diff --git a/src/apps/canvas/component/structure-representation.tsx b/src/apps/canvas/component/structure-representation.tsx
index d282e8e41fd53d705dd00990bd519263f80daf8a..4249ddea2d2a3c4c0ba727884ebc5a9ed4ebc57a 100644
--- a/src/apps/canvas/component/structure-representation.tsx
+++ b/src/apps/canvas/component/structure-representation.tsx
@@ -26,8 +26,8 @@ export interface StructureRepresentationComponentState {
flatShaded?: boolean
resolutionFactor?: number
- probeRadius?: number
- isoValue?: number
+ radiusOffset?: number
+ smoothness?: number
}
export class StructureRepresentationComponent extends React.Component<StructureRepresentationComponentProps, StructureRepresentationComponentState> {
@@ -40,8 +40,8 @@ export class StructureRepresentationComponent extends React.Component<StructureR
flatShaded: (this.props.representation.props as any).flatShaded,
resolutionFactor: (this.props.representation.props as any).resolutionFactor,
- probeRadius: (this.props.representation.props as any).probeRadius,
- isoValue: (this.props.representation.props as any).isoValue,
+ radiusOffset: (this.props.representation.props as any).radiusOffset,
+ smoothness: (this.props.representation.props as any).smoothness,
}
componentWillMount() {
@@ -57,8 +57,8 @@ export class StructureRepresentationComponent extends React.Component<StructureR
flatShaded: (repr.props as any).flatShaded,
resolutionFactor: (repr.props as any).resolutionFactor,
- probeRadius: (repr.props as any).probeRadius,
- isoValue: (repr.props as any).isoValue,
+ radiusOffset: (repr.props as any).probeRadius,
+ smoothness: (repr.props as any).smoothness,
})
}
@@ -73,8 +73,8 @@ export class StructureRepresentationComponent extends React.Component<StructureR
if (state.flatShaded !== undefined) (props as any).flatShaded = state.flatShaded
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
+ if (state.radiusOffset !== undefined) (props as any).probeRadius = state.radiusOffset
+ if (state.smoothness !== undefined) (props as any).smoothness = state.smoothness
await repr.createOrUpdate(props).run(
progress => console.log(Progress.format(progress))
@@ -161,25 +161,25 @@ export class StructureRepresentationComponent extends React.Component<StructureR
>
</input>
</div> : '' }
- { this.state.isoValue !== undefined ? <div>
- <span>Iso Value </span>
+ { this.state.smoothness !== undefined ? <div>
+ <span>Smoothness </span>
<input type='range'
- defaultValue={this.state.isoValue.toString()}
+ defaultValue={this.state.smoothness.toString()}
min='1'
max='3'
step='0.1'
- onInput={(e) => this.update({ isoValue: parseFloat(e.currentTarget.value) })}
+ onInput={(e) => this.update({ smoothness: parseFloat(e.currentTarget.value) })}
>
</input>
</div> : '' }
- { this.state.probeRadius !== undefined ? <div>
- <span>Probe Radius </span>
+ { this.state.radiusOffset !== undefined ? <div>
+ <span>Radius Offset </span>
<input type='range'
- defaultValue={this.state.probeRadius.toString()}
+ defaultValue={this.state.radiusOffset.toString()}
min='0'
max='10'
step='0.1'
- onInput={(e) => this.update({ probeRadius: parseFloat(e.currentTarget.value) })}
+ onInput={(e) => this.update({ radiusOffset: parseFloat(e.currentTarget.value) })}
>
</input>
</div> : '' }
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index 62ef041ddfb753af90e335284ec85e431ae03c3e..e4acd4e8e3deea2217ac17b790f826bd74becdcb 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -68,10 +68,10 @@ 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: true,
+ spacefill: false,
distanceRestraint: false,
symmetryAxes: false,
// polymerSphere: false,
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 13dfc293a317d10d8ba4e7f38d788f111efc3090..a29ab4fdaac7f9505b15f8adf3fbe996f2e3c6fc 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -29,8 +29,8 @@ export const DefaultStructureMeshProps = {
export type StructureMeshProps = typeof DefaultStructureMeshProps
export const DefaultStructurePointProps = {
+ ...Point.DefaultProps,
...DefaultStructureProps,
- ...Point.DefaultProps
}
export type StructurePointProps = typeof DefaultStructurePointProps
diff --git a/src/mol-geo/representation/structure/representation/surface.ts b/src/mol-geo/representation/structure/representation/surface.ts
index 5d8c77e678ae58ae8db45558eed608f4576f8f16..d9237e575d449c7215b937ae1ec7c8390af0780d 100644
--- a/src/mol-geo/representation/structure/representation/surface.ts
+++ b/src/mol-geo/representation/structure/representation/surface.ts
@@ -38,7 +38,7 @@ export function SurfaceRepresentation(): SurfaceRepresentation {
currentProps = Object.assign({}, DefaultSurfaceProps, currentProps, props)
return Task.create('Creating SurfaceRepresentation', async ctx => {
await gaussianSurfaceRepr.createOrUpdate(currentProps, structure).runInContext(ctx)
- await gaussianPointRepr.createOrUpdate(currentProps, structure).runInContext(ctx)
+ // await gaussianPointRepr.createOrUpdate(currentProps, structure).runInContext(ctx)
})
},
getLoci: (pickingId: PickingId) => {
diff --git a/src/mol-geo/representation/structure/visual/gaussian-density-point.ts b/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
index 7bc2d1c9d671bad4c69321708b4b25ea99af4621..b6c3efd2ea2b92c48de6f4d520dcf695f644d9f0 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
@@ -10,36 +10,22 @@ import { UnitsVisual, VisualUpdateState } from '..';
import { StructureElementIterator } from './util/element';
import { EmptyLoci } from 'mol-model/loci';
import { Vec3 } from 'mol-math/linear-algebra';
-import { SizeThemeProps } from 'mol-view/theme/size';
import { UnitsPointVisual, DefaultUnitsPointProps } from '../units-visual';
-import { computeGaussianDensity } from './util/gaussian';
-import { Color } from 'mol-util/color';
-import { ColorThemeProps } from 'mol-view/theme/color';
+import { computeGaussianDensity, DefaultGaussianDensityProps } from './util/gaussian';
import { Point } from '../../../geometry/point/point';
import { PointBuilder } from '../../../geometry/point/point-builder';
+import { SizeThemeProps } from 'mol-view/theme/size';
export const DefaultGaussianDensityPointProps = {
...DefaultUnitsPointProps,
+ ...DefaultGaussianDensityProps,
- sizeTheme: { name: 'uniform', value: 1.5 } as SizeThemeProps,
- colorTheme: { name: 'uniform', value: Color(0xAAAAAA) } as ColorThemeProps,
+ sizeTheme: { name: 'uniform', value: 1 } as SizeThemeProps,
pointSizeAttenuation: false,
-
- resolutionFactor: 7,
- probeRadius: 0,
- isoValue: 1.5,
}
export type GaussianDensityPointProps = typeof DefaultGaussianDensityPointProps
-export interface GaussianDensityProps {
- sizeTheme: SizeThemeProps
-
- resolutionFactor: number
- probeRadius: number
- isoValue: number
-}
-
-export async function createGaussianDensityPoint(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps, point?: Point) {
+export async function createGaussianDensityPoint(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityPointProps, point?: Point) {
const { transform, field: { space, data } } = await computeGaussianDensity(unit, structure, props).runAsChild(ctx)
const { dimensions, get } = space
@@ -77,7 +63,9 @@ export function GaussianDensityPointVisual(): UnitsVisual<GaussianDensityPointPr
getLoci: () => EmptyLoci,
mark: () => false,
setUpdateState: (state: VisualUpdateState, newProps: GaussianDensityPointProps, currentProps: GaussianDensityPointProps) => {
-
+ if (newProps.resolutionFactor !== currentProps.resolutionFactor) state.createGeometry = true
+ if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+ if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
}
})
}
\ No newline at end of file
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 8966ca864a445e4ae546d338d66a73f151c231af..59485b6727f1f20830516cdd34265b523ef608ae 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -11,33 +11,17 @@ import { Mesh } from '../../../geometry/mesh/mesh';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { StructureElementIterator, getElementLoci, markElement } from './util/element';
import { computeMarchingCubes } from '../../../util/marching-cubes/algorithm';
-import { SizeThemeProps } from 'mol-view/theme/size';
-import { Color } from 'mol-util/color';
-import { computeGaussianDensity } from './util/gaussian';
-import { ColorThemeProps } from 'mol-view/theme/color';
+import { computeGaussianDensity, DefaultGaussianDensityProps } from './util/gaussian';
-export interface GaussianSurfaceMeshProps {
- sizeTheme: SizeThemeProps
-
- resolutionFactor: number
- probeRadius: number
- isoValue: number
-}
-
-async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
- const { isoValue } = props
-
- console.time('surface density')
+async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceProps, mesh?: Mesh): Promise<Mesh> {
+ const { smoothness } = props
const { transform, field } = await computeGaussianDensity(unit, structure, props).runAsChild(ctx)
- console.timeEnd('surface density')
- console.time('surface mc')
const surface = await computeMarchingCubes({
- isoLevel: Math.exp(-isoValue),
+ isoLevel: Math.exp(-smoothness),
scalarField: field,
oldSurface: mesh
}).runAsChild(ctx)
- console.timeEnd('surface mc')
Mesh.transformImmediate(surface, transform)
Mesh.computeNormalsImmediate(surface)
@@ -47,19 +31,9 @@ async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, struct
export const DefaultGaussianSurfaceProps = {
...DefaultUnitsMeshProps,
- linearSegments: 8,
- radialSegments: 12,
- aspectRatio: 5,
- arrowFactor: 1.5,
-
- flipSided: true,
- // flatShaded: true,
- alpha: 0.7,
- colorTheme: { name: 'uniform' as 'uniform', value: Color(0xDDDDDD) } as ColorThemeProps,
+ ...DefaultGaussianDensityProps,
- resolutionFactor: 7,
- probeRadius: 0,
- isoValue: 1.5,
+ flipSided: true, // TODO should not be required
}
export type GaussianSurfaceProps = typeof DefaultGaussianSurfaceProps
@@ -72,8 +46,8 @@ export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
mark: markElement,
setUpdateState: (state: VisualUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {
if (newProps.resolutionFactor !== currentProps.resolutionFactor) state.createGeometry = true
- if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true
- if (newProps.isoValue !== currentProps.isoValue) state.createGeometry = true
+ if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+ if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
}
})
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/gaussian.ts b/src/mol-geo/representation/structure/visual/util/gaussian.ts
index 1607bbb7fb3f71ce0a4e5d0998da9fa1c05289de..20505c1f1573567723ed0b1ef8b5813e82a3ee4f 100644
--- a/src/mol-geo/representation/structure/visual/util/gaussian.ts
+++ b/src/mol-geo/representation/structure/visual/util/gaussian.ts
@@ -8,24 +8,21 @@ import { Unit, Structure, StructureElement } from 'mol-model/structure';
import { RuntimeContext, Task } from 'mol-task'
import { Tensor, Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Box3D } from 'mol-math/geometry';
-import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
+import { SizeTheme } from 'mol-view/theme/size';
-export interface GaussianDensityProps {
- sizeTheme: SizeThemeProps
-
- resolutionFactor: number
- probeRadius: number
- isoValue: number
+export const DefaultGaussianDensityProps = {
+ resolutionFactor: 7,
+ radiusOffset: 0,
+ smoothness: 1.5,
}
+export type GaussianDensityProps = typeof DefaultGaussianDensityProps
function getDelta(box: Box3D, resolutionFactor: number) {
const extent = Vec3.sub(Vec3.zero(), box.max, box.min)
-
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()
- // Vec3.scale(size, extent, s)
Vec3.ceil(size, Vec3.scale(size, extent, s))
const delta = Vec3.div(Vec3.zero(), extent, size)
return delta
@@ -40,18 +37,18 @@ export function computeGaussianDensity(unit: Unit, structure: Structure, props:
}
export async function GaussianDensity(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps): Promise<Density> {
- const { resolutionFactor, probeRadius, isoValue } = props
+ const { resolutionFactor, radiusOffset, smoothness } = props
const { elements } = unit;
const elementCount = elements.length;
- const sizeTheme = SizeTheme(props.sizeTheme)
+ const sizeTheme = SizeTheme({ name: 'physical' })
const v = Vec3.zero()
const p = Vec3.zero()
const pos = unit.conformation.invariantPosition
const l = StructureElement.create(unit)
- const pad = (probeRadius + 3) * 3 // TODO calculate max radius
+ const pad = (radiusOffset + 3) * 3 // TODO calculate max radius
const box = unit.lookup3d.boundary.box
const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad));
const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
@@ -67,9 +64,9 @@ export async function GaussianDensity(ctx: RuntimeContext, unit: Unit, structure
const c = Vec3.zero()
- const alpha = isoValue // smoothness
+ const alpha = smoothness
- const _r2 = (probeRadius + 1.4 * 2)
+ const _r2 = (radiusOffset + 1.4 * 2)
const _radius2 = Vec3.create(_r2, _r2, _r2)
Vec3.mul(_radius2, _radius2, delta)
const updateChunk = Math.ceil(10000 / (_radius2[0] * _radius2[1] * _radius2[2]))
@@ -84,10 +81,10 @@ export async function GaussianDensity(ctx: RuntimeContext, unit: Unit, structure
Vec3.sub(v, v, min)
Vec3.mul(c, v, delta)
- const radius = sizeTheme.size(l) + probeRadius
+ const radius = sizeTheme.size(l) + radiusOffset
const rSq = radius * radius
- const r2 = (probeRadius + radius * 2)
+ const r2 = (radiusOffset + radius * 2)
const radius2 = Vec3.create(r2, r2, r2)
Vec3.mul(radius2, radius2, delta)
const r2sq = r2 * r2