From 6e5c20f442af01a85aff27e2bad956280532630d Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 19 Mar 2022 12:21:55 -0700
Subject: [PATCH] improve surface bounding-sphere
- use exact max radius to expand structure/unit sphere
---
CHANGELOG.md | 2 ++
src/mol-math/geometry/common.ts | 5 ++--
src/mol-math/geometry/gaussian-density.ts | 4 ++--
src/mol-math/geometry/gaussian-density/cpu.ts | 4 ++--
src/mol-math/geometry/gaussian-density/gpu.ts | 15 ++++++------
src/mol-math/geometry/molecular-surface.ts | 4 ++--
.../visual/gaussian-density-volume.ts | 5 ++--
.../structure/visual/gaussian-surface-mesh.ts | 16 ++++++-------
.../visual/gaussian-surface-wireframe.ts | 7 +++---
.../visual/molecular-surface-mesh.ts | 6 ++---
.../visual/molecular-surface-wireframe.ts | 8 +++----
src/mol-repr/structure/visual/util/common.ts | 24 +------------------
12 files changed, 40 insertions(+), 60 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bb3b9cfd4..1d991f9b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+- Fix issues with bounding-sphere & color-smoothing (mostly for small geometries)
+
## [v3.4.0] - 2022-03-13
- Fix handling of mmcif with empty ``label_*`` fields
diff --git a/src/mol-math/geometry/common.ts b/src/mol-math/geometry/common.ts
index 01b0e804a..0651bc448 100644
--- a/src/mol-math/geometry/common.ts
+++ b/src/mol-math/geometry/common.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -26,7 +26,8 @@ export type DensityData = {
transform: Mat4,
field: Tensor,
idField: Tensor,
- resolution: number
+ resolution: number,
+ maxRadius: number,
}
export type DensityTextureData = {
diff --git a/src/mol-math/geometry/gaussian-density.ts b/src/mol-math/geometry/gaussian-density.ts
index 44d36fa44..05ad13cd1 100644
--- a/src/mol-math/geometry/gaussian-density.ts
+++ b/src/mol-math/geometry/gaussian-density.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -21,12 +21,12 @@ export type GaussianDensityProps = typeof DefaultGaussianDensityProps
export type GaussianDensityData = {
radiusFactor: number
- resolution: number
} & DensityData
export type GaussianDensityTextureData = {
radiusFactor: number
resolution: number
+ maxRadius: number
} & DensityTextureData
export function computeGaussianDensity(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps) {
diff --git a/src/mol-math/geometry/gaussian-density/cpu.ts b/src/mol-math/geometry/gaussian-density/cpu.ts
index 50a33fbeb..faa293f84 100644
--- a/src/mol-math/geometry/gaussian-density/cpu.ts
+++ b/src/mol-math/geometry/gaussian-density/cpu.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -129,5 +129,5 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
Mat4.setTranslation(transform, expandedBox.min);
- return { field, idField, transform, radiusFactor: 1, resolution };
+ return { field, idField, transform, radiusFactor: 1, resolution, maxRadius };
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/gaussian-density/gpu.ts b/src/mol-math/geometry/gaussian-density/gpu.ts
index d53c1f658..5d3214248 100644
--- a/src/mol-math/geometry/gaussian-density/gpu.ts
+++ b/src/mol-math/geometry/gaussian-density/gpu.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -70,12 +70,12 @@ export function GaussianDensityGPU(position: PositionData, box: Box3D, radius: (
// it's faster than texture3d
// console.time('GaussianDensityTexture2d')
const tmpTexture = getTexture('tmp', webgl, 'image-uint8', 'rgba', 'ubyte', 'linear');
- const { scale, bbox, texture, gridDim, gridTexDim, radiusFactor, resolution } = calcGaussianDensityTexture2d(webgl, position, box, radius, false, props, tmpTexture);
+ const { scale, bbox, texture, gridDim, gridTexDim, radiusFactor, resolution, maxRadius } = calcGaussianDensityTexture2d(webgl, position, box, radius, false, props, tmpTexture);
// webgl.waitForGpuCommandsCompleteSync()
// console.timeEnd('GaussianDensityTexture2d')
const { field, idField } = fieldFromTexture2d(webgl, texture, gridDim, gridTexDim);
- return { field, idField, transform: getTransform(scale, bbox), radiusFactor, resolution };
+ return { field, idField, transform: getTransform(scale, bbox), radiusFactor, resolution, maxRadius };
}
export function GaussianDensityTexture(webgl: WebGLContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps, oldTexture?: Texture): GaussianDensityTextureData {
@@ -92,8 +92,8 @@ export function GaussianDensityTexture3d(webgl: WebGLContext, position: Position
return finalizeGaussianDensityTexture(calcGaussianDensityTexture3d(webgl, position, box, radius, props, oldTexture));
}
-function finalizeGaussianDensityTexture({ texture, scale, bbox, gridDim, gridTexDim, gridTexScale, radiusFactor, resolution }: _GaussianDensityTextureData): GaussianDensityTextureData {
- return { transform: getTransform(scale, bbox), texture, bbox, gridDim, gridTexDim, gridTexScale, radiusFactor, resolution };
+function finalizeGaussianDensityTexture({ texture, scale, bbox, gridDim, gridTexDim, gridTexScale, radiusFactor, resolution, maxRadius }: _GaussianDensityTextureData): GaussianDensityTextureData {
+ return { transform: getTransform(scale, bbox), texture, bbox, gridDim, gridTexDim, gridTexScale, radiusFactor, resolution, maxRadius };
}
function getTransform(scale: Vec3, bbox: Box3D) {
@@ -114,6 +114,7 @@ type _GaussianDensityTextureData = {
gridTexScale: Vec2
radiusFactor: number
resolution: number
+ maxRadius: number
}
function calcGaussianDensityTexture2d(webgl: WebGLContext, position: PositionData, box: Box3D, radius: (index: number) => number, powerOfTwo: boolean, props: GaussianDensityProps, texture?: Texture): _GaussianDensityTextureData {
@@ -198,7 +199,7 @@ function calcGaussianDensityTexture2d(webgl: WebGLContext, position: PositionDat
// printTexture(webgl, minDistTex, 0.75);
- return { texture, scale, bbox: expandedBox, gridDim: dim, gridTexDim, gridTexScale, radiusFactor, resolution };
+ return { texture, scale, bbox: expandedBox, gridDim: dim, gridTexDim, gridTexScale, radiusFactor, resolution, maxRadius };
}
function calcGaussianDensityTexture3d(webgl: WebGLContext, position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps, texture?: Texture): _GaussianDensityTextureData {
@@ -254,7 +255,7 @@ function calcGaussianDensityTexture3d(webgl: WebGLContext, position: PositionDat
setupGroupIdRendering(webgl, renderable);
render(texture, false);
- return { texture, scale, bbox: expandedBox, gridDim: dim, gridTexDim: dim, gridTexScale, radiusFactor, resolution };
+ return { texture, scale, bbox: expandedBox, gridDim: dim, gridTexDim: dim, gridTexScale, radiusFactor, resolution, maxRadius };
}
//
diff --git a/src/mol-math/geometry/molecular-surface.ts b/src/mol-math/geometry/molecular-surface.ts
index b361c100b..3b43a5c18 100644
--- a/src/mol-math/geometry/molecular-surface.ts
+++ b/src/mol-math/geometry/molecular-surface.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Fred Ludlow <fred.ludlow@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -370,5 +370,5 @@ export async function calcMolecularSurface(ctx: RuntimeContext, position: Requir
Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
Mat4.setTranslation(transform, expandedBox.min);
// console.log({ field, idField, transform, updateChunk })
- return { field, idField, transform, resolution };
+ return { field, idField, transform, resolution, maxRadius };
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index e29b13d76..21deb9c37 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -16,7 +16,6 @@ import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
import { eachElement, eachSerialElement, ElementIterator, getElementLoci, getSerialElementLoci } from './util/element';
import { Sphere3D } from '../../../mol-math/geometry';
import { UnitsDirectVolumeParams, UnitsVisual, UnitsDirectVolumeVisual } from '../units-visual';
-import { getStructureExtraRadius, getUnitExtraRadius } from './util/common';
async function createGaussianDensityVolume(ctx: VisualContext, structure: Structure, theme: Theme, props: GaussianDensityProps, directVolume?: DirectVolume): Promise<DirectVolume> {
const { runtime, webgl } = ctx;
@@ -34,7 +33,7 @@ async function createGaussianDensityVolume(ctx: VisualContext, structure: Struct
const axisOrder = Vec3.create(0, 1, 2);
const vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
- const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+ const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
vol.setBoundingSphere(sphere);
return vol;
@@ -90,7 +89,7 @@ async function createUnitsGaussianDensityVolume(ctx: VisualContext, unit: Unit,
const axisOrder = Vec3.create(0, 1, 2);
const vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
- const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+ const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
vol.setBoundingSphere(sphere);
return vol;
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index a9ca1e085..f5116e435 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -18,7 +18,7 @@ import { TextureMesh } from '../../../mol-geo/geometry/texture-mesh/texture-mesh
import { extractIsosurface } from '../../../mol-gl/compute/marching-cubes/isosurface';
import { Sphere3D } from '../../../mol-math/geometry';
import { ComplexVisual, ComplexMeshParams, ComplexMeshVisual, ComplexTextureMeshVisual, ComplexTextureMeshParams } from '../complex-visual';
-import { getUnitExtraRadius, getStructureExtraRadius, getVolumeSliceInfo, StructureGroup } from './util/common';
+import { getVolumeSliceInfo, StructureGroup } from './util/common';
import { WebGLContext } from '../../../mol-gl/webgl/context';
import { MeshValues } from '../../../mol-gl/renderable/mesh';
import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
@@ -89,7 +89,7 @@ type GaussianSurfaceMeta = {
async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
const { smoothness } = props;
- const { transform, field, idField, radiusFactor, resolution } = await computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime);
+ const { transform, field, idField, radiusFactor, resolution, maxRadius } = await computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: Math.exp(-smoothness) / radiusFactor,
@@ -102,7 +102,7 @@ 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 + getUnitExtraRadius(unit));
+ const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
return surface;
@@ -150,7 +150,7 @@ export function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<Gauss
async function createStructureGaussianSurfaceMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
const { smoothness } = props;
- const { transform, field, idField, radiusFactor, resolution } = await computeStructureGaussianDensity(structure, theme.size, props).runInContext(ctx.runtime);
+ const { transform, field, idField, radiusFactor, resolution, maxRadius } = await computeStructureGaussianDensity(structure, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: Math.exp(-smoothness) / radiusFactor,
@@ -163,7 +163,7 @@ 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 + getStructureExtraRadius(structure));
+ const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
return surface;
@@ -235,7 +235,7 @@ async function createGaussianSurfaceTextureMesh(ctx: VisualContext, unit: Unit,
const buffer = textureMesh?.doubleBuffer.get();
const gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer?.vertex, buffer?.group, buffer?.normal);
- const boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+ const boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
const surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
(surface.meta as GaussianSurfaceMeta).resolution = densityTextureData.resolution;
@@ -312,7 +312,7 @@ async function createStructureGaussianSurfaceTextureMesh(ctx: VisualContext, str
const buffer = textureMesh?.doubleBuffer.get();
const gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer?.vertex, buffer?.group, buffer?.normal);
- const boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
+ const boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
const surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
(surface.meta as GaussianSurfaceMeta).resolution = densityTextureData.resolution;
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index d62f849ba..aa5cddb98 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -15,11 +15,10 @@ import { UnitsLinesParams, UnitsVisual, UnitsLinesVisual } from '../units-visual
import { ElementIterator, getElementLoci, eachElement } from './util/element';
import { VisualUpdateState } from '../../util';
import { Sphere3D } from '../../../mol-math/geometry';
-import { getUnitExtraRadius } from './util/common';
async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
const { smoothness } = props;
- const { transform, field, idField } = await computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime);
+ const { transform, field, idField, maxRadius } = await computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: Math.exp(-smoothness),
@@ -30,7 +29,7 @@ async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure
Lines.transform(wireframe, transform);
- const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
+ const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
wireframe.setBoundingSphere(sphere);
return wireframe;
diff --git a/src/mol-repr/structure/visual/molecular-surface-mesh.ts b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
index 306bccb0c..173a5181c 100644
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -15,7 +15,7 @@ import { computeUnitMolecularSurface } from './util/molecular-surface';
import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
import { ElementIterator, getElementLoci, eachElement } from './util/element';
import { VisualUpdateState } from '../../util';
-import { CommonSurfaceParams, getUnitExtraRadius } from './util/common';
+import { CommonSurfaceParams } from './util/common';
import { Sphere3D } from '../../../mol-math/geometry';
import { MeshValues } from '../../../mol-gl/renderable/mesh';
import { Texture } from '../../../mol-gl/webgl/texture';
@@ -40,7 +40,7 @@ type MolecularSurfaceMeta = {
//
async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: MolecularSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
- const { transform, field, idField, resolution } = await computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime);
+ const { transform, field, idField, resolution, maxRadius } = await computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: props.probeRadius,
@@ -57,7 +57,7 @@ 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, getUnitExtraRadius(unit));
+ const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
surface.setBoundingSphere(sphere);
(surface.meta as MolecularSurfaceMeta).resolution = resolution;
diff --git a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
index 516d62fb7..f3a2c0778 100644
--- a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -15,7 +15,7 @@ import { computeUnitMolecularSurface, MolecularSurfaceProps } from './util/molec
import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/algorithm';
import { ElementIterator, getElementLoci, eachElement } from './util/element';
import { VisualUpdateState } from '../../util';
-import { CommonSurfaceParams, getUnitExtraRadius } from './util/common';
+import { CommonSurfaceParams } from './util/common';
import { Sphere3D } from '../../../mol-math/geometry';
export const MolecularSurfaceWireframeParams = {
@@ -29,7 +29,7 @@ export type MolecularSurfaceWireframeParams = typeof MolecularSurfaceWireframePa
//
async function createMolecularSurfaceWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: MolecularSurfaceProps, lines?: Lines): Promise<Lines> {
- const { transform, field, idField } = await computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime);
+ const { transform, field, idField, maxRadius } = await computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime);
const params = {
isoLevel: props.probeRadius,
scalarField: field,
@@ -39,7 +39,7 @@ async function createMolecularSurfaceWireframe(ctx: VisualContext, unit: Unit, s
Lines.transform(wireframe, transform);
- const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius + getUnitExtraRadius(unit));
+ const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, maxRadius);
wireframe.setBoundingSphere(sphere);
return wireframe;
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index cb2655645..c0eaf6269 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -298,25 +298,3 @@ export function isTrace(unit: Unit, element: ElementIndex) {
if (atomId === 'CA' || atomId === 'BB' || atomId === 'P') return true;
return false;
}
-
-export function getUnitExtraRadius(unit: Unit) {
- if (Unit.isAtomic(unit)) return 4;
-
- let max = 0;
- const { elements } = unit;
- const { r } = unit.conformation;
- for (let i = 0, _i = elements.length; i < _i; i++) {
- const _r = r(elements[i]);
- if (_r > max) max = _r;
- }
- return max + 1;
-}
-
-export function getStructureExtraRadius(structure: Structure) {
- let max = 0;
- for (const ug of structure.unitSymmetryGroups) {
- const r = getUnitExtraRadius(ug.units[0]);
- if (r > max) max = r;
- }
- return max;
-}
\ No newline at end of file
--
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