureElement.create()
-
- function colorFn(locationValue: LocationValue): Color {
- const { location } = locationValue
- if (StructureElement.isLocation(location)) {
- const map = location.unit.model.properties.asymIdSerialMap
- const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
- const asym_id = getAsymId(location.unit)
- return scale.color(map.get(asym_id(location)) || 0)
- } else if (Link.isLocation(location)) {
- const map = location.aUnit.model.properties.asymIdSerialMap
- const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
- const asym_id = getAsymId(location.aUnit)
- l.unit = location.aUnit
- l.element = location.aUnit.elements[location.aIndex]
- return scale.color(map.get(asym_id(l)) || 0)
+const DefaultColor = 0xCCCCCC;
+
+export function carbohydrateSymbolColorData(locationIt: LocationIterator, props: ColorTheme, colorData?: ColorData) {
+ let colorFn: (locationValue: LocationValue) => Color
+
+ if (props.structure) {
+ const { elements, getElementIndex, getAnomericCarbon } = props.structure.carbohydrates
+
+ const getColor = (unit: Unit, index: ElementIndex) => {
+ const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index[index]
+ const anomericCarbon = getAnomericCarbon(unit, residueIndex)
+ if (anomericCarbon !== undefined) {
+ const idx = getElementIndex(unit, anomericCarbon)
+ if (idx !== undefined) return elements[idx].component.color
+ }
+ return DefaultColor
+ }
+
+ colorFn = (locationValue: LocationValue) => {
+ const { location: l } = locationValue
+ if (locationValue.isSecondary) {
+ return SaccharideColors.Secondary
+ } else {
+ if (StructureElement.isLocation(l)) {
+ return getColor(l.unit, l.element)
+ } else if (Link.isLocation(l)) {
+ return getColor(l.aUnit, l.aUnit.elements[l.aIndex])
+ }
+ }
+ return DefaultColor
}
- return 0
+ } else {
+ colorFn = () => DefaultColor
}
return createElementColor(locationIt, colorFn, colorData)
diff --git a/src/mol-math/linear-algebra/3d/mat4.ts b/src/mol-math/linear-algebra/3d/mat4.ts
index ddd7eaafd42725f55018bfdbd35f4185b581a9af..968870259862fd95d033d32f347598ab264a04e1 100644
--- a/src/mol-math/linear-algebra/3d/mat4.ts
+++ b/src/mol-math/linear-algebra/3d/mat4.ts
@@ -873,18 +873,26 @@ namespace Mat4 {
return out;
}
- /** Rotation matrix for 90deg rotation around x-axis */
+ /** Rotation matrix for 90deg 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 */
+ /** Rotation matrix for 180deg around x-axis */
+ export const rotX180: ReadonlyMat4 = Mat4.fromRotation(Mat4.identity(), degToRad(180), Vec3.create(1, 0, 0))
+ /** Rotation matrix for 90deg 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 */
+ /** Rotation matrix for 180deg around y-axis */
+ export const rotY180: ReadonlyMat4 = Mat4.fromRotation(Mat4.identity(), degToRad(180), Vec3.create(0, 1, 0))
+ /** Rotation matrix for 90deg 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 */
+ /** Rotation matrix for 180deg around z-axis */
+ export const rotZ180: ReadonlyMat4 = Mat4.fromRotation(Mat4.identity(), degToRad(180), Vec3.create(0, 0, 1))
+ /** Rotation matrix for 90deg 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 */
+ /** Rotation matrix for 90deg 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 */
+ /** Rotation matrix for 90deg around first z-axis and then y-axis and then z-axis */
export const rotZYZ90: ReadonlyMat4 = Mat4.mul(Mat4.identity(), rotZY90, rotZ90)
+ /** Rotation matrix for 90deg around first z-axis and then 180deg around x-axis */
+ export const rotZ90X180: ReadonlyMat4 = Mat4.mul(Mat4.identity(), rotZ90, rotX180)
}
export default Mat4
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index ebf52e14c8dee07e214c32fa59b26fe8d5a1481a..d983593c0036ca5c3107a784781e6406c984e366 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -315,5 +315,22 @@ function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[
return linkMap.get(linkKey(unitA, anomericCarbonA, unitB, anomericCarbonB))
}
- return { getElementIndex, getLinkIndex }
+ // anomeric carbon lookup
+
+ function anomericCarbonKey(unit: Unit, residueIndex: ResidueIndex) {
+ return `${unit.id}|${residueIndex}`
+ }
+
+ const anomericCarbonMap = new Map<string, ElementIndex>()
+ for (let i = 0, il = elements.length; i < il; ++i) {
+ const { unit, anomericCarbon } = elements[i]
+ const residueIndex = unit.model.atomicHierarchy.residueAtomSegments.index[anomericCarbon]
+ anomericCarbonMap.set(anomericCarbonKey(unit, residueIndex), anomericCarbon)
+ }
+
+ function getAnomericCarbon(unit: Unit, residueIndex: ResidueIndex) {
+ return anomericCarbonMap.get(anomericCarbonKey(unit, residueIndex))
+ }
+
+ return { getElementIndex, getLinkIndex, getAnomericCarbon }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index a6c16844db26d6db7587be46f6ba822d37c3e7e2..4de9309289ece0ed1d09ea6f6bdcdd05a326875b 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -12,8 +12,7 @@ export const enum SaccharideShapes {
FlatBox, FilledStar, FilledDiamond, FlatDiamond, FlatHexagon, Pentagon
}
-// TODO move to theme
-const enum SaccharideColors {
+export const enum SaccharideColors {
Blue = 0x0090bc,
Green = 0x00a651,
Yellow = 0xffd400,
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index c69bde439533cd91c36936588394870fde68c83f..4afcf03e445fc2c9671ac8aee04e84ab7a1edb60 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -44,4 +44,5 @@ export interface Carbohydrates {
partialElements: ReadonlyArray<PartialCarbohydrateElement>
getElementIndex: (unit: Unit, anomericCarbon: ElementIndex) => number | undefined
getLinkIndex: (unitA: Unit, anomericCarbonA: ElementIndex, unitB: Unit, anomericCarbonB: ElementIndex) => number | undefined
+ getAnomericCarbon: (unit: Unit, residueIndex: ResidueIndex) => ElementIndex | undefined
}
\ No newline at end of file
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index ed5ce1cc1e9c53bb933dab8bc12afa39c5c25e3c..6b0998765d054be89468eeb56d14e5f21235a57f 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -78,7 +78,7 @@ export class Stage {
// this.loadPdbid('1hrv') // viral assembly
// this.loadPdbid('1rb8') // virus
// this.loadPdbid('1blu') // metal coordination
- this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
+ // this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
// this.loadPdbid('2np2') // dna
@@ -98,7 +98,7 @@ 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