diff --git a/src/apps/canvas/component/structure-representation.tsx b/src/apps/canvas/component/structure-representation.tsx
index bdc194b701b259a28ff093d15372dcc861b75672..497fa6e8b324d631f44afe2dfe45bf4bd3e5347f 100644
--- a/src/apps/canvas/component/structure-representation.tsx
+++ b/src/apps/canvas/component/structure-representation.tsx
@@ -10,6 +10,7 @@ import Viewer from 'mol-view/viewer';
import { VisualQuality, VisualQualityNames } from 'mol-geo/representation/util';
import { ColorThemeProps, ColorThemeName, ColorThemeNames, ColorTheme } from 'mol-view/theme/color';
import { Color } from 'mol-util/color';
+import { Progress } from 'mol-task';
export interface StructureRepresentationComponentProps {
viewer: Viewer
@@ -22,6 +23,10 @@ export interface StructureRepresentationComponentState {
alpha: number
quality: VisualQuality
colorTheme: ColorThemeProps
+
+ resolutionFactor?: number
+ probeRadius?: number
+ isoValue?: number
}
export class StructureRepresentationComponent extends React.Component<StructureRepresentationComponentProps, StructureRepresentationComponentState> {
@@ -31,6 +36,10 @@ export class StructureRepresentationComponent extends React.Component<StructureR
alpha: this.props.representation.props.alpha,
quality: this.props.representation.props.quality,
colorTheme: this.props.representation.props.colorTheme,
+
+ resolutionFactor: (this.props.representation.props as any).resolutionFactor,
+ probeRadius: (this.props.representation.props as any).probeRadius,
+ isoValue: (this.props.representation.props as any).isoValue,
}
componentWillMount() {
@@ -43,6 +52,10 @@ export class StructureRepresentationComponent extends React.Component<StructureR
alpha: repr.props.alpha,
quality: repr.props.quality,
colorTheme: repr.props.colorTheme,
+
+ resolutionFactor: (repr.props as any).resolutionFactor,
+ probeRadius: (repr.props as any).probeRadius,
+ isoValue: (repr.props as any).isoValue,
})
}
@@ -55,17 +68,36 @@ export class StructureRepresentationComponent extends React.Component<StructureR
if (state.alpha !== undefined) props.alpha = state.alpha
if (state.colorTheme !== undefined) props.colorTheme = state.colorTheme
- await repr.createOrUpdate(props).run()
+ if (state.resolutionFactor !== undefined) (props as any).resolutionFactor = state.resolutionFactor
+ if (state.probeRadius !== undefined) (props as any).probeRadius = state.probeRadius
+ if (state.isoValue !== undefined) (props as any).isoValue = state.isoValue
+
+ await repr.createOrUpdate(props).run(
+ progress => console.log(Progress.format(progress)), 100
+ )
this.props.viewer.add(repr)
- this.props.viewer.requestDraw(true)
+ this.props.viewer.draw(true)
console.log(this.props.viewer.stats)
+ console.log(
+ 'drawCount',
+ repr.renderObjects[0].values.drawCount.ref.version,
+ repr.renderObjects[0].values.drawCount.ref.value,
+ 'dColorType',
+ repr.renderObjects[0].values.dColorType.ref.version,
+ repr.renderObjects[0].values.dColorType.ref.value
+ )
+
const newState = {
...this.state,
visible: repr.props.visible,
quality: repr.props.quality,
alpha: repr.props.alpha,
colorTheme: repr.props.colorTheme,
+
+ resolutionFactor: (repr.props as any).resolutionFactor,
+ probeRadius: (repr.props as any).probeRadius,
+ isoValue: (repr.props as any).isoValue,
}
this.setState(newState)
}
@@ -107,6 +139,39 @@ export class StructureRepresentationComponent extends React.Component<StructureR
>
</input>
</div>
+ { this.state.resolutionFactor !== undefined ? <div>
+ <span>Resolution Factor </span>
+ <input type='range'
+ defaultValue={this.state.resolutionFactor.toString()}
+ min='4'
+ max='9'
+ step='1'
+ onInput={(e) => this.update({ resolutionFactor: parseInt(e.currentTarget.value) })}
+ >
+ </input>
+ </div> : '' }
+ { this.state.isoValue !== undefined ? <div>
+ <span>Iso Value </span>
+ <input type='range'
+ defaultValue={this.state.isoValue.toString()}
+ min='0.1'
+ max='2'
+ step='0.1'
+ onInput={(e) => this.update({ isoValue: parseFloat(e.currentTarget.value) })}
+ >
+ </input>
+ </div> : '' }
+ { this.state.probeRadius !== undefined ? <div>
+ <span>Probe Radius </span>
+ <input type='range'
+ defaultValue={this.state.probeRadius.toString()}
+ min='0'
+ max='10'
+ step='0.1'
+ onInput={(e) => this.update({ probeRadius: parseFloat(e.currentTarget.value) })}
+ >
+ </input>
+ </div> : '' }
<div>
<span>Color Theme </span>
<select value={colorTheme.name} onChange={(e) => this.update({ colorTheme: { name: e.target.value as ColorThemeName } }) }>
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index c5674578f27d99dae9056db73f63464279da2c44..a4fe44feed193911127e579e17b324b87b39e1cc 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -25,6 +25,7 @@ import { BehaviorSubject } from 'rxjs';
import { SpacefillRepresentation } from 'mol-geo/representation/structure/representation/spacefill';
import { DistanceRestraintRepresentation } from 'mol-geo/representation/structure/representation/distance-restraint';
import { SurfaceRepresentation } from 'mol-geo/representation/structure/representation/surface';
+import { Progress } from 'mol-task';
export interface StructureView {
readonly viewer: Viewer
@@ -67,7 +68,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const active: { [k: string]: boolean } = {
cartoon: true,
point: false,
- surface: true,
+ surface: false,
ballAndStick: false,
carbohydrate: false,
spacefill: false,
@@ -208,7 +209,9 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
console.log('createStructureRepr')
for (const k in structureRepresentations) {
if (active[k]) {
- await structureRepresentations[k].createOrUpdate({}, structure).run()
+ await structureRepresentations[k].createOrUpdate({}, structure).run(
+ progress => console.log(Progress.format(progress)), 100
+ )
viewer.add(structureRepresentations[k])
} else {
viewer.remove(structureRepresentations[k])
@@ -247,7 +250,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
updated.next(null)
viewer.requestDraw(true)
- console.log(viewer.stats)
+ console.log('stats', viewer.stats)
}
async function createSymmetryRepr() {
diff --git a/src/mol-geo/representation/structure/complex-representation.ts b/src/mol-geo/representation/structure/complex-representation.ts
index 3f624d4af188435dccb9238decbf223f9de2665c..66d65d10272ef0da7794495e7899c89f7c45d875 100644
--- a/src/mol-geo/representation/structure/complex-representation.ts
+++ b/src/mol-geo/representation/structure/complex-representation.ts
@@ -20,7 +20,7 @@ export function ComplexRepresentation<P extends StructureProps>(label: string, v
function createOrUpdate(props: Partial<P> = {}, structure?: Structure) {
_props = Object.assign({}, _props, props)
- return Task.create('Creating StructureRepresentation', async ctx => {
+ return Task.create('Creating or updating ComplexRepresentation', async ctx => {
if (!visual) visual = visualCtor()
await visual.createOrUpdate(ctx, _props, structure)
});
diff --git a/src/mol-geo/representation/structure/units-visual.ts b/src/mol-geo/representation/structure/units-visual.ts
index a98620a7f37577c8370be896af55bbbc0213c6a0..0644d5bbf19dfa1f510a77d245df5b0ec2eeef3a 100644
--- a/src/mol-geo/representation/structure/units-visual.ts
+++ b/src/mol-geo/representation/structure/units-visual.ts
@@ -126,14 +126,19 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
if (!group && !currentGroup) {
throw new Error('missing group')
} else if (group && (!currentGroup || !renderObject)) {
+ // console.log('unit-visual first create')
await create(ctx, group, props)
} else if (group && group.hashCode !== currentGroup.hashCode) {
+ // console.log('unit-visual group.hashCode !== currentGroup.hashCode')
await create(ctx, group, props)
} else {
- if (group && !areGroupsIdentical(group, currentGroup)) {
+ // console.log('unit-visual update')
+ if (group && !sameGroupConformation(group, currentGroup)) {
+ // console.log('unit-visual new conformation')
currentGroup = group
+ } else {
+ await update(ctx, props)
}
- await update(ctx, props)
}
},
getLoci(pickingId: PickingId) {
@@ -168,7 +173,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
}
}
-function areGroupsIdentical(groupA: Unit.SymmetryGroup, groupB: Unit.SymmetryGroup) {
+function sameGroupConformation(groupA: Unit.SymmetryGroup, groupB: Unit.SymmetryGroup) {
return (
groupA.units.length === groupB.units.length &&
Unit.conformationId(groupA.units[0]) === Unit.conformationId(groupB.units[0])
diff --git a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
index 7176fe48f39a07687b107da400ac16753521c6c0..ec42e86a277c57daf381941e0c2a0d2e7bd30432 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -13,18 +13,21 @@ import { StructureElementIterator, getElementLoci, markElement } from './util/el
import { computeMarchingCubes } from '../../../util/marching-cubes/algorithm';
import { Tensor, Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Box3D } from 'mol-math/geometry';
-import { ValueCell } from 'mol-util';
import { smoothstep } from 'mol-math/interpolate';
-import { LocationIterator } from '../../../util/location-iterator';
+import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
export interface GaussianSurfaceMeshProps {
+ sizeTheme: SizeThemeProps
+ resolutionFactor: number
+ probeRadius: number
+ isoValue: number
}
-function getDelta(box: Box3D) {
+function getDelta(box: Box3D, resolutionFactor: number) {
const extent = Vec3.sub(Vec3.zero(), box.max, box.min)
- const n = Math.pow(128, 3)
+ const n = Math.pow(Math.pow(2, resolutionFactor), 3)
const f = (extent[0] * extent[1] * extent[2]) / n
const s = Math.pow(f, 1 / 3)
const size = Vec3.zero()
@@ -35,17 +38,21 @@ function getDelta(box: Box3D) {
}
async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
+ const { resolutionFactor, probeRadius, isoValue } = props
const { elements } = unit;
const elementCount = elements.length;
-
- const r = 2.5;
+ const sizeTheme = SizeTheme(props.sizeTheme)
const v = Vec3.zero()
const p = Vec3.zero()
const pos = unit.conformation.invariantPosition
+ const l = StructureElement.create()
+ l.unit = unit
+
+ const pad = (probeRadius + 2) * 2 // TODO calculate max radius
const box = unit.lookup3d.boundary.box
- const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(r*3, r*3, r*3));
+ const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad));
const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
const min = expandedBox.min
@@ -63,7 +70,7 @@ async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, struct
// console.log('s', s)
// console.log('size', size)
// console.log('delta', delta)
- const delta = getDelta(Box3D.expand(Box3D.empty(), structure.boundary.box, Vec3.create(r*3, r*3, r*3)))
+ const delta = getDelta(Box3D.expand(Box3D.empty(), structure.boundary.box, Vec3.create(pad, pad, pad)), resolutionFactor)
const dim = Vec3.zero()
Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
// console.log('dim', dim, dim[0] * dim[1] * dim[2])
@@ -73,11 +80,12 @@ async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, struct
const field = Tensor.create(space, data)
for (let i = 0; i < elementCount; i++) {
+ l.element = elements[i]
pos(elements[i], v)
Vec3.mul(v, Vec3.sub(v, v, min), delta)
- const size = r
+ const size = sizeTheme.size(l) + probeRadius
const radius = size * delta[0]
const minX = Math.floor(v[0] - radius)
@@ -107,11 +115,10 @@ async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, struct
// console.log('data', data)
const surface = await computeMarchingCubes({
- isoLevel: 0.1,
+ isoLevel: isoValue,
scalarField: field,
oldSurface: mesh
-
- }).runAsChild(ctx);
+ }).runAsChild(ctx)
const t = Mat4.identity()
Mat4.fromUniformScaling(t, 1 / delta[0])
@@ -132,6 +139,10 @@ export const DefaultGaussianSurfaceProps = {
flipSided: true,
// flatShaded: true,
+
+ resolutionFactor: 7,
+ probeRadius: 1.4,
+ isoValue: 0.1,
}
export type GaussianSurfaceProps = typeof DefaultGaussianSurfaceProps
@@ -142,19 +153,10 @@ export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
- setUpdateState: (state: MeshUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {}
+ setUpdateState: (state: MeshUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {
+ if (newProps.resolutionFactor !== currentProps.resolutionFactor) state.createMesh = true
+ if (newProps.probeRadius !== currentProps.probeRadius) state.createMesh = true
+ if (newProps.isoValue !== currentProps.isoValue) state.createMesh = true
+ }
})
-}
-
-// function SingleGroupLocationIterator(group: Unit.SymmetryGroup): LocationIterator {
-// const groupCount = 1
-// const instanceCount = group.units.length
-// const location = StructureElement.create()
-// const getLocation = (groupIndex: number, instanceIndex: number) => {
-// const unit = group.units[instanceIndex]
-// location.unit = unit
-// location.element = unit.elements[groupIndex]
-// return location
-// }
-// return LocationIterator(groupCount, instanceCount, getLocation)
-// }
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 32ee9549a7f82a4f165bac0411bb03b11d2f70f3..651b823e02ef7f383cc070bac8bd8e8231b3b336 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -28,7 +28,7 @@ export interface MarchingCubesParameters {
export function computeMarchingCubes(parameters: MarchingCubesParameters) {
return Task.create('Marching Cubes', async ctx => {
- let comp = new MarchingCubesComputation(parameters, ctx);
+ const comp = new MarchingCubesComputation(parameters, ctx);
return await comp.run();
});
}
@@ -64,17 +64,18 @@ class MarchingCubesComputation {
this.state.clearEdgeVertexIndexSlice(k);
}
- private finish() {
+ private finish(): Mesh {
const vb = ChunkedArray.compact(this.state.vertexBuffer, true) as Float32Array;
const ib = ChunkedArray.compact(this.state.triangleBuffer, true) as Uint32Array;
const gb = ChunkedArray.compact(this.state.groupBuffer, true) as Float32Array;
this.state.vertexBuffer = <any>void 0;
this.state.verticesOnEdges = <any>void 0;
+ this.state.groupBuffer = <any>void 0;
const os = this.parameters.oldSurface
- const ret: Mesh = {
+ return {
vertexCount: this.state.vertexCount,
triangleCount: this.state.triangleCount,
vertexBuffer: os ? ValueCell.update(os.vertexBuffer, vb) : ValueCell.create(vb),
@@ -83,8 +84,6 @@ class MarchingCubesComputation {
normalBuffer: os ? os.normalBuffer : ValueCell.create(new Float32Array(0)),
normalsComputed: false
}
-
- return ret;
}
async run() {
@@ -94,11 +93,8 @@ class MarchingCubesComputation {
return this.finish();
}
- constructor(
- parameters: MarchingCubesParameters,
- private ctx: RuntimeContext) {
-
- let params = { ...parameters };
+ constructor(parameters: MarchingCubesParameters, private ctx: RuntimeContext) {
+ const params = { ...parameters };
this.parameters = params;
if (!params.bottomLeft) params.bottomLeft = [0, 0, 0];
@@ -148,8 +144,8 @@ class MarchingCubesState {
}
private interpolate(edgeNum: number) {
- const info = EdgeIdInfo[edgeNum],
- edgeId = 3 * this.get3dOffsetFromEdgeInfo(info) + info.e;
+ const info = EdgeIdInfo[edgeNum];
+ const edgeId = 3 * this.get3dOffsetFromEdgeInfo(info) + info.e;
const ret = this.verticesOnEdges[edgeId];
if (ret > 0) return (ret - 1) | 0;
@@ -247,7 +243,7 @@ class MarchingCubesState {
if ((edgeInfo & 1024) > 0) this.vertList[10] = this.interpolate(10); // 2 6
if ((edgeInfo & 2048) > 0) this.vertList[11] = this.interpolate(11); // 3 7
- let triInfo = TriTable[tableIndex];
+ const triInfo = TriTable[tableIndex];
for (let t = 0; t < triInfo.length; t += 3) {
this.triangleCount++;
ChunkedArray.add3(this.triangleBuffer, this.vertList[triInfo[t]], this.vertList[triInfo[t + 1]], this.vertList[triInfo[t + 2]]);