use unit/structure bounding-sphere in visuals geometry

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -21,6 +21,7 @@ import { Interval, OrderedSet } from '../../../mol-data/int';
 import { isHydrogen } from './util/common';
 import { BondType } from '../../../mol-model/structure/model/types';
 import { ignoreBondType, BondCylinderParams, BondIterator } from './util/bond';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 function createIntraUnitBondCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitBondParams>, mesh?: Mesh) {
     if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -92,7 +93,12 @@ function createIntraUnitBondCylinderMesh(ctx: VisualContext, unit: Unit, structu
         ignore: (edgeIndex: number) => ignoreHydrogen(edgeIndex) || ignoreBondType(include, exclude, _flags[edgeIndex])
     }
 
-    return createLinkCylinderMesh(ctx, builderProps, props, mesh)
+    const m = createLinkCylinderMesh(ctx, builderProps, props, mesh)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const IntraUnitBondParams = {

src/mol-repr/structure/visual/element-point.ts

@@ -14,6 +14,7 @@ import { PointsBuilder } from '../../../mol-geo/geometry/points/points-builder';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { VisualUpdateState } from '../../util';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const ElementPointParams = {
     ...UnitsPointsParams,
@@ -39,7 +40,13 @@ export function createElementPoint(ctx: VisualContext, unit: Unit, structure: St
         pos(elements[i], p)
         builder.add(p[0], p[1], p[2], i)
     }
-    return builder.getPoints()
+
+    const pt = builder.getPoints()
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    pt.setBoundingSphere(sphere)
+
+    return pt
 }
 
 export function ElementPointVisual(materialId: number): UnitsVisual<ElementPointParams> {

src/mol-repr/structure/visual/ellipsoid-mesh.ts

@@ -20,6 +20,7 @@ import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
 import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property/anisotropic'
 import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
 import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const EllipsoidMeshParams = {
     ...UnitsMeshParams,
@@ -66,7 +67,7 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
     if (!atomSiteAnisotrop) return Mesh.createEmpty(mesh)
 
     const v = Vec3()
-    const m = Mat3()
+    const mat = Mat3()
     const eigvals = Vec3()
     const eigvec1 = Vec3()
     const eigvec2 = Vec3()
@@ -87,11 +88,11 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
         pos(ei, v)
 
         builderState.currentGroup = i
-        Tensor.toMat3(m, space, U.value(ai))
-        Mat3.symmtricFromLower(m, m)
-        Mat3.symmetricEigenvalues(eigvals, m)
-        Mat3.eigenvector(eigvec1, m, eigvals[1])
-        Mat3.eigenvector(eigvec2, m, eigvals[2])
+        Tensor.toMat3(mat, space, U.value(ai))
+        Mat3.symmtricFromLower(mat, mat)
+        Mat3.symmetricEigenvalues(eigvals, mat)
+        Mat3.eigenvector(eigvec1, mat, eigvals[1])
+        Mat3.eigenvector(eigvec2, mat, eigvals[2])
         for (let j = 0; j < 3; ++j) {
             // show 50% probability surface, needs sqrt as U matrix is in angstrom-squared
             // take abs of eigenvalue to avoid reflection
@@ -106,5 +107,10 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
         }
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }

src/mol-repr/structure/visual/gaussian-surface-mesh.ts

@@ -49,6 +49,9 @@ async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structu
     Mesh.transform(surface, transform)
     if (ctx.webgl && !ctx.webgl.isWebGL2) Mesh.uniformTriangleGroup(surface)
 
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset)
+    surface.setBoundingSphere(sphere)
+
     return surface
 }
 
@@ -93,6 +96,9 @@ async function createStructureGaussianSurfaceMesh(ctx: VisualContext, structure:
     Mesh.transform(surface, transform)
     if (ctx.webgl && !ctx.webgl.isWebGL2) Mesh.uniformTriangleGroup(surface)
 
+    const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset)
+    surface.setBoundingSphere(sphere)
+
     return surface
 }
 

src/mol-repr/structure/visual/gaussian-surface-wireframe.ts

@@ -14,6 +14,7 @@ import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/
 import { UnitsLinesParams, UnitsVisual, UnitsLinesVisual } from '../units-visual';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { VisualUpdateState } from '../../util';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
     const { smoothness } = props
@@ -28,6 +29,9 @@ async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure
 
     Lines.transform(wireframe, transform)
 
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset)
+    wireframe.setBoundingSphere(sphere)
+
     return wireframe
 }
 

src/mol-repr/structure/visual/molecular-surface-mesh.ts

@@ -16,6 +16,7 @@ import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/a
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { VisualUpdateState } from '../../util';
 import { CommonSurfaceParams } from './util/common';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const MolecularSurfaceMeshParams = {
     ...UnitsMeshParams,
@@ -38,6 +39,9 @@ async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, struct
     Mesh.transform(surface, transform)
     if (ctx.webgl && !ctx.webgl.isWebGL2) Mesh.uniformTriangleGroup(surface)
 
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius)
+    surface.setBoundingSphere(sphere)
+
     return surface
 }
 

src/mol-repr/structure/visual/molecular-surface-wireframe.ts

@@ -16,6 +16,7 @@ import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { VisualUpdateState } from '../../util';
 import { CommonSurfaceParams } from './util/common';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const MolecularSurfaceWireframeParams = {
     ...UnitsLinesParams,
@@ -38,6 +39,9 @@ async function createMolecularSurfaceWireframe(ctx: VisualContext, unit: Unit, s
 
     Lines.transform(wireframe, transform)
 
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius)
+    wireframe.setBoundingSphere(sphere)
+
     return wireframe
 }
 

src/mol-repr/structure/visual/nucleotide-block-mesh.ts

@@ -20,6 +20,7 @@ import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { NucleotideLocationIterator, getNucleotideElementLoci, eachNucleotideElement } from './util/nucleotide';
 import { VisualUpdateState } from '../../util';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 const p1 = Vec3.zero()
 const p2 = Vec3.zero()
@@ -134,7 +135,12 @@ function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: St
         }
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const NucleotideBlockParams = {

src/mol-repr/structure/visual/nucleotide-ring-mesh.ts

@@ -21,6 +21,7 @@ import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { NucleotideLocationIterator, getNucleotideElementLoci, eachNucleotideElement } from './util/nucleotide';
 import { VisualUpdateState } from '../../util';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 const pTrace = Vec3.zero()
 const pN1 = Vec3.zero()
@@ -189,7 +190,12 @@ function createNucleotideRingMesh(ctx: VisualContext, unit: Unit, structure: Str
         }
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const NucleotideRingParams = {

src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts

@@ -14,7 +14,7 @@ import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
-import { Axes3D } from '../../../mol-math/geometry';
+import { Axes3D, Sphere3D } from '../../../mol-math/geometry';
 import { PickingId } from '../../../mol-geo/geometry/picking';
 import { OrderedSet, Interval } from '../../../mol-data/int';
 import { EmptyLoci, Loci } from '../../../mol-model/loci';
@@ -82,7 +82,12 @@ export function createOrientationEllipsoidMesh(ctx: VisualContext, unit: Unit, s
     builderState.currentGroup = 0
     addEllipsoid(builderState, origin, dirA, dirB, radiusScale, detail)
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 //

src/mol-repr/structure/visual/polymer-backbone-cylinder.ts

@@ -19,6 +19,7 @@ import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { VisualUpdateState } from '../../util';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const PolymerBackboneCylinderParams = {
     sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
@@ -58,7 +59,12 @@ function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, struc
         addCylinder(builderState, pB, pA, 0.5, cylinderProps)
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const PolymerBackboneParams = {

src/mol-repr/structure/visual/polymer-direction-wedge.ts

@@ -16,6 +16,7 @@ import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment,
 import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/model/types';
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 const t = Mat4.identity()
 const sVec = Vec3.zero()
@@ -82,7 +83,12 @@ function createPolymerDirectionWedgeMesh(ctx: VisualContext, unit: Unit, structu
         ++i
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const PolymerDirectionParams = {

src/mol-repr/structure/visual/polymer-gap-cylinder.ts

@@ -17,6 +17,7 @@ import { addFixedCountDashedCylinder } from '../../../mol-geo/geometry/mesh/buil
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
 // import { TriangularPyramid } from '../../../mol-geo/primitive/pyramid';
 
 const segmentCount = 10
@@ -77,7 +78,12 @@ function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, structure:
         i += 2
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const PolymerGapParams = {

src/mol-repr/structure/visual/polymer-trace-mesh.ts

@@ -21,6 +21,7 @@ import { addRibbon } from '../../../mol-geo/geometry/mesh/builder/ribbon';
 import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const PolymerTraceMeshParams = {
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
@@ -147,7 +148,12 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
         ++i
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const PolymerTraceParams = {

src/mol-repr/structure/visual/polymer-tube-mesh.ts

@@ -20,6 +20,7 @@ import { addRibbon } from '../../../mol-geo/geometry/mesh/builder/ribbon';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export const PolymerTubeMeshParams = {
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
@@ -100,7 +101,12 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
         ++i
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export const PolymerTubeParams = {

src/mol-repr/structure/visual/util/element.ts

@@ -21,6 +21,7 @@ import { StructureGroup } from '../../../../mol-repr/structure/units-visual';
 import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
 import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-builder';
 import { isHydrogen } from './common';
+import { Sphere3D } from '../../../../mol-math/geometry';
 
 export interface ElementSphereMeshProps {
     detail: number,
@@ -51,7 +52,12 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
         addSphere(builderState, v, theme.size.size(l) * sizeFactor, detail)
     }
 
-    return MeshBuilder.getMesh(builderState)
+    const m = MeshBuilder.getMesh(builderState)
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * sizeFactor)
+    m.setBoundingSphere(sphere)
+
+    return m
 }
 
 export interface ElementSphereImpostorProps {
@@ -74,7 +80,12 @@ export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, stru
         builder.add(v[0], v[1], v[2], i)
     }
 
-    return builder.getSpheres()
+    const s = builder.getSpheres()
+
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1)
+    s.setBoundingSphere(sphere)
+
+    return s
 }
 
 export function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {