diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index e4cbb0c6981ccd54f621e2dc3eff90ef55334b5b..1f0d7149f9e1448b31bc362619ad84299b2cf198 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -70,7 +70,7 @@ export async function StructureView(app: App, viewer: Viewer, models: ReadonlyAr
const active: { [k: string]: boolean } = {
cartoon: true,
point: false,
- surface: true,
+ surface: false,
ballAndStick: false,
carbohydrate: false,
spacefill: false,
diff --git a/src/mol-geo/representation/structure/representation/surface.ts b/src/mol-geo/representation/structure/representation/surface.ts
index 344034f7f3775a4c7886b42237387f7617400934..d397bd3eaeee8f085f66217061542aba11329756 100644
--- a/src/mol-geo/representation/structure/representation/surface.ts
+++ b/src/mol-geo/representation/structure/representation/surface.ts
@@ -13,6 +13,7 @@ import { Loci } from 'mol-model/loci';
import { PickingId } from '../../../geometry/picking';
import { Task } from 'mol-task';
import { DefaultGaussianWireframeProps, GaussianWireframeVisual } from '../visual/gaussian-surface-wireframe';
+import { getQualityProps } from '../../util';
export const DefaultSurfaceProps = {
...DefaultGaussianSurfaceProps,
@@ -41,8 +42,9 @@ export function SurfaceRepresentation(): SurfaceRepresentation {
return { ...gaussianSurfaceRepr.props, ...gaussianWireframeRepr.props, visuals: currentProps.visuals }
},
createOrUpdate: (props: Partial<SurfaceProps> = {}, structure?: Structure) => {
- currentProps = Object.assign({}, DefaultSurfaceProps, currentProps, props)
if (structure) currentStructure = structure
+ const qualityProps = getQualityProps(Object.assign({}, currentProps, props), currentStructure)
+ currentProps = Object.assign({}, DefaultSurfaceProps, currentProps, props, qualityProps)
return Task.create('Creating SurfaceRepresentation', async ctx => {
if (currentProps.visuals.surface) await gaussianSurfaceRepr.createOrUpdate(currentProps, currentStructure).runInContext(ctx)
if (currentProps.visuals.wireframe) await gaussianWireframeRepr.createOrUpdate(currentProps, currentStructure).runInContext(ctx)
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 86d32e2818dfeb76d333f91ef4b9f47973cf3b46..27689484e79dc816298db88a79096cab8dc084f5 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
@@ -63,7 +63,7 @@ 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.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
}
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 38dc49375d0cf04b4742718cbcf4a678f9657967..331ed499a67ff25cda8f2b6c635aed3f98b5972a 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -45,7 +45,7 @@ export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
getLoci: getElementLoci,
mark: markElement,
setUpdateState: (state: VisualUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {
- if (newProps.resolutionFactor !== currentProps.resolutionFactor) state.createGeometry = true
+ if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
}
diff --git a/src/mol-geo/representation/structure/visual/gaussian-surface-wireframe.ts b/src/mol-geo/representation/structure/visual/gaussian-surface-wireframe.ts
index 6f43a0c9917ead166d686312062be0be95e2d012..3d2635a3a3a7a690e0e7ce1de732d861eb993fdb 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-wireframe.ts
@@ -43,7 +43,7 @@ export function GaussianWireframeVisual(): UnitsVisual<GaussianWireframeProps> {
getLoci: getElementLoci,
mark: markElement,
setUpdateState: (state: VisualUpdateState, newProps: GaussianWireframeProps, currentProps: GaussianWireframeProps) => {
- if (newProps.resolutionFactor !== currentProps.resolutionFactor) state.createGeometry = true
+ if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
}
diff --git a/src/mol-geo/representation/util.ts b/src/mol-geo/representation/util.ts
index b16444f081f7431283f8807e3aab802f1d388953..dbcedd0636eedb1bd7a26b4c07be784967115336 100644
--- a/src/mol-geo/representation/util.ts
+++ b/src/mol-geo/representation/util.ts
@@ -13,6 +13,7 @@ export interface QualityProps {
detail: number
radialSegments: number
linearSegments: number
+ resolution: number
}
export function getQualityProps(props: Partial<QualityProps>, structure?: Structure) {
@@ -20,6 +21,7 @@ export function getQualityProps(props: Partial<QualityProps>, structure?: Struct
let detail = defaults(props.detail, 1)
let radialSegments = defaults(props.radialSegments, 12)
let linearSegments = defaults(props.linearSegments, 8)
+ let resolution = defaults(props.resolution, 1)
if (quality === 'auto' && structure) {
let score = structure.elementCount
@@ -40,26 +42,31 @@ export function getQualityProps(props: Partial<QualityProps>, structure?: Struct
detail = 3
radialSegments = 36
linearSegments = 18
+ resolution = 0.5
break
case 'high':
detail = 2
radialSegments = 24
linearSegments = 12
+ resolution = 1.0
break
case 'medium':
detail = 1
radialSegments = 12
linearSegments = 8
+ resolution = 1.5
break
case 'low':
detail = 0
radialSegments = 8
linearSegments = 3
+ resolution = 3
break
case 'lowest':
detail = 0
radialSegments = 4
linearSegments = 2
+ resolution = 6
break
case 'custom':
// use defaults or given props as set above
@@ -69,6 +76,7 @@ export function getQualityProps(props: Partial<QualityProps>, structure?: Struct
return {
detail,
radialSegments,
- linearSegments
+ linearSegments,
+ resolution
}
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/gaussian-density.ts b/src/mol-math/geometry/gaussian-density.ts
index d6d2d8cd1249949b3239aa096bed3c906e859d8f..23778fa4b61a5b952ed35a7a9cc763b9d40b1e8c 100644
--- a/src/mol-math/geometry/gaussian-density.ts
+++ b/src/mol-math/geometry/gaussian-density.ts
@@ -11,20 +11,16 @@ import { PositionData, DensityData } from './common';
import { OrderedSet } from 'mol-data/int';
export const DefaultGaussianDensityProps = {
- resolutionFactor: 6,
+ resolution: 1,
radiusOffset: 0,
- smoothness: 1.5,
- box: Box3D.empty() // TODO remove
+ smoothness: 1.5
}
export type GaussianDensityProps = typeof DefaultGaussianDensityProps
-function getDelta(box: Box3D, resolutionFactor: number) {
+function getDelta(box: Box3D, resolution: 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.ceil(size, Vec3.scale(size, extent, s))
+ Vec3.ceil(size, Vec3.scale(size, extent, resolution))
const delta = Vec3.div(Vec3.zero(), extent, size)
return delta
}
@@ -34,7 +30,7 @@ export function computeGaussianDensity(position: PositionData, box: Box3D, radiu
}
export async function GaussianDensity(ctx: RuntimeContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Promise<DensityData> {
- const { resolutionFactor, radiusOffset, smoothness } = props
+ const { resolution, radiusOffset, smoothness } = props
const { indices, x, y, z } = position
const n = OrderedSet.size(indices)
@@ -47,7 +43,7 @@ export async function GaussianDensity(ctx: RuntimeContext, position: PositionDat
const extent = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min)
const min = expandedBox.min
- const delta = getDelta(Box3D.expand(Box3D.empty(), props.box, Vec3.create(pad, pad, pad)), resolutionFactor)
+ const delta = getDelta(Box3D.expand(Box3D.empty(), box, Vec3.create(pad, pad, pad)), resolution)
const dim = Vec3.zero()
Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
diff --git a/src/mol-model/structure/structure/unit/gaussian-density.ts b/src/mol-model/structure/structure/unit/gaussian-density.ts
index df7bf0a89595b15a9b82d014902dd5c969e97fd1..1c9d5b4f10f649a9d92d298e90f22bff627fc5ef 100644
--- a/src/mol-model/structure/structure/unit/gaussian-density.ts
+++ b/src/mol-model/structure/structure/unit/gaussian-density.ts
@@ -11,7 +11,7 @@ import { Task, RuntimeContext } from 'mol-task';
import { DensityData } from 'mol-math/geometry';
export const DefaultGaussianDensityProps = {
- resolutionFactor: 6,
+ resolution: 1,
radiusOffset: 0,
smoothness: 1.5,
}
@@ -43,12 +43,12 @@ export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityPro
}
return Task.create('Gaussian Density', async ctx => {
- return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, { ...props, box: unit.lookup3d.boundary.box });
+ return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, props);
});
}
export async function computeUnitGaussianDensityCached(unit: Unit, props: GaussianDensityProps, cache: Map<string, DensityData>, ctx?: RuntimeContext) {
- const key = `${props.radiusOffset}|${props.resolutionFactor}|${props.smoothness}`
+ const key = `${props.radiusOffset}|${props.resolution}|${props.smoothness}`
let density = cache.get(key)
if (density) return density
density = ctx ? await computeUnitGaussianDensity(unit, props).runInContext(ctx) : await computeUnitGaussianDensity(unit, props).run()