diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index e803e1e18137fb68787e7cc4d36db8507eb2201e..e4bb91a6478cdd47c652ba66c949f382b3e41d0f 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -26,15 +26,17 @@ import { MarkerAction } from 'mol-geo/geometry/marker-data';
import { Loci, EmptyLoci, isEmptyLoci } from 'mol-model/loci';
import { Color } from 'mol-util/color';
import { Camera } from './camera';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
-export const DefaultCanvas3DProps = {
+export const Canvas3DParams = {
// TODO: FPS cap?
- // maxFps: 30,
- cameraPosition: Vec3.create(0, 0, 50),
- cameraMode: 'perspective' as Camera.Mode,
- backgroundColor: Color(0x000000),
+ // maxFps: PD.Numeric(30),
+ cameraPosition: PD.Vec3(Vec3.create(0, 0, 50)), // TODO or should it be in a seperate 'state' property?
+ cameraMode: PD.Select('perspective', [['perspective', 'Perspective'], ['orthographic', 'Orthographic']]),
+ backgroundColor: PD.Color(Color(0x000000)),
+ pickingAlphaThreshold: PD.Numeric(0.5, { min: 0.0, max: 1.0, step: 0.01 }, { description: 'The minimum opacity value needed for an object to be pickable.' }),
}
-export type Canvas3DProps = typeof DefaultCanvas3DProps
+export type Canvas3DParams = typeof Canvas3DParams
export { Canvas3D }
@@ -64,18 +66,18 @@ interface Canvas3D {
readonly camera: Camera
downloadScreenshot: () => void
getImageData: (variant: RenderVariant) => ImageData
- setProps: (props: Partial<Canvas3DProps>) => void
+ setProps: (props: Partial<PD.Values<Canvas3DParams>>) => void
/** Returns a copy of the current Canvas3D instance props */
- readonly props: Canvas3DProps
+ readonly props: PD.Values<Canvas3DParams>
readonly input: InputObserver
readonly stats: RendererStats
dispose: () => void
}
namespace Canvas3D {
- export function create(canvas: HTMLCanvasElement, container: Element, props: Partial<Canvas3DProps> = {}): Canvas3D {
- const p = { ...props, ...DefaultCanvas3DProps }
+ export function create(canvas: HTMLCanvasElement, container: Element, props: Partial<PD.Values<Canvas3DParams>> = {}): Canvas3D {
+ const p = { ...PD.getDefaultValues(Canvas3DParams), ...props }
const reprRenderObjects = new Map<Representation.Any, Set<RenderObject>>()
const reprUpdatedSubscriptions = new Map<Representation.Any, Subscription>()
@@ -353,13 +355,16 @@ namespace Canvas3D {
}
},
didDraw,
- setProps: (props: Partial<Canvas3DProps>) => {
+ setProps: (props: Partial<PD.Values<Canvas3DParams>>) => {
if (props.cameraMode !== undefined && props.cameraMode !== camera.state.mode) {
camera.setState({ mode: props.cameraMode })
}
if (props.backgroundColor !== undefined && props.backgroundColor !== renderer.props.clearColor) {
renderer.setClearColor(props.backgroundColor)
}
+ if (props.pickingAlphaThreshold !== undefined && props.pickingAlphaThreshold !== renderer.props.pickingAlphaThreshold) {
+ renderer.setPickingAlphaThreshold(props.pickingAlphaThreshold)
+ }
requestDraw(true)
},
@@ -367,7 +372,8 @@ namespace Canvas3D {
return {
cameraPosition: Vec3.clone(camera.position),
cameraMode: camera.state.mode,
- backgroundColor: renderer.props.clearColor
+ backgroundColor: renderer.props.clearColor,
+ pickingAlphaThreshold: renderer.props.pickingAlphaThreshold,
}
},
get input() {
diff --git a/src/mol-geo/geometry/geometry.ts b/src/mol-geo/geometry/geometry.ts
index 190e21d27a4cf9ebfe361c2d1b280902e26ebef9..8533bc34244aa8a4691e389d249d7e50655aeee2 100644
--- a/src/mol-geo/geometry/geometry.ts
+++ b/src/mol-geo/geometry/geometry.ts
@@ -104,6 +104,7 @@ export namespace Geometry {
export function createRenderableState(props: PD.Values<Geometry.Params>): RenderableState {
return {
visible: true,
+ pickable: true,
depthMask: props.depthMask
}
}
diff --git a/src/mol-gl/_spec/renderer.spec.ts b/src/mol-gl/_spec/renderer.spec.ts
index 51552ebf2dac61950224535024a725c0574b78d6..e62c5415f7be59b638ff97167f2ca012d6d2c34a 100644
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -85,6 +85,7 @@ function createPoints() {
}
const state: RenderableState = {
visible: true,
+ pickable: true,
depthMask: true,
}
diff --git a/src/mol-gl/renderable.ts b/src/mol-gl/renderable.ts
index 370437898cfee60a0df4e37d155640412c21a6fb..6d9d55ac3e5612ea01df7663062484f09dcf4503 100644
--- a/src/mol-gl/renderable.ts
+++ b/src/mol-gl/renderable.ts
@@ -9,9 +9,11 @@ import { RenderableValues, Values, RenderableSchema } from './renderable/schema'
import { RenderVariant, RenderItem } from './webgl/render-item';
import { Sphere3D } from 'mol-math/geometry';
import { Vec3 } from 'mol-math/linear-algebra';
+import { ValueCell } from 'mol-util';
export type RenderableState = {
visible: boolean
+ pickable: boolean
depthMask: boolean
}
@@ -41,7 +43,12 @@ export function createRenderable<T extends Values<RenderableSchema>>(renderItem:
},
get opaque () { return values.uAlpha && values.uAlpha.ref.value === 1 },
- render: (variant: RenderVariant) => renderItem.render(variant),
+ render: (variant: RenderVariant) => {
+ if (values.uPickable) {
+ ValueCell.updateIfChanged(values.uPickable, state.pickable ? 1 : 0)
+ }
+ renderItem.render(variant)
+ },
getProgram: (variant: RenderVariant) => renderItem.getProgram(variant),
update: () => renderItem.update(),
dispose: () => renderItem.destroy()
diff --git a/src/mol-gl/renderable/direct-volume.ts b/src/mol-gl/renderable/direct-volume.ts
index 63b2424ed608744a5e6b6651d284b2a991a5412a..27ce4e40668fb0b78c587187fbb6564d0fb006f3 100644
--- a/src/mol-gl/renderable/direct-volume.ts
+++ b/src/mol-gl/renderable/direct-volume.ts
@@ -57,7 +57,8 @@ export type DirectVolumeValues = Values<DirectVolumeSchema>
export function DirectVolumeRenderable(ctx: WebGLContext, id: number, values: DirectVolumeValues, state: RenderableState): Renderable<DirectVolumeValues> {
const schema = { ...GlobalUniformSchema, ...InternalSchema, ...DirectVolumeSchema }
const internalValues: InternalValues = {
- uObjectId: ValueCell.create(id)
+ uObjectId: ValueCell.create(id),
+ uPickable: ValueCell.create(state.pickable ? 1 : 0)
}
const shaderCode = DirectVolumeShaderCode
const renderItem = createRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues })
diff --git a/src/mol-gl/renderable/lines.ts b/src/mol-gl/renderable/lines.ts
index 31ebfd493eca89c14021d916f7dc81a93987a62e..54e62c5b448bf5b4bf8bcf88037092564fcf52ce 100644
--- a/src/mol-gl/renderable/lines.ts
+++ b/src/mol-gl/renderable/lines.ts
@@ -28,7 +28,8 @@ export type LinesValues = Values<LinesSchema>
export function LinesRenderable(ctx: WebGLContext, id: number, values: LinesValues, state: RenderableState): Renderable<LinesValues> {
const schema = { ...GlobalUniformSchema, ...InternalSchema, ...LinesSchema }
const internalValues: InternalValues = {
- uObjectId: ValueCell.create(id)
+ uObjectId: ValueCell.create(id),
+ uPickable: ValueCell.create(state.pickable ? 1 : 0)
}
const shaderCode = LinesShaderCode
const renderItem = createRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues })
diff --git a/src/mol-gl/renderable/mesh.ts b/src/mol-gl/renderable/mesh.ts
index e79f78159a7ecbc1500a6adbfe796d08b1b4b7af..a3d70909409dda202f1649ab5397ae0cc47e8d29 100644
--- a/src/mol-gl/renderable/mesh.ts
+++ b/src/mol-gl/renderable/mesh.ts
@@ -26,7 +26,8 @@ export type MeshValues = Values<MeshSchema>
export function MeshRenderable(ctx: WebGLContext, id: number, values: MeshValues, state: RenderableState): Renderable<MeshValues> {
const schema = { ...GlobalUniformSchema, ...InternalSchema, ...MeshSchema }
const internalValues: InternalValues = {
- uObjectId: ValueCell.create(id)
+ uObjectId: ValueCell.create(id),
+ uPickable: ValueCell.create(state.pickable ? 1 : 0)
}
const shaderCode = MeshShaderCode
const renderItem = createRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues })
diff --git a/src/mol-gl/renderable/points.ts b/src/mol-gl/renderable/points.ts
index 95a45cceda95c18e52b6c1829b94b8deeff5169b..f4d87921f388afdefe195965d0b290dc6465ea9e 100644
--- a/src/mol-gl/renderable/points.ts
+++ b/src/mol-gl/renderable/points.ts
@@ -25,7 +25,8 @@ export type PointsValues = Values<PointsSchema>
export function PointsRenderable(ctx: WebGLContext, id: number, values: PointsValues, state: RenderableState): Renderable<PointsValues> {
const schema = { ...GlobalUniformSchema, ...InternalSchema, ...PointsSchema }
const internalValues: InternalValues = {
- uObjectId: ValueCell.create(id)
+ uObjectId: ValueCell.create(id),
+ uPickable: ValueCell.create(state.pickable ? 1 : 0)
}
const shaderCode = PointsShaderCode
const renderItem = createRenderItem(ctx, 'points', shaderCode, schema, { ...values, ...internalValues })
diff --git a/src/mol-gl/renderable/schema.ts b/src/mol-gl/renderable/schema.ts
index bac604bea5230fd1a8f6eb2d8f453d14a9247d00..7050ee13bbd19865f39421d3722a6046e71ff6e0 100644
--- a/src/mol-gl/renderable/schema.ts
+++ b/src/mol-gl/renderable/schema.ts
@@ -149,12 +149,15 @@ export const GlobalUniformSchema = {
uFogNear: UniformSpec('f'),
uFogFar: UniformSpec('f'),
uFogColor: UniformSpec('v3'),
+
+ uPickingAlphaThreshold: UniformSpec('f'),
}
export type GlobalUniformSchema = typeof GlobalUniformSchema
export type GlobalUniformValues = { [k in keyof GlobalUniformSchema]: ValueCell<any> }
export const InternalSchema = {
uObjectId: UniformSpec('i'),
+ uPickable: UniformSpec('i'),
}
export type InternalSchema = typeof InternalSchema
export type InternalValues = { [k in keyof InternalSchema]: ValueCell<any> }
diff --git a/src/mol-gl/renderer.ts b/src/mol-gl/renderer.ts
index c7d4ce3a4fec1c3b17a1dd68cd02d8d020f80a49..26c1845e523e11baea123a2c13a9569b7222a0a9 100644
--- a/src/mol-gl/renderer.ts
+++ b/src/mol-gl/renderer.ts
@@ -39,20 +39,22 @@ interface Renderer {
render: (scene: Scene, variant: RenderVariant) => void
setViewport: (x: number, y: number, width: number, height: number) => void
setClearColor: (color: Color) => void
+ setPickingAlphaThreshold: (value: number) => void
getImageData: () => ImageData
dispose: () => void
}
export const DefaultRendererProps = {
clearColor: Color(0x000000),
- viewport: Viewport.create(0, 0, 0, 0)
+ viewport: Viewport.create(0, 0, 0, 0),
+ pickingAlphaThreshold: 0.5,
}
export type RendererProps = typeof DefaultRendererProps
namespace Renderer {
export function create(ctx: WebGLContext, camera: Camera, props: Partial<RendererProps> = {}): Renderer {
const { gl } = ctx
- let { clearColor, viewport: _viewport } = { ...DefaultRendererProps, ...props }
+ let { clearColor, viewport: _viewport, pickingAlphaThreshold } = { ...DefaultRendererProps, ...props }
const viewport = Viewport.clone(_viewport)
const viewportVec4 = Viewport.toVec4(Vec4.zero(), viewport)
@@ -98,6 +100,8 @@ namespace Renderer {
uFogNear: ValueCell.create(camera.state.near),
uFogFar: ValueCell.create(camera.state.far / 50),
uFogColor: ValueCell.create(Vec3.clone(fogColor)),
+
+ uPickingAlphaThreshold: ValueCell.create(pickingAlphaThreshold),
}
let currentProgramId = -1
@@ -175,6 +179,10 @@ namespace Renderer {
render,
setClearColor,
+ setPickingAlphaThreshold: (value: number) => {
+ pickingAlphaThreshold = value
+ ValueCell.update(globalUniforms.uPickingAlphaThreshold, pickingAlphaThreshold)
+ },
setViewport: (x: number, y: number, width: number, height: number) => {
Viewport.set(viewport, x, y, width, height)
gl.viewport(x, y, width, height)
@@ -192,6 +200,7 @@ namespace Renderer {
get props() {
return {
clearColor,
+ pickingAlphaThreshold,
viewport
}
},
diff --git a/src/mol-gl/shader/chunks/assign-material-color.glsl b/src/mol-gl/shader/chunks/assign-material-color.glsl
index bc56340c25f74d749e9c8cc6377ac9ca265b2035..81758eabcd3b6630f7e7cd1cf3f2f819f419695e 100644
--- a/src/mol-gl/shader/chunks/assign-material-color.glsl
+++ b/src/mol-gl/shader/chunks/assign-material-color.glsl
@@ -3,5 +3,5 @@
#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
vec4 material = vec4(vColor.rgb, uAlpha);
#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
- vec4 material = vColor;
+ vec4 material = uPickable == 1 ? vColor : vec4(0.0, 0.0, 0.0, 1.0); // set to empty picking id
#endif
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/common-frag-params.glsl b/src/mol-gl/shader/chunks/common-frag-params.glsl
index c757d1b2f5afa54efad4236d533b9f4535bc64da..dc62dbe9bec92fae2018665d136b5f10e624f71b 100644
--- a/src/mol-gl/shader/chunks/common-frag-params.glsl
+++ b/src/mol-gl/shader/chunks/common-frag-params.glsl
@@ -12,4 +12,6 @@ uniform float uFogNear;
uniform float uFogFar;
uniform vec3 uFogColor;
-uniform float uAlpha;
\ No newline at end of file
+uniform float uAlpha;
+uniform float uPickingAlphaThreshold;
+uniform int uPickable;
\ No newline at end of file
diff --git a/src/mol-gl/shader/direct-volume.frag b/src/mol-gl/shader/direct-volume.frag
index 6be0ab731366d502314f61722f6b124b308dc092..7baa242c02aae1f90c6b47ebf9678152ff1f3cef 100644
--- a/src/mol-gl/shader/direct-volume.frag
+++ b/src/mol-gl/shader/direct-volume.frag
@@ -123,6 +123,11 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 viewDir) {
tmp = ((prevValue - uIsoValue) / ((prevValue - uIsoValue) - (value - uIsoValue)));
isoPos = mix(pos - step, pos, tmp);
+ #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+ if (uAlpha < uPickingAlphaThreshold)
+ discard; // ignore so the element below can be picked
+ #else
+
#if defined(dColorType_objectPicking)
return vec4(encodeIdRGB(float(uObjectId)), 1.0);
#elif defined(dColorType_instancePicking)
diff --git a/src/mol-gl/shader/lines.frag b/src/mol-gl/shader/lines.frag
index 98caeadbf7fd714c79fb17425b2fd7f44ec24de8..ec512988b00b2fabea4fc65183284fc200a3d347 100644
--- a/src/mol-gl/shader/lines.frag
+++ b/src/mol-gl/shader/lines.frag
@@ -14,6 +14,8 @@ void main(){
#pragma glslify: import('./chunks/assign-material-color.glsl')
#if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+ if (uAlpha < uPickingAlphaThreshold)
+ discard; // ignore so the element below can be picked
gl_FragColor = material;
#else
gl_FragColor = material;
diff --git a/src/mol-gl/shader/mesh.frag b/src/mol-gl/shader/mesh.frag
index 2195060272cbc736d150e39d3d58166569d1f2b3..93858961510496217a7121ee8182aee085218313 100644
--- a/src/mol-gl/shader/mesh.frag
+++ b/src/mol-gl/shader/mesh.frag
@@ -33,7 +33,8 @@ void main() {
#pragma glslify: import('./chunks/assign-material-color.glsl')
#if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
- // gl_FragColor = vec4(material.r, material.g, material.a, 1.0);
+ if (uAlpha < uPickingAlphaThreshold)
+ discard; // ignore so the element below can be picked
gl_FragColor = material;
#else
// determine surface to light direction
diff --git a/src/mol-gl/shader/points.frag b/src/mol-gl/shader/points.frag
index 5ef4153d4cfc66a9f10177a2eca17ecc3a836c36..67f8aa47d44abdbfe229c868e2a64d1e12e16374 100644
--- a/src/mol-gl/shader/points.frag
+++ b/src/mol-gl/shader/points.frag
@@ -21,6 +21,8 @@ void main(){
#pragma glslify: import('./chunks/assign-material-color.glsl')
#if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
+ if (uAlpha < uPickingAlphaThreshold)
+ discard; // ignore so the element below can be picked
gl_FragColor = material;
#else
gl_FragColor = material;
diff --git a/src/mol-math/geometry/gaussian-density/gpu.ts b/src/mol-math/geometry/gaussian-density/gpu.ts
index e14fb754a15fa825b4b1b98dcfda5593a076c65e..d0429a36dfee714b53ba6de3a59c0cae93856e9a 100644
--- a/src/mol-math/geometry/gaussian-density/gpu.ts
+++ b/src/mol-math/geometry/gaussian-density/gpu.ts
@@ -232,6 +232,7 @@ function getGaussianDensityRenderObject(webgl: WebGLContext, drawCount: number,
}
const state: RenderableState = {
visible: true,
+ pickable: false,
depthMask: false
}
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 729e7bb56c1b38207f8297e19a457212eec0cd27..d86ed125b4f6d796b02453c432a0017ebb9a89fc 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -262,8 +262,9 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
}
- // get carbohydrate links induced by inter-unit bonds
- // (e.g. for structures from the PDB archive __before__ carbohydrate remediation)
+ // get carbohydrate links induced by inter-unit bonds, that is
+ // terminal links plus inter monosaccharide links for structures from the
+ // PDB archive __before__ carbohydrate remediation
for (let i = 0, il = structure.units.length; i < il; ++i) {
const unit = structure.units[i]
if (!Unit.isAtomic(unit)) continue
@@ -309,10 +310,10 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
})
}
- return { links, terminalLinks, elements, partialElements, ...buildLookups(elements, links) }
+ return { links, terminalLinks, elements, partialElements, ...buildLookups(elements, links, terminalLinks) }
}
-function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[]) {
+function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[], terminalLinks: CarbohydrateTerminalLink[]) {
// element lookup
function elementKey(unit: Unit, anomericCarbon: ElementIndex) {
@@ -347,6 +348,27 @@ function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[
return linkMap.get(linkKey(unitA, anomericCarbonA, unitB, anomericCarbonB))
}
+ // terminal link lookup
+
+ function terminalLinkKey(unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) {
+ return `${unitA.id}|${elementA}|${unitB.id}|${elementB}`
+ }
+
+ const terminalLinkMap = new Map<string, number>()
+ for (let i = 0, il = terminalLinks.length; i < il; ++i) {
+ const { fromCarbohydrate, carbohydrateIndex, elementUnit, elementIndex } = terminalLinks[i]
+ const { unit, anomericCarbon } = elements[carbohydrateIndex]
+ if (fromCarbohydrate) {
+ terminalLinkMap.set(terminalLinkKey(unit, anomericCarbon, elementUnit, elementUnit.elements[elementIndex]), i)
+ } else {
+ terminalLinkMap.set(terminalLinkKey(elementUnit, elementUnit.elements[elementIndex], unit, anomericCarbon), i)
+ }
+ }
+
+ function getTerminalLinkIndex(unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) {
+ return terminalLinkMap.get(terminalLinkKey(unitA, elementA, unitB, elementB))
+ }
+
// anomeric carbon lookup
function anomericCarbonKey(unit: Unit, residueIndex: ResidueIndex) {
@@ -364,5 +386,5 @@ function buildLookups (elements: CarbohydrateElement[], links: CarbohydrateLink[
return anomericCarbonMap.get(anomericCarbonKey(unit, residueIndex))
}
- return { getElementIndex, getLinkIndex, getAnomericCarbon }
+ return { getElementIndex, getLinkIndex, getTerminalLinkIndex, getAnomericCarbon }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/carbohydrates/data.ts b/src/mol-model/structure/structure/carbohydrates/data.ts
index 0a8d383755bac79c9ffde4be7de61a4b8f331cf0..7743bd0ba2ab580cd9a5226c07bd0678253953af 100644
--- a/src/mol-model/structure/structure/carbohydrates/data.ts
+++ b/src/mol-model/structure/structure/carbohydrates/data.ts
@@ -8,6 +8,7 @@ import Unit from '../unit';
import { Vec3 } from 'mol-math/linear-algebra';
import { ResidueIndex, ElementIndex } from '../../model';
import { SaccharideComponent } from './constants';
+import StructureElement from '../element';
export interface CarbohydrateLink {
readonly carbohydrateIndexA: number
@@ -16,7 +17,7 @@ export interface CarbohydrateLink {
export interface CarbohydrateTerminalLink {
readonly carbohydrateIndex: number
- readonly elementIndex: number
+ readonly elementIndex: StructureElement.UnitIndex
readonly elementUnit: Unit
/** specifies direction of the link */
readonly fromCarbohydrate: boolean
@@ -31,7 +32,7 @@ export interface CarbohydrateElement {
readonly ringAltId: string,
}
-// partial carbohydrate with no ring present
+/** partial carbohydrate with no ring present */
export interface PartialCarbohydrateElement {
readonly unit: Unit.Atomic,
readonly residueIndex: ResidueIndex,
@@ -45,5 +46,6 @@ export interface Carbohydrates {
partialElements: ReadonlyArray<PartialCarbohydrateElement>
getElementIndex: (unit: Unit, anomericCarbon: ElementIndex) => number | undefined
getLinkIndex: (unitA: Unit, anomericCarbonA: ElementIndex, unitB: Unit, anomericCarbonB: ElementIndex) => number | undefined
+ getTerminalLinkIndex: (unitA: Unit, elementA: ElementIndex, unitB: Unit, elementB: ElementIndex) => number | undefined
getAnomericCarbon: (unit: Unit, residueIndex: ResidueIndex) => ElementIndex | undefined
}
\ No newline at end of file
diff --git a/src/mol-plugin/ui/controls/parameters.tsx b/src/mol-plugin/ui/controls/parameters.tsx
index 2f2604382c0c1ac56da6b66f978b1200a21e2bcf..86c955cb0c2336f8e10b27e87406da2cf36ee82f 100644
--- a/src/mol-plugin/ui/controls/parameters.tsx
+++ b/src/mol-plugin/ui/controls/parameters.tsx
@@ -44,6 +44,7 @@ function controlFor(param: PD.Any): ParamControl | undefined {
case 'converted': return ConvertedControl;
case 'multi-select': return MultiSelectControl;
case 'color': return ColorControl;
+ case 'vec3': return Vec3Control;
case 'select': return SelectControl;
case 'text': return TextControl;
case 'interval': return IntervalControl;
@@ -166,6 +167,17 @@ export class ColorControl extends SimpleParam<PD.Color> {
}
}
+export class Vec3Control extends SimpleParam<PD.Vec3> {
+ // onChange = (e: React.ChangeEvent<HTMLSelectElement>) => {
+ // this.setState({ value: e.target.value });
+ // this.props.onChange(e.target.value);
+ // }
+
+ renderControl() {
+ return <span>vec3 TODO</span>;
+ }
+}
+
export class MultiSelectControl extends React.PureComponent<ParamProps<PD.MultiSelect<any>>, { isExpanded: boolean }> {
state = { isExpanded: false }
diff --git a/src/mol-repr/representation.ts b/src/mol-repr/representation.ts
index 1325c1481edc2963cb4cff2584431022142599da..d271a2f35b28f501a3921444c79394c1f436e1c9 100644
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/representation.ts
@@ -15,7 +15,7 @@ import { getQualityProps } from './util';
import { ColorTheme } from 'mol-theme/color';
import { SizeTheme } from 'mol-theme/size';
import { Theme, ThemeRegistryContext } from 'mol-theme/theme';
-import { BehaviorSubject } from 'rxjs';
+import { Subject } from 'rxjs';
// export interface RepresentationProps {
// visuals?: string[]
@@ -80,7 +80,7 @@ export interface RepresentationContext {
export { Representation }
interface Representation<D, P extends PD.Params = {}> {
readonly label: string
- readonly updated: BehaviorSubject<number>
+ readonly updated: Subject<number>
readonly renderObjects: ReadonlyArray<RenderObject>
readonly props: Readonly<PD.Values<P>>
readonly params: Readonly<P>
@@ -88,23 +88,26 @@ interface Representation<D, P extends PD.Params = {}> {
getLoci: (pickingId: PickingId) => Loci
mark: (loci: Loci, action: MarkerAction) => boolean
setVisibility: (value: boolean) => void
+ setPickable: (value: boolean) => void
destroy: () => void
}
namespace Representation {
export type Any = Representation<any>
export const Empty: Any = {
- label: '', renderObjects: [], props: {}, params: {}, updated: new BehaviorSubject(0),
+ label: '', renderObjects: [], props: {}, params: {}, updated: new Subject(),
createOrUpdate: () => Task.constant('', undefined),
getLoci: () => EmptyLoci,
mark: () => false,
setVisibility: () => {},
+ setPickable: () => {},
destroy: () => {}
}
export type Def<D, P extends PD.Params = {}> = { [k: string]: (getParams: RepresentationParamsGetter<D, P>) => Representation<any, P> }
export function createMulti<D, P extends PD.Params = {}>(label: string, getParams: RepresentationParamsGetter<D, P>, reprDefs: Def<D, P>): Representation<D, P> {
- const updated = new BehaviorSubject(0)
+ let version = 0
+ const updated = new Subject<number>()
let currentParams: P
let currentProps: PD.Values<P>
@@ -153,7 +156,7 @@ namespace Representation {
await reprList[i].createOrUpdate(ctx, currentProps, currentData).runInContext(runtime)
}
}
- updated.next(updated.getValue() + 1)
+ updated.next(version++)
})
},
getLoci: (pickingId: PickingId) => {
@@ -175,6 +178,11 @@ namespace Representation {
reprList[i].setVisibility(value)
}
},
+ setPickable: (value: boolean) => {
+ for (let i = 0, il = reprList.length; i < il; ++i) {
+ reprList[i].setPickable(value)
+ }
+ },
destroy() {
for (let i = 0, il = reprList.length; i < il; ++i) {
reprList[i].destroy()
@@ -197,5 +205,6 @@ export interface Visual<D, P extends PD.Params> {
getLoci: (pickingId: PickingId) => Loci
mark: (loci: Loci, action: MarkerAction) => boolean
setVisibility: (value: boolean) => void
+ setPickable: (value: boolean) => void
destroy: () => void
}
\ No newline at end of file
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index 27c7d9e7339a29438bce609f766c8cc2d8bf3570..c8e7ac8db60ea143a510f4358cf3b153cc233f6c 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/src/mol-repr/shape/representation.ts
@@ -19,7 +19,7 @@ import { PickingId } from 'mol-geo/geometry/picking';
import { MarkerAction, applyMarkerAction } from 'mol-geo/geometry/marker-data';
import { LocationIterator } from 'mol-geo/util/location-iterator';
import { createTheme } from 'mol-theme/theme';
-import { BehaviorSubject } from 'rxjs';
+import { Subject } from 'rxjs';
export interface ShapeRepresentation<P extends ShapeParams> extends Representation<Shape, P> { }
@@ -31,7 +31,8 @@ export const ShapeParams = {
export type ShapeParams = typeof ShapeParams
export function ShapeRepresentation<P extends ShapeParams>(): ShapeRepresentation<P> {
- const updated = new BehaviorSubject(0)
+ let version = 0
+ const updated = new Subject<number>()
const renderObjects: RenderObject[] = []
let _renderObject: MeshRenderObject | undefined
let _shape: Shape
@@ -57,7 +58,7 @@ export function ShapeRepresentation<P extends ShapeParams>(): ShapeRepresentatio
_renderObject = createMeshRenderObject(values, state)
renderObjects.push(_renderObject)
- updated.next(updated.getValue() + 1)
+ updated.next(version++)
});
}
@@ -103,6 +104,9 @@ export function ShapeRepresentation<P extends ShapeParams>(): ShapeRepresentatio
setVisibility(value: boolean) {
renderObjects.forEach(ro => ro.state.visible = value)
},
+ setPickable(value: boolean) {
+ renderObjects.forEach(ro => ro.state.pickable = value)
+ },
destroy() {
// TODO
renderObjects.length = 0
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index f74d0551005db1201cd232d17b9b23321ade0838..816f84d4ddb0d95897f6930695a1fb6d22a23b35 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -15,10 +15,11 @@ import { MarkerAction } from 'mol-geo/geometry/marker-data';
import { RepresentationContext, RepresentationParamsGetter } from 'mol-repr/representation';
import { Theme, createTheme } from 'mol-theme/theme';
import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { BehaviorSubject } from 'rxjs';
+import { Subject } from 'rxjs';
export function ComplexRepresentation<P extends StructureParams>(label: string, getParams: RepresentationParamsGetter<Structure, P>, visualCtor: () => ComplexVisual<P>): StructureRepresentation<P> {
- const updated = new BehaviorSubject(0)
+ let version = 0
+ const updated = new Subject<number>()
let visual: ComplexVisual<P> | undefined
let _structure: Structure
@@ -38,7 +39,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
return Task.create('Creating or updating ComplexRepresentation', async runtime => {
if (!visual) visual = visualCtor()
await visual.createOrUpdate({ ...ctx, runtime }, _theme, _props, structure)
- updated.next(updated.getValue() + 1)
+ updated.next(version++)
});
}
@@ -54,6 +55,10 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
if (visual) visual.setVisibility(value)
}
+ function setPickable(value: boolean) {
+ if (visual) visual.setPickable(value)
+ }
+
function destroy() {
if (visual) visual.destroy()
}
@@ -70,6 +75,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
getLoci,
mark,
setVisibility,
+ setPickable,
destroy
}
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 25823c82f05c06438cb4c61af328390ad3a87395..ffccd126bec7138a427b8cdeb6c739f4ea7681c6 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -165,6 +165,9 @@ export function ComplexVisual<P extends ComplexParams>(builder: ComplexVisualGeo
setVisibility(value: boolean) {
if (renderObject) renderObject.state.visible = value
},
+ setPickable(value: boolean) {
+ if (renderObject) renderObject.state.pickable = value
+ },
destroy() {
// TODO
renderObject = undefined
@@ -187,7 +190,7 @@ export function ComplexMeshVisual<P extends ComplexMeshParams>(builder: ComplexM
...builder,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
- if (SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
+ if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
},
createEmptyGeometry: Mesh.createEmpty,
createRenderObject: createComplexMeshRenderObject,
diff --git a/src/mol-repr/structure/representation/carbohydrate.ts b/src/mol-repr/structure/representation/carbohydrate.ts
index 82660da3fb1f0eba58ad787a8843cca7684450bb..ac2e0d87bd53066ddf807ea3b39c2c2f73c3cc2f 100644
--- a/src/mol-repr/structure/representation/carbohydrate.ts
+++ b/src/mol-repr/structure/representation/carbohydrate.ts
@@ -6,6 +6,7 @@
import { CarbohydrateSymbolVisual, CarbohydrateSymbolParams } from '../visual/carbohydrate-symbol-mesh';
import { CarbohydrateLinkVisual, CarbohydrateLinkParams } from '../visual/carbohydrate-link-cylinder';
+import { CarbohydrateTerminalLinkParams, CarbohydrateTerminalLinkVisual } from '../visual/carbohydrate-terminal-link-cylinder';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { ComplexRepresentation } from '../complex-representation';
import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
@@ -17,6 +18,7 @@ import { BuiltInColorThemeOptions, getBuiltInColorThemeParams } from 'mol-theme/
const CarbohydrateVisuals = {
'carbohydrate-symbol': (getParams: RepresentationParamsGetter<Structure, CarbohydrateSymbolParams>) => ComplexRepresentation('Carbohydrate symbol mesh', getParams, CarbohydrateSymbolVisual),
'carbohydrate-link': (getParams: RepresentationParamsGetter<Structure, CarbohydrateLinkParams>) => ComplexRepresentation('Carbohydrate link cylinder', getParams, CarbohydrateLinkVisual),
+ 'carbohydrate-terminal-link': (getParams: RepresentationParamsGetter<Structure, CarbohydrateTerminalLinkParams>) => ComplexRepresentation('Carbohydrate terminal link cylinder', getParams, CarbohydrateTerminalLinkVisual),
}
type CarbohydrateVisualName = keyof typeof CarbohydrateVisuals
const CarbohydrateVisualOptions = Object.keys(CarbohydrateVisuals).map(name => [name, name] as [CarbohydrateVisualName, string])
@@ -24,8 +26,9 @@ const CarbohydrateVisualOptions = Object.keys(CarbohydrateVisuals).map(name => [
export const CarbohydrateParams = {
...CarbohydrateSymbolParams,
...CarbohydrateLinkParams,
+ ...CarbohydrateTerminalLinkParams,
colorTheme: PD.Mapped('carbohydrate-symbol', BuiltInColorThemeOptions, getBuiltInColorThemeParams),
- visuals: PD.MultiSelect<CarbohydrateVisualName>(['carbohydrate-symbol', 'carbohydrate-link'], CarbohydrateVisualOptions),
+ visuals: PD.MultiSelect<CarbohydrateVisualName>(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], CarbohydrateVisualOptions),
}
PD.getDefaultValues(CarbohydrateParams).colorTheme.name
export type CarbohydrateParams = typeof CarbohydrateParams
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 42bb3fb8604b8660664dbdf7476772105c6cab63..84aed6c3de81b45c5dd44ff2b813e0b01d2e17dc 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -17,7 +17,7 @@ import { MarkerAction } from 'mol-geo/geometry/marker-data';
import { Theme, createTheme } from 'mol-theme/theme';
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { UnitKind, UnitKindOptions } from './visual/util/common';
-import { BehaviorSubject } from 'rxjs';
+import { Subject } from 'rxjs';
export const UnitsParams = {
...StructureParams,
@@ -28,7 +28,8 @@ export type UnitsParams = typeof UnitsParams
export interface UnitsVisual<P extends UnitsParams> extends Visual<StructureGroup, P> { }
export function UnitsRepresentation<P extends UnitsParams>(label: string, getParams: RepresentationParamsGetter<Structure, P>, visualCtor: () => UnitsVisual<P>): StructureRepresentation<P> {
- const updated = new BehaviorSubject(0)
+ let version = 0
+ const updated = new Subject<number>()
let visuals = new Map<number, { group: Unit.SymmetryGroup, visual: UnitsVisual<P> }>()
let _structure: Structure
@@ -120,7 +121,7 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
}
}
if (structure) _structure = structure
- updated.next(updated.getValue() + 1)
+ updated.next(version++)
});
}
@@ -147,6 +148,12 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
})
}
+ function setPickable(value: boolean) {
+ visuals.forEach(({ visual }) => {
+ visual.setPickable(value)
+ })
+ }
+
function destroy() {
visuals.forEach(({ visual }) => visual.destroy())
visuals.clear()
@@ -163,11 +170,12 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, getPar
},
get props() { return _props },
get params() { return _params },
- get updated() { return updated },
+ updated,
createOrUpdate,
getLoci,
mark,
setVisibility,
+ setPickable,
destroy
}
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index f5cc5a4a58ce0ae94f8eb3bd551a47d0d49565f8..abb5dccb56234f38b41d0e16ff71d2c48953787c 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -195,6 +195,9 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
setVisibility(value: boolean) {
if (renderObject) renderObject.state.visible = value
},
+ setPickable(value: boolean) {
+ if (renderObject) renderObject.state.pickable = value
+ },
destroy() {
// TODO
renderObject = undefined
@@ -216,7 +219,7 @@ export function UnitsMeshVisual<P extends UnitsMeshParams>(builder: UnitsMeshVis
...builder,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
- if (SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
+ if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
},
createEmptyGeometry: Mesh.createEmpty,
createRenderObject: createUnitsMeshRenderObject,
@@ -240,7 +243,7 @@ export function UnitsPointsVisual<P extends UnitsPointsParams>(builder: UnitsPoi
createRenderObject: createUnitsPointsRenderObject,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
- if (SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
+ if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
},
updateValues: Points.updateValues
})
@@ -262,7 +265,7 @@ export function UnitsLinesVisual<P extends UnitsLinesParams>(builder: UnitsLines
createRenderObject: createUnitsLinesRenderObject,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
- if (SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
+ if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.updateSize = true
},
updateValues: Lines.updateValues
})
@@ -284,7 +287,7 @@ export function UnitsDirectVolumeVisual<P extends UnitsDirectVolumeParams>(build
createRenderObject: createUnitsDirectVolumeRenderObject,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme) => {
builder.setUpdateState(state, newProps, currentProps, newTheme, currentTheme)
- if (SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
+ if (!SizeTheme.areEqual(newTheme.size, currentTheme.size)) state.createGeometry = true
},
updateValues: DirectVolume.updateValues
})
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index e58322f57d5b6f1eb90db7832db26dbe61007433..05d5a04b0d66afd2c4bf649fb66826835538fe13 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -7,7 +7,7 @@
import { Structure, Link, StructureElement } from 'mol-model/structure';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { Vec3 } from 'mol-math/linear-algebra';
-import { createLinkCylinderMesh, LinkCylinderProps, LinkCylinderParams } from './util/link';
+import { createLinkCylinderMesh, LinkCylinderParams } from './util/link';
import { OrderedSet, Interval } from 'mol-data/int';
import { ComplexMeshVisual, ComplexVisual } from '../complex-visual';
import { LinkType } from 'mol-model/structure/model/types';
@@ -21,22 +21,10 @@ import { VisualUpdateState } from '../../util';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-// TODO create seperate visual
-// for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {
-// const tl = carbohydrates.terminalLinks[i]
-// const center = carbohydrates.elements[tl.carbohydrateIndex].geometry.center
-// tl.elementUnit.conformation.position(tl.elementUnit.elements[tl.elementIndex], p)
-// if (tl.fromCarbohydrate) {
-// builder.addCylinder(center, p, 0.5, linkParams)
-// } else {
-// builder.addCylinder(p, center, 0.5, linkParams)
-// }
-// }
-
-const radiusFactor = 0.3
-
-async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: LinkCylinderProps, mesh?: Mesh) {
+async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateLinkParams>, mesh?: Mesh) {
const { links, elements } = structure.carbohydrates
+ const { linkSizeFactor } = props
+
const location = StructureElement.create()
const builderProps = {
@@ -53,7 +41,7 @@ async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure:
const l = links[edgeIndex]
location.unit = elements[l.carbohydrateIndexA].unit
location.element = elements[l.carbohydrateIndexA].anomericCarbon
- return theme.size.size(location) * radiusFactor
+ return theme.size.size(location) * linkSizeFactor
}
}
@@ -64,6 +52,7 @@ export const CarbohydrateLinkParams = {
...UnitsMeshParams,
...LinkCylinderParams,
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }),
}
export type CarbohydrateLinkParams = typeof CarbohydrateLinkParams
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index 440d6e834e948a8b2ae6de8cdf85855686316368..7a5acbf598fc3d6b1241632712d95c97ee30358e 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -30,8 +30,7 @@ const t = Mat4.identity()
const sVec = Vec3.zero()
const pd = Vec3.zero()
-const sideFactor = 1.75 * 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
-const radiusFactor = 1.75
+const SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)
const box = Box()
const perforatedBox = PerforatedBox()
@@ -47,7 +46,7 @@ const hexagonalPrism = HexagonalPrism()
async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateSymbolParams>, mesh?: Mesh) {
const builder = MeshBuilder.create(256, 128, mesh)
- const { detail } = props
+ const { detail, sizeFactor } = props
const carbohydrates = structure.carbohydrates
const n = carbohydrates.elements.length
@@ -60,8 +59,8 @@ async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Struc
l.unit = c.unit
l.element = c.unit.elements[c.anomericCarbon]
const size = theme.size.size(l)
- const radius = size * radiusFactor
- const side = size * sideFactor
+ const radius = size * sizeFactor
+ const side = size * sizeFactor * SideFactor
const { center, normal, direction } = c.geometry
Vec3.add(pd, center, direction)
@@ -148,6 +147,7 @@ async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Struc
export const CarbohydrateSymbolParams = {
...ComplexMeshParams,
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ sizeFactor: PD.Numeric(1.75, { min: 0, max: 10, step: 0.01 }),
}
export type CarbohydrateSymbolParams = typeof CarbohydrateSymbolParams
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7d594fd788a192d1fa5fb1df4e2ec6f2bff9ca65
--- /dev/null
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -0,0 +1,147 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Structure, Link, StructureElement } from 'mol-model/structure';
+import { Loci, EmptyLoci } from 'mol-model/loci';
+import { Vec3 } from 'mol-math/linear-algebra';
+import { createLinkCylinderMesh, LinkCylinderParams } from './util/link';
+import { OrderedSet, Interval } from 'mol-data/int';
+import { ComplexMeshVisual, ComplexVisual } from '../complex-visual';
+import { LinkType } from 'mol-model/structure/model/types';
+import { BitFlags } from 'mol-util';
+import { UnitsMeshParams } from '../units-visual';
+import { ParamDefinition as PD } from 'mol-util/param-definition';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
+import { LocationIterator } from 'mol-geo/util/location-iterator';
+import { PickingId } from 'mol-geo/geometry/picking';
+import { VisualUpdateState } from '../../util';
+import { VisualContext } from 'mol-repr/representation';
+import { Theme } from 'mol-theme/theme';
+
+async function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateTerminalLinkParams>, mesh?: Mesh) {
+ const { terminalLinks, elements } = structure.carbohydrates
+ const { linkSizeFactor } = props
+
+ const location = StructureElement.create()
+
+ const builderProps = {
+ linkCount: terminalLinks.length,
+ referencePosition: (edgeIndex: number) => null,
+ position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
+ const l = terminalLinks[edgeIndex]
+ if (l.fromCarbohydrate) {
+ Vec3.copy(posA, elements[l.carbohydrateIndex].geometry.center)
+ l.elementUnit.conformation.position(l.elementIndex, posB)
+ } else {
+ l.elementUnit.conformation.position(l.elementIndex, posA)
+ Vec3.copy(posB, elements[l.carbohydrateIndex].geometry.center)
+ }
+ },
+ order: (edgeIndex: number) => 1,
+ flags: (edgeIndex: number) => BitFlags.create(LinkType.Flag.None),
+ radius: (edgeIndex: number) => {
+ const l = terminalLinks[edgeIndex]
+ if (l.fromCarbohydrate) {
+ location.unit = elements[l.carbohydrateIndex].unit
+ location.element = elements[l.carbohydrateIndex].anomericCarbon
+ } else {
+ location.unit = l.elementUnit
+ location.element = l.elementUnit.elements[l.elementIndex]
+ }
+ return theme.size.size(location) * linkSizeFactor
+ }
+ }
+
+ return createLinkCylinderMesh(ctx, builderProps, props, mesh)
+}
+
+export const CarbohydrateTerminalLinkParams = {
+ ...UnitsMeshParams,
+ ...LinkCylinderParams,
+ detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }),
+}
+export type CarbohydrateTerminalLinkParams = typeof CarbohydrateTerminalLinkParams
+
+export function CarbohydrateTerminalLinkVisual(): ComplexVisual<CarbohydrateTerminalLinkParams> {
+ return ComplexMeshVisual<CarbohydrateTerminalLinkParams>({
+ defaultProps: PD.getDefaultValues(CarbohydrateTerminalLinkParams),
+ createGeometry: createCarbohydrateTerminalLinkCylinderMesh,
+ createLocationIterator: CarbohydrateTerminalLinkIterator,
+ getLoci: getTerminalLinkLoci,
+ mark: markTerminalLink,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<CarbohydrateTerminalLinkParams>, currentProps: PD.Values<CarbohydrateTerminalLinkParams>) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
+ }
+ })
+}
+
+function CarbohydrateTerminalLinkIterator(structure: Structure): LocationIterator {
+ const { elements, terminalLinks } = structure.carbohydrates
+ const groupCount = terminalLinks.length
+ const instanceCount = 1
+ const location = Link.Location()
+ const getLocation = (groupIndex: number) => {
+ const terminalLink = terminalLinks[groupIndex]
+ const carb = elements[terminalLink.carbohydrateIndex]
+ const indexCarb = OrderedSet.indexOf(carb.unit.elements, carb.anomericCarbon)
+ if (terminalLink.fromCarbohydrate) {
+ location.aUnit = carb.unit
+ location.aIndex = indexCarb as StructureElement.UnitIndex
+ location.bUnit = terminalLink.elementUnit
+ location.bIndex = terminalLink.elementIndex
+ } else {
+ location.aUnit = terminalLink.elementUnit
+ location.aIndex = terminalLink.elementIndex
+ location.bUnit = carb.unit
+ location.bIndex = indexCarb as StructureElement.UnitIndex
+ }
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation, true)
+}
+
+function getTerminalLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
+ const { objectId, groupId } = pickingId
+ if (id === objectId) {
+ const { terminalLinks, elements } = structure.carbohydrates
+ const l = terminalLinks[groupId]
+ const carb = elements[l.carbohydrateIndex]
+ const carbIndex = OrderedSet.indexOf(carb.unit.elements, carb.anomericCarbon)
+
+ if (l.fromCarbohydrate) {
+ return Link.Loci(structure, [
+ Link.Location(
+ carb.unit, carbIndex as StructureElement.UnitIndex,
+ l.elementUnit, l.elementIndex
+ )
+ ])
+ } else {
+ return Link.Loci(structure, [
+ Link.Location(
+ l.elementUnit, l.elementIndex,
+ carb.unit, carbIndex as StructureElement.UnitIndex
+ )
+ ])
+ }
+ }
+ return EmptyLoci
+}
+
+function markTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+ const { getTerminalLinkIndex } = structure.carbohydrates
+
+ let changed = false
+ if (Link.isLoci(loci)) {
+ for (const l of loci.links) {
+ const idx = getTerminalLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
+ if (idx !== undefined) {
+ if (apply(Interval.ofSingleton(idx))) changed = true
+ }
+ }
+ }
+ return changed
+}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
index 31e82c69c78b9f1e5bad8b5022b02b3a2f7e7e8c..f85233d3541260ded2037f1c37c814e17e00be24 100644
--- a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
@@ -7,7 +7,7 @@
import { Link, Structure, StructureElement } from 'mol-model/structure';
import { ComplexVisual } from '../representation';
import { VisualUpdateState } from '../../util';
-import { LinkCylinderProps, createLinkCylinderMesh, LinkIterator, LinkCylinderParams } from './util/link';
+import { createLinkCylinderMesh, LinkIterator, LinkCylinderParams } from './util/link';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { ComplexMeshVisual, ComplexMeshParams } from '../complex-visual';
@@ -19,9 +19,10 @@ import { PickingId } from 'mol-geo/geometry/picking';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: LinkCylinderProps, mesh?: Mesh) {
+async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitLinkParams>, mesh?: Mesh) {
const links = structure.links
const { bondCount, bonds } = links
+ const { sizeFactor } = props
if (!bondCount) return Mesh.createEmpty(mesh)
@@ -42,7 +43,7 @@ async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: St
const b = bonds[edgeIndex]
location.unit = b.unitA
location.element = b.unitA.elements[b.indexA]
- return theme.size.size(location)
+ return theme.size.size(location) * sizeFactor
}
}
@@ -52,6 +53,7 @@ async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: St
export const InterUnitLinkParams = {
...ComplexMeshParams,
...LinkCylinderParams,
+ sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
}
export type InterUnitLinkParams = typeof InterUnitLinkParams
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index 12e24cdf1cd98895bb3e61971202c9aea2a1b5b8..075c02c8a417f4671251242aeac212d5387d6132 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -20,7 +20,7 @@ import { NullLocation } from 'mol-model/location';
import { VisualUpdateState } from 'mol-repr/util';
import { ValueCell } from 'mol-util';
import { Theme, createTheme } from 'mol-theme/theme';
-import { BehaviorSubject } from 'rxjs';
+import { Subject } from 'rxjs';
export interface VolumeVisual<P extends VolumeParams> extends Visual<VolumeData, P> { }
@@ -39,7 +39,7 @@ interface VolumeVisualGeometryBuilder<P extends VolumeParams, G extends Geometry
updateValues(values: RenderableValues, newProps: PD.Values<P>): void
}
-export function VolumeVisual<P extends VolumeParams>(builder: VolumeVisualGeometryBuilder<P, Geometry>) {
+export function VolumeVisual<P extends VolumeParams>(builder: VolumeVisualGeometryBuilder<P, Geometry>): VolumeVisual<P> {
const { defaultProps, createGeometry, getLoci, mark, setUpdateState } = builder
const { createRenderObject, updateValues } = builder
const updateState = VisualUpdateState.create()
@@ -120,6 +120,9 @@ export function VolumeVisual<P extends VolumeParams>(builder: VolumeVisualGeomet
setVisibility(value: boolean) {
if (renderObject) renderObject.state.visible = value
},
+ setPickable(value: boolean) {
+ if (renderObject) renderObject.state.pickable = value
+ },
destroy() {
// TODO
renderObject = undefined
@@ -140,7 +143,8 @@ export const VolumeParams = {
export type VolumeParams = typeof VolumeParams
export function VolumeRepresentation<P extends VolumeParams>(label: string, getParams: RepresentationParamsGetter<VolumeData, P>, visualCtor: (volume: VolumeData) => VolumeVisual<P>): VolumeRepresentation<P> {
- const updated = new BehaviorSubject(0)
+ let version = 0
+ const updated = new Subject<number>()
let visual: VolumeVisual<P>
let _volume: VolumeData
@@ -174,7 +178,7 @@ export function VolumeRepresentation<P extends VolumeParams>(label: string, getP
await visual.createOrUpdate({ ...ctx, runtime }, _theme, _props, volume)
busy = false
}
- updated.next(updated.getValue() + 1)
+ updated.next(version++)
});
}
@@ -194,6 +198,10 @@ export function VolumeRepresentation<P extends VolumeParams>(label: string, getP
if (visual) visual.setVisibility(value)
}
+ function setPickable(value: boolean) {
+ if (visual) visual.setPickable(value)
+ }
+
return {
label,
get renderObjects() {
@@ -206,6 +214,7 @@ export function VolumeRepresentation<P extends VolumeParams>(label: string, getP
getLoci,
mark,
setVisibility,
+ setPickable,
destroy
}
}
\ No newline at end of file
diff --git a/src/mol-util/param-definition.ts b/src/mol-util/param-definition.ts
index 2c1922a953cad32e68a35fea67d6719389d5826b..8bb45df5b470cdb53cbe3acb8d691de78ed21b92 100644
--- a/src/mol-util/param-definition.ts
+++ b/src/mol-util/param-definition.ts
@@ -7,7 +7,7 @@
import { Color as ColorData } from './color';
import { shallowEqual } from 'mol-util';
-import { Vec2 } from 'mol-math/linear-algebra';
+import { Vec2 as Vec2Data, Vec3 as Vec3Data } from 'mol-math/linear-algebra';
import { deepClone } from './object';
export namespace ParamDefinition {
@@ -75,6 +75,13 @@ export namespace ParamDefinition {
return setInfo<Color>({ type: 'color', defaultValue }, info)
}
+ export interface Vec3 extends Base<Vec3Data> {
+ type: 'vec3'
+ }
+ export function Vec3(defaultValue: Vec3Data, info?: Info): Vec3 {
+ return setInfo<Vec3>({ type: 'vec3', defaultValue }, info)
+ }
+
export interface Range {
/** If given treat as a range. */
min?: number
@@ -108,10 +115,10 @@ export namespace ParamDefinition {
return setInfo<Interval>(setRange({ type: 'interval', defaultValue }, range), info)
}
- export interface LineGraph extends Base<Vec2[]> {
+ export interface LineGraph extends Base<Vec2Data[]> {
type: 'line-graph'
}
- export function LineGraph(defaultValue: Vec2[], info?: Info): LineGraph {
+ export function LineGraph(defaultValue: Vec2Data[], info?: Info): LineGraph {
return setInfo<LineGraph>({ type: 'line-graph', defaultValue }, info)
}
@@ -149,7 +156,7 @@ export namespace ParamDefinition {
return { type: 'converted', defaultValue: toValue(converted.defaultValue), converted, fromValue, toValue };
}
- export type Any = Value<any> | Select<any> | MultiSelect<any> | Boolean | Text | Color | Numeric | Interval | LineGraph | Group<any> | Mapped<any> | Converted<any, any>
+ export type Any = Value<any> | Select<any> | MultiSelect<any> | Boolean | Text | Color | Vec3 | Numeric | Interval | LineGraph | Group<any> | Mapped<any> | Converted<any, any>
export type Params = { [k: string]: Any }
export type Values<T extends Params> = { [k in keyof T]: T[k]['defaultValue'] }
@@ -210,9 +217,11 @@ export namespace ParamDefinition {
const u = a as LineGraph['defaultValue'], v = b as LineGraph['defaultValue'];
if (u.length !== v.length) return false;
for (let i = 0, _i = u.length; i < _i; i++) {
- if (!Vec2.areEqual(u[i], v[i])) return false;
+ if (!Vec2Data.areEqual(u[i], v[i])) return false;
}
return true;
+ } else if (p.type === 'vec3') {
+ return Vec3Data.equals(a, b);
} else if (typeof a === 'object' && typeof b === 'object') {
return shallowEqual(a, b);
}