tweaked gausian surface resolution handling

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,

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)

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
         }

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
         }

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
         }

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

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))
 

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()