diff --git a/src/apps/canvas/assembly-symmetry.ts b/src/apps/canvas/assembly-symmetry.ts
index 69fee7dd07fd6acfb60c87a354f719dd556a2493..ee4d6832753ef4a2f379f5004ede22078ff26eab 100644
--- a/src/apps/canvas/assembly-symmetry.ts
+++ b/src/apps/canvas/assembly-symmetry.ts
@@ -7,10 +7,10 @@
import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
import { Table } from 'mol-data/db';
import { Color, ColorScale } from 'mol-util/color';
-import { MeshBuilder } from 'mol-geo/mesh/mesh-builder';
+import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
import { Tensor } from 'mol-math/linear-algebra';
-import { addSphere } from 'mol-geo/mesh/builder/sphere';
-import { addCylinder } from 'mol-geo/mesh/builder/cylinder';
+import { addSphere } from 'mol-geo/geometry/mesh/builder/sphere';
+import { addCylinder } from 'mol-geo/geometry/mesh/builder/cylinder';
import { Shape } from 'mol-model/shape';
import { ColorTheme } from 'mol-view/theme/color';
import { Location } from 'mol-model/location';
diff --git a/src/apps/canvas/component/structure-representation.tsx b/src/apps/canvas/component/structure-representation.tsx
index d81cc3f3d1a179dcd825217bddb3de60403dfad6..d282e8e41fd53d705dd00990bd519263f80daf8a 100644
--- a/src/apps/canvas/component/structure-representation.tsx
+++ b/src/apps/canvas/component/structure-representation.tsx
@@ -7,10 +7,10 @@
import * as React from 'react'
import { StructureRepresentation, StructureProps } from 'mol-geo/representation/structure';
import Viewer from 'mol-view/viewer';
-import { VisualQuality, VisualQualityNames } from 'mol-geo/representation/util';
import { ColorThemeProps, ColorThemeName, ColorThemeNames, ColorTheme } from 'mol-view/theme/color';
import { Color } from 'mol-util/color';
import { Progress } from 'mol-task';
+import { VisualQuality, VisualQualityNames } from 'mol-geo/geometry/geometry';
export interface StructureRepresentationComponentProps {
viewer: Viewer
@@ -165,7 +165,7 @@ export class StructureRepresentationComponent extends React.Component<StructureR
<span>Iso Value </span>
<input type='range'
defaultValue={this.state.isoValue.toString()}
- min='0.1'
+ min='1'
max='3'
step='0.1'
onInput={(e) => this.update({ isoValue: parseFloat(e.currentTarget.value) })}
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index d13cfb6ef6852840cf2241900d7d67f5f68cbe32..62ef041ddfb753af90e335284ec85e431ae03c3e 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -25,7 +25,7 @@ import { BehaviorSubject } from 'rxjs';
import { SpacefillRepresentation } from 'mol-geo/representation/structure/representation/spacefill';
import { DistanceRestraintRepresentation } from 'mol-geo/representation/structure/representation/distance-restraint';
import { SurfaceRepresentation } from 'mol-geo/representation/structure/representation/surface';
-import { Progress } from 'mol-task';
+// import { Progress } from 'mol-task';
export interface StructureView {
readonly viewer: Viewer
@@ -210,7 +210,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
for (const k in structureRepresentations) {
if (active[k]) {
await structureRepresentations[k].createOrUpdate({}, structure).run(
- progress => console.log(Progress.format(progress))
+ // progress => console.log(Progress.format(progress))
)
viewer.add(structureRepresentations[k])
} else {
diff --git a/src/mol-app/ui/transform/backbone.tsx b/src/mol-app/ui/transform/backbone.tsx
index 76270473768242f05fbe3744541c7aed9243ee49..93a4a3392618673ea30514e515ef0d8f3dff0d6c 100644
--- a/src/mol-app/ui/transform/backbone.tsx
+++ b/src/mol-app/ui/transform/backbone.tsx
@@ -19,8 +19,8 @@ import { ColorThemeProps, ColorThemeNames, ColorThemeName } from 'mol-view/theme
import { SizeThemeProps } from 'mol-view/theme/size';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
-import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
+import { VisualQuality } from 'mol-geo/geometry/geometry';
interface BackboneState {
doubleSided: boolean
diff --git a/src/mol-app/ui/transform/ball-and-stick.tsx b/src/mol-app/ui/transform/ball-and-stick.tsx
index 61d621f988f5d6aa7f89e89fe5309dc2d6c7c63b..38320c2b07341ef93674381c3cb52718b9008af0 100644
--- a/src/mol-app/ui/transform/ball-and-stick.tsx
+++ b/src/mol-app/ui/transform/ball-and-stick.tsx
@@ -19,8 +19,8 @@ import { ColorThemeProps, ColorThemeNames, ColorThemeName } from 'mol-view/theme
import { SizeThemeProps } from 'mol-view/theme/size';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
-import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
+import { VisualQuality } from 'mol-geo/geometry/geometry';
interface BallAndStickState {
doubleSided: boolean
diff --git a/src/mol-app/ui/transform/carbohydrate.tsx b/src/mol-app/ui/transform/carbohydrate.tsx
index 66e4b3a4c02c3a5ad99bb582097252666821a979..e725131474ef63d60261eab264c4c925a3f8ad31 100644
--- a/src/mol-app/ui/transform/carbohydrate.tsx
+++ b/src/mol-app/ui/transform/carbohydrate.tsx
@@ -19,8 +19,8 @@ import { ColorThemeProps, ColorThemeNames, ColorThemeName } from 'mol-view/theme
import { SizeThemeProps } from 'mol-view/theme/size';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
-import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
+import { VisualQuality } from 'mol-geo/geometry/geometry';
interface CarbohydrateState {
doubleSided: boolean
diff --git a/src/mol-app/ui/transform/cartoon.tsx b/src/mol-app/ui/transform/cartoon.tsx
index b78e8c91e8969d254e06e9c877c7ee20a157e9a9..994934214126b6fbf9909791a65ac5777b883fdd 100644
--- a/src/mol-app/ui/transform/cartoon.tsx
+++ b/src/mol-app/ui/transform/cartoon.tsx
@@ -19,8 +19,8 @@ import { ColorThemeProps, ColorThemeNames, ColorThemeName } from 'mol-view/theme
import { SizeThemeProps } from 'mol-view/theme/size';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
-import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
+import { VisualQuality } from 'mol-geo/geometry/geometry';
interface CartoonState {
doubleSided: boolean
diff --git a/src/mol-app/ui/transform/distance-restraint.tsx b/src/mol-app/ui/transform/distance-restraint.tsx
index 981cd83ef69d1b188259428233a782414f37ec52..037532629bf76078090abee3e4600f5cc8698ce2 100644
--- a/src/mol-app/ui/transform/distance-restraint.tsx
+++ b/src/mol-app/ui/transform/distance-restraint.tsx
@@ -19,8 +19,8 @@ import { ColorThemeProps, ColorThemeNames, ColorThemeName } from 'mol-view/theme
import { SizeThemeProps } from 'mol-view/theme/size';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
-import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
+import { VisualQuality } from 'mol-geo/geometry/geometry';
interface DistanceRestraintState {
doubleSided: boolean
diff --git a/src/mol-app/ui/transform/spacefill.tsx b/src/mol-app/ui/transform/spacefill.tsx
index 53c22660e267a2f66cab426cb531bd54b8454478..d9694e10eae9c0b7bd3e392112290a40bd1b85a7 100644
--- a/src/mol-app/ui/transform/spacefill.tsx
+++ b/src/mol-app/ui/transform/spacefill.tsx
@@ -19,8 +19,8 @@ import { ColorThemeProps, ColorThemeNames, ColorThemeName } from 'mol-view/theme
import { SizeThemeProps } from 'mol-view/theme/size';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
-import { VisualQuality } from 'mol-geo/representation/util';
import { Unit } from 'mol-model/structure';
+import { VisualQuality } from 'mol-geo/geometry/geometry';
interface SpacefillState {
doubleSided: boolean
diff --git a/src/mol-geo/geometry/geometry.ts b/src/mol-geo/geometry/geometry.ts
new file mode 100644
index 0000000000000000000000000000000000000000..a2f6f940808f3be306625f02329e422eb05c0712
--- /dev/null
+++ b/src/mol-geo/geometry/geometry.ts
@@ -0,0 +1,125 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mesh } from './mesh/mesh';
+import { Point } from './point/point';
+import { PointValues, MeshValues, RenderableState } from 'mol-gl/renderable';
+import { MeshRenderObject, PointRenderObject } from 'mol-gl/render-object';
+import { ValueCell } from 'mol-util';
+import { BaseValues } from 'mol-gl/renderable/schema';
+
+export type GeometryKindType = { 'mesh': Mesh, 'point': Point }
+export type GeometryKind = keyof GeometryKindType
+export type Geometry = Helpers.ValueOf<GeometryKindType>
+
+export type GeometryDef = {
+ 'mesh': { 'props': MeshProps, 'values': MeshValues, 'renderObject': MeshRenderObject }
+ 'point': { 'props': PointProps, 'values': PointValues, 'renderObject': PointRenderObject }
+}
+
+export namespace Geometry {
+ export function getDrawCount(geometry: Geometry) {
+ switch (geometry.kind) {
+ case 'mesh': return geometry.triangleCount * 3
+ case 'point': return geometry.vertexCount
+ }
+ }
+}
+
+//
+
+export const VisualQualityInfo = {
+ 'custom': {},
+ 'auto': {},
+ 'highest': {},
+ 'high': {},
+ 'medium': {},
+ 'low': {},
+ 'lowest': {},
+}
+export type VisualQuality = keyof typeof VisualQualityInfo
+export const VisualQualityNames = Object.keys(VisualQualityInfo)
+
+//
+
+export const DefaultBaseProps = {
+ alpha: 1,
+ visible: true,
+ depthMask: true,
+ useFog: false,
+ quality: 'auto' as VisualQuality
+}
+export type BaseProps = typeof DefaultBaseProps
+
+export const DefaultMeshProps = {
+ ...DefaultBaseProps,
+ doubleSided: false,
+ flipSided: false,
+ flatShaded: false,
+}
+export type MeshProps = typeof DefaultMeshProps
+
+export const DefaultPointProps = {
+ ...DefaultBaseProps,
+ pointSizeAttenuation: true
+}
+export type PointProps = typeof DefaultPointProps
+
+type Counts = { drawCount: number, groupCount: number, instanceCount: number }
+
+export function createBaseValues(props: BaseProps, counts: Counts) {
+ return {
+ uAlpha: ValueCell.create(props.alpha),
+ uGroupCount: ValueCell.create(counts.groupCount),
+ drawCount: ValueCell.create(counts.drawCount),
+ dUseFog: ValueCell.create(props.useFog),
+ }
+}
+
+export function createMeshValues(props: MeshProps, counts: Counts) {
+ return {
+ ...createBaseValues(props, counts),
+ dDoubleSided: ValueCell.create(props.doubleSided),
+ dFlatShaded: ValueCell.create(props.flatShaded),
+ dFlipSided: ValueCell.create(props.flipSided),
+ }
+}
+
+export function createPointValues(props: PointProps, counts: Counts) {
+ return {
+ ...createBaseValues(props, counts),
+ dPointSizeAttenuation: ValueCell.create(props.pointSizeAttenuation),
+ }
+}
+
+export function createRenderableState(props: BaseProps): RenderableState {
+ return {
+ visible: props.visible,
+ depthMask: props.depthMask
+ }
+}
+
+export function updateBaseValues(values: BaseValues, props: BaseProps) {
+ ValueCell.updateIfChanged(values.uAlpha, props.alpha)
+ ValueCell.updateIfChanged(values.dUseFog, props.useFog)
+}
+
+export function updateMeshValues(values: MeshValues, props: MeshProps) {
+ updateBaseValues(values, props)
+ ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided)
+ ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded)
+ ValueCell.updateIfChanged(values.dFlipSided, props.flipSided)
+}
+
+export function updatePointValues(values: PointValues, props: PointProps) {
+ updateBaseValues(values, props)
+ ValueCell.updateIfChanged(values.dPointSizeAttenuation, props.pointSizeAttenuation)
+}
+
+export function updateRenderableState(state: RenderableState, props: BaseProps) {
+ state.visible = props.visible
+ state.depthMask = props.depthMask
+}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/line/line-builder.ts b/src/mol-geo/geometry/line/line-builder.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0ffdd02fcbce683e436c0030ffe0517135c6ceda
--- /dev/null
+++ b/src/mol-geo/geometry/line/line-builder.ts
@@ -0,0 +1 @@
+// TODO
\ No newline at end of file
diff --git a/src/mol-geo/geometry/line/line.ts b/src/mol-geo/geometry/line/line.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0ffdd02fcbce683e436c0030ffe0517135c6ceda
--- /dev/null
+++ b/src/mol-geo/geometry/line/line.ts
@@ -0,0 +1 @@
+// TODO
\ No newline at end of file
diff --git a/src/mol-geo/mesh/builder/bounding-box.ts b/src/mol-geo/geometry/mesh/builder/bounding-box.ts
similarity index 97%
rename from src/mol-geo/mesh/builder/bounding-box.ts
rename to src/mol-geo/geometry/mesh/builder/bounding-box.ts
index ba36360454d6d689d8b392631543a2be861ff9cb..0781953361505721dd31b15aef6279f4a4d6b83a 100644
--- a/src/mol-geo/mesh/builder/bounding-box.ts
+++ b/src/mol-geo/geometry/mesh/builder/bounding-box.ts
@@ -7,7 +7,7 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { Box3D } from 'mol-math/geometry';
import { MeshBuilder } from '../mesh-builder';
-import { CylinderProps } from '../../primitive/cylinder';
+import { CylinderProps } from '../../../primitive/cylinder';
import { addCylinder } from './cylinder';
import { addSphere } from './sphere';
diff --git a/src/mol-geo/mesh/builder/cylinder.ts b/src/mol-geo/geometry/mesh/builder/cylinder.ts
similarity index 96%
rename from src/mol-geo/mesh/builder/cylinder.ts
rename to src/mol-geo/geometry/mesh/builder/cylinder.ts
index b4538c1c81a0a802392a622ece8199e2f997e77e..a4b978f3fd4e2ed7e8770278034e47d210d136a2 100644
--- a/src/mol-geo/mesh/builder/cylinder.ts
+++ b/src/mol-geo/geometry/mesh/builder/cylinder.ts
@@ -6,8 +6,8 @@
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { MeshBuilder } from '../mesh-builder';
-import { Primitive } from '../../primitive/primitive';
-import { Cylinder, CylinderProps } from '../../primitive/cylinder';
+import { Primitive } from '../../../primitive/primitive';
+import { Cylinder, CylinderProps } from '../../../primitive/cylinder';
const cylinderMap = new Map<string, Primitive>()
const up = Vec3.create(0, 1, 0)
diff --git a/src/mol-geo/mesh/builder/sheet.ts b/src/mol-geo/geometry/mesh/builder/sheet.ts
similarity index 100%
rename from src/mol-geo/mesh/builder/sheet.ts
rename to src/mol-geo/geometry/mesh/builder/sheet.ts
diff --git a/src/mol-geo/mesh/builder/sphere.ts b/src/mol-geo/geometry/mesh/builder/sphere.ts
similarity index 88%
rename from src/mol-geo/mesh/builder/sphere.ts
rename to src/mol-geo/geometry/mesh/builder/sphere.ts
index d9196c3a2840223e833369e133c79c237b3e4c63..4d04616b642e2819432c4463c5346c409bc618c7 100644
--- a/src/mol-geo/mesh/builder/sphere.ts
+++ b/src/mol-geo/geometry/mesh/builder/sphere.ts
@@ -6,8 +6,8 @@
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { MeshBuilder } from '../mesh-builder';
-import { Primitive } from '../../primitive/primitive';
-import { Sphere } from '../../primitive/sphere';
+import { Primitive } from '../../../primitive/primitive';
+import { Sphere } from '../../../primitive/sphere';
const sphereMap = new Map<number, Primitive>()
const tmpSphereMat = Mat4.identity()
diff --git a/src/mol-geo/mesh/builder/tube.ts b/src/mol-geo/geometry/mesh/builder/tube.ts
similarity index 100%
rename from src/mol-geo/mesh/builder/tube.ts
rename to src/mol-geo/geometry/mesh/builder/tube.ts
diff --git a/src/mol-geo/mesh/mesh-builder.ts b/src/mol-geo/geometry/mesh/mesh-builder.ts
similarity index 96%
rename from src/mol-geo/mesh/mesh-builder.ts
rename to src/mol-geo/geometry/mesh/mesh-builder.ts
index d7d264bfc777b0a5548aa229e43b620862c6af95..ecd8dfeec52c1d756ff3c5e45b4c9e215084ce75 100644
--- a/src/mol-geo/mesh/mesh-builder.ts
+++ b/src/mol-geo/geometry/mesh/mesh-builder.ts
@@ -8,8 +8,8 @@ import { ValueCell } from 'mol-util/value-cell'
import { Vec3, Mat4, Mat3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
import { Mesh } from './mesh';
-import { getNormalMatrix } from '../util';
-import { Primitive } from '../primitive/primitive';
+import { getNormalMatrix } from '../../util';
+import { Primitive } from '../../primitive/primitive';
export interface MeshBuilderState {
readonly currentGroup: number
@@ -67,6 +67,7 @@ export namespace MeshBuilder {
const nb = ChunkedArray.compact(normals, true) as Float32Array
const gb = ChunkedArray.compact(groups, true) as Float32Array
return {
+ kind: 'mesh',
vertexCount: vertices.elementCount,
triangleCount: indices.elementCount,
vertexBuffer: mesh ? ValueCell.update(mesh.vertexBuffer, vb) : ValueCell.create(vb),
diff --git a/src/mol-geo/mesh/mesh.ts b/src/mol-geo/geometry/mesh/mesh.ts
similarity index 99%
rename from src/mol-geo/mesh/mesh.ts
rename to src/mol-geo/geometry/mesh/mesh.ts
index adb7cae231e800863e5b4d7d5fa53b69d1e4246e..e600eef6370dfc6460926a66853199a5734a010f 100644
--- a/src/mol-geo/mesh/mesh.ts
+++ b/src/mol-geo/geometry/mesh/mesh.ts
@@ -8,9 +8,11 @@ import { Task } from 'mol-task'
import { ValueCell } from 'mol-util'
import { Vec3, Mat4 } from 'mol-math/linear-algebra'
import { Sphere3D } from 'mol-math/geometry'
-import { transformPositionArray/* , transformDirectionArray, getNormalMatrix */ } from '../util';
+import { transformPositionArray/* , transformDirectionArray, getNormalMatrix */ } from '../../util';
export interface Mesh {
+ readonly kind: 'mesh',
+
/** Number of vertices in the mesh */
vertexCount: number,
/** Number of triangles in the mesh */
@@ -39,6 +41,7 @@ export namespace Mesh {
const nb = mesh ? mesh.normalBuffer.ref.value : new Float32Array(0)
const gb = mesh ? mesh.groupBuffer.ref.value : new Float32Array(0)
return {
+ kind: 'mesh',
vertexCount: 0,
triangleCount: 0,
vertexBuffer: mesh ? ValueCell.update(mesh.vertexBuffer, vb) : ValueCell.create(vb),
diff --git a/src/mol-geo/geometry/point/point-builder.ts b/src/mol-geo/geometry/point/point-builder.ts
new file mode 100644
index 0000000000000000000000000000000000000000..e00a9e06e3da840a267c19100e9ffb412242ccdd
--- /dev/null
+++ b/src/mol-geo/geometry/point/point-builder.ts
@@ -0,0 +1,38 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ValueCell } from 'mol-util/value-cell'
+import { ChunkedArray } from 'mol-data/util';
+import { Point } from './point';
+
+export interface PointBuilder {
+ add(x: number, y: number, z: number, group: number): void
+ getPoint(): Point
+}
+
+export namespace PointBuilder {
+ export function create(initialCount = 2048, chunkSize = 1024, point?: Point): PointBuilder {
+ const vertices = ChunkedArray.create(Float32Array, 3, chunkSize, point ? point.vertexBuffer.ref.value : initialCount);
+ const groups = ChunkedArray.create(Float32Array, 1, chunkSize, point ? point.groupBuffer.ref.value : initialCount);
+
+ return {
+ add: (x: number, y: number, z: number, group: number) => {
+ ChunkedArray.add3(vertices, x, y, z);
+ ChunkedArray.add(groups, group);
+ },
+ getPoint: () => {
+ const vb = ChunkedArray.compact(vertices, true) as Float32Array
+ const gb = ChunkedArray.compact(groups, true) as Float32Array
+ return {
+ kind: 'point',
+ vertexCount: vertices.elementCount,
+ vertexBuffer: point ? ValueCell.update(point.vertexBuffer, vb) : ValueCell.create(vb),
+ groupBuffer: point ? ValueCell.update(point.groupBuffer, gb) : ValueCell.create(gb),
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/point/point.ts b/src/mol-geo/geometry/point/point.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2b5a810e6a95a3bcbc078663da46f21d502c7f9c
--- /dev/null
+++ b/src/mol-geo/geometry/point/point.ts
@@ -0,0 +1,43 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ValueCell } from 'mol-util'
+import { Mat4 } from 'mol-math/linear-algebra'
+import { transformPositionArray/* , transformDirectionArray, getNormalMatrix */ } from '../../util';
+
+/** Point cloud */
+export interface Point {
+ readonly kind: 'point',
+ /** Number of vertices in the point cloud */
+ vertexCount: number,
+ /** Vertex buffer as array of xyz values wrapped in a value cell */
+ readonly vertexBuffer: ValueCell<Float32Array>,
+ /** Group buffer as array of group ids for each vertex wrapped in a value cell */
+ readonly groupBuffer: ValueCell<Float32Array>,
+}
+
+export namespace Point {
+ export function createEmpty(point?: Point): Point {
+ const vb = point ? point.vertexBuffer.ref.value : new Float32Array(0)
+ const gb = point ? point.groupBuffer.ref.value : new Float32Array(0)
+ return {
+ kind: 'point',
+ vertexCount: 0,
+ vertexBuffer: point ? ValueCell.update(point.vertexBuffer, vb) : ValueCell.create(vb),
+ groupBuffer: point ? ValueCell.update(point.groupBuffer, gb) : ValueCell.create(gb),
+ }
+ }
+
+ export function transformImmediate(point: Point, t: Mat4) {
+ transformRangeImmediate(point, t, 0, point.vertexCount)
+ }
+
+ export function transformRangeImmediate(point: Point, t: Mat4, offset: number, count: number) {
+ const v = point.vertexBuffer.ref.value
+ transformPositionArray(t, v, offset, count)
+ ValueCell.update(point.vertexBuffer, v);
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/shape/index.ts b/src/mol-geo/representation/shape/index.ts
index c5b86178a700bd021cbd759e1dcfe36ee43c5df2..fcb1800524150c6262e0cd3966377c4944456418 100644
--- a/src/mol-geo/representation/shape/index.ts
+++ b/src/mol-geo/representation/shape/index.ts
@@ -10,7 +10,6 @@ import { RepresentationProps, Representation } from '..';
import { PickingId } from '../../util/picking';
import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, createMarkers } from '../../util/marker-data';
-import { createRenderableState, createMeshValues, DefaultMeshProps } from '../util';
import { getMeshData } from '../../util/mesh-data';
import { MeshValues } from 'mol-gl/renderable';
import { ValueCell } from 'mol-util';
@@ -20,6 +19,7 @@ import { LocationIterator } from '../../util/location-iterator';
import { createColors } from '../structure/visual/util/common';
import { OrderedSet, Interval } from 'mol-data/int';
import { createIdentityTransform } from '../../util/transform-data';
+import { DefaultMeshProps, createMeshValues, createRenderableState } from '../../geometry/geometry';
export interface ShapeRepresentation<P extends RepresentationProps = {}> extends Representation<Shape, P> { }
diff --git a/src/mol-geo/representation/structure/complex-visual.ts b/src/mol-geo/representation/structure/complex-visual.ts
index 53a59c6d4ed75890f3a3463971c138f14445192b..e9bf510643a5c30bb7b25fd173b3ce41fc18a0f8 100644
--- a/src/mol-geo/representation/structure/complex-visual.ts
+++ b/src/mol-geo/representation/structure/complex-visual.ts
@@ -7,17 +7,17 @@
import { Structure } from 'mol-model/structure';
import { Visual } from '..';
import { MeshRenderObject } from 'mol-gl/render-object';
-import { Mesh } from '../../mesh/mesh';
+import { Mesh } from '../../geometry/mesh/mesh';
import { RuntimeContext } from 'mol-task';
import { LocationIterator } from '../../util/location-iterator';
import { createComplexMeshRenderObject, createColors } from './visual/util/common';
-import { StructureProps, DefaultStructureMeshProps, MeshUpdateState } from '.';
+import { StructureProps, DefaultStructureMeshProps, VisualUpdateState } from '.';
import { deepEqual, ValueCell } from 'mol-util';
-import { updateMeshValues, updateRenderableState } from '../util';
import { PickingId } from '../../util/picking';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction } from '../../util/marker-data';
import { Interval } from 'mol-data/int';
+import { updateMeshValues, updateRenderableState } from '../../geometry/geometry';
export interface ComplexVisual<P extends StructureProps> extends Visual<Structure, P> { }
@@ -32,12 +32,12 @@ export interface ComplexMeshVisualBuilder<P extends ComplexMeshProps> {
createLocationIterator(structure: Structure): LocationIterator
getLoci(pickingId: PickingId, structure: Structure, id: number): Loci
mark(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean,
- setUpdateState(state: MeshUpdateState, newProps: P, currentProps: P): void
+ setUpdateState(state: VisualUpdateState, newProps: P, currentProps: P): void
}
export function ComplexMeshVisual<P extends ComplexMeshProps>(builder: ComplexMeshVisualBuilder<P>): ComplexVisual<P> {
const { defaultProps, createMesh, createLocationIterator, getLoci, mark, setUpdateState } = builder
- const updateState = MeshUpdateState.create()
+ const updateState = VisualUpdateState.create()
let renderObject: MeshRenderObject | undefined
let currentProps: P
@@ -65,22 +65,22 @@ export function ComplexMeshVisual<P extends ComplexMeshProps>(builder: ComplexMe
if (!renderObject) return false
locationIt.reset()
- MeshUpdateState.reset(updateState)
+ VisualUpdateState.reset(updateState)
setUpdateState(updateState, newProps, currentProps)
const newConformationHash = Structure.conformationHash(currentStructure)
if (newConformationHash !== conformationHash) {
conformationHash = newConformationHash
- updateState.createMesh = true
+ updateState.createGeometry = true
}
- if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) updateState.createMesh = true
+ if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) updateState.createGeometry = true
if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) updateState.updateColor = true
// if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createMesh = true // TODO
//
- if (updateState.createMesh) {
+ if (updateState.createGeometry) {
mesh = await createMesh(ctx, currentStructure, newProps, mesh)
ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
updateState.updateColor = true
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 7628d9e084ba81ff6ef7e9705638532e73ee2c77..e6f6610418cb9fbf08a3669fc0157cc62bcd828a 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -9,7 +9,7 @@ import { Structure } from 'mol-model/structure';
import { ColorThemeProps } from 'mol-view/theme/color';
import { SizeThemeProps } from 'mol-view/theme/size';
import { Representation, RepresentationProps } from '..';
-import { DefaultBaseProps, DefaultMeshProps } from '../util';
+import { DefaultMeshProps, DefaultBaseProps, DefaultPointProps } from '../../geometry/geometry';
export interface StructureRepresentation<P extends RepresentationProps = {}> extends Representation<Structure, P> { }
@@ -26,23 +26,32 @@ export const DefaultStructureMeshProps = {
}
export type StructureMeshProps = typeof DefaultStructureMeshProps
-export interface MeshUpdateState {
+export const DefaultStructurePointProps = {
+ ...DefaultStructureProps,
+ ...DefaultPointProps
+}
+export type StructurePointProps = typeof DefaultStructurePointProps
+
+export interface VisualUpdateState {
updateTransform: boolean
updateColor: boolean
- createMesh: boolean
+ updateSize: boolean
+ createGeometry: boolean
}
-export namespace MeshUpdateState {
- export function create(): MeshUpdateState {
+export namespace VisualUpdateState {
+ export function create(): VisualUpdateState {
return {
updateTransform: false,
updateColor: false,
- createMesh: false
+ updateSize: false,
+ createGeometry: false
}
}
- export function reset(state: MeshUpdateState) {
+ export function reset(state: VisualUpdateState) {
state.updateTransform = false
state.updateColor = false
- state.createMesh = false
+ state.updateSize = false
+ state.createGeometry = false
}
}
diff --git a/src/mol-geo/representation/structure/representation/surface.ts b/src/mol-geo/representation/structure/representation/surface.ts
index 7e95466e6ffa51421b7973b8436b2a5ef1e9a6d8..92a0d48e2d610244eb7e0e1dc1e32e326ba3a52c 100644
--- a/src/mol-geo/representation/structure/representation/surface.ts
+++ b/src/mol-geo/representation/structure/representation/surface.ts
@@ -11,9 +11,12 @@ import { Structure } from 'mol-model/structure';
import { MarkerAction } from '../../../util/marker-data';
import { Loci } from 'mol-model/loci';
import { PickingId } from '../../../util/picking';
+import { Task } from 'mol-task';
+import { GaussianDensityPointVisual, DefaultGaussianDensityPointProps } from '../visual/gaussian-density-point';
export const DefaultSurfaceProps = {
...DefaultGaussianSurfaceProps,
+ ...DefaultGaussianDensityPointProps,
}
export type SurfaceProps = typeof DefaultSurfaceProps
@@ -21,27 +24,32 @@ export type SurfaceRepresentation = StructureRepresentation<SurfaceProps>
export function SurfaceRepresentation(): SurfaceRepresentation {
let currentProps: SurfaceProps
- const gaussianRepr = UnitsRepresentation('Gaussian surface', GaussianSurfaceVisual)
+ const gaussianSurfaceRepr = UnitsRepresentation('Gaussian surface', GaussianSurfaceVisual)
+ const gaussianPointRepr = UnitsRepresentation('Gaussian point grid', GaussianDensityPointVisual)
return {
label: 'Surface',
get renderObjects() {
- return [ ...gaussianRepr.renderObjects ]
+ return [ ...gaussianSurfaceRepr.renderObjects, ...gaussianPointRepr.renderObjects ]
},
get props() {
- return { ...gaussianRepr.props }
+ return { ...gaussianSurfaceRepr.props, ...gaussianPointRepr.props }
},
createOrUpdate: (props: Partial<SurfaceProps> = {}, structure?: Structure) => {
currentProps = Object.assign({}, DefaultSurfaceProps, currentProps, props)
- return gaussianRepr.createOrUpdate(currentProps, structure)
+ return Task.create('Creating SurfaceRepresentation', async ctx => {
+ await gaussianSurfaceRepr.createOrUpdate(currentProps, structure).runInContext(ctx)
+ await gaussianPointRepr.createOrUpdate(currentProps, structure).runInContext(ctx)
+ })
},
getLoci: (pickingId: PickingId) => {
- return gaussianRepr.getLoci(pickingId)
+ return gaussianSurfaceRepr.getLoci(pickingId)
},
mark: (loci: Loci, action: MarkerAction) => {
- return gaussianRepr.mark(loci, action)
+ return gaussianSurfaceRepr.mark(loci, action)
},
destroy() {
- gaussianRepr.destroy()
+ gaussianSurfaceRepr.destroy()
+ gaussianPointRepr.destroy()
}
}
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/units-visual.ts b/src/mol-geo/representation/structure/units-visual.ts
index e017c8494135ebee56678f719378cbd6e4abba51..b7feb79de7a9ed01693317afc8517d9d115857d3 100644
--- a/src/mol-geo/representation/structure/units-visual.ts
+++ b/src/mol-geo/representation/structure/units-visual.ts
@@ -5,20 +5,21 @@
*/
import { Unit, Structure } from 'mol-model/structure';
-import { RepresentationProps, Visual } from '..';
-import { DefaultStructureMeshProps, MeshUpdateState } from '.';
+import { RepresentationProps, Visual } from '../';
+import { DefaultStructureMeshProps, VisualUpdateState, DefaultStructurePointProps } from '.';
import { RuntimeContext } from 'mol-task';
import { PickingId } from '../../util/picking';
import { LocationIterator } from '../../util/location-iterator';
-import { Mesh } from '../../mesh/mesh';
+import { Mesh } from '../../geometry/mesh/mesh';
import { MarkerAction, applyMarkerAction, createMarkers } from '../../util/marker-data';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
-import { MeshRenderObject } from 'mol-gl/render-object';
-import { createUnitsMeshRenderObject, createColors } from './visual/util/common';
+import { MeshRenderObject, PointRenderObject } from 'mol-gl/render-object';
+import { createUnitsMeshRenderObject, createColors, createUnitsPointRenderObject } from './visual/util/common';
import { deepEqual, ValueCell, UUID } from 'mol-util';
-import { updateMeshValues, updateRenderableState } from '../util';
import { Interval } from 'mol-data/int';
import { createTransforms } from '../../util/transform-data';
+import { updateMeshValues, updateRenderableState, updatePointValues } from '../../geometry/geometry';
+import { Point } from '../../geometry/point/point';
export type StructureGroup = { structure: Structure, group: Unit.SymmetryGroup }
@@ -36,12 +37,12 @@ export interface UnitsMeshVisualBuilder<P extends UnitsMeshProps> {
createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
getLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number): Loci
mark(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Interval) => boolean): boolean
- setUpdateState(state: MeshUpdateState, newProps: P, currentProps: P): void
+ setUpdateState(state: VisualUpdateState, newProps: P, currentProps: P): void
}
export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisualBuilder<P>): UnitsVisual<P> {
const { defaultProps, createMesh, createLocationIterator, getLoci, mark, setUpdateState } = builder
- const updateState = MeshUpdateState.create()
+ const updateState = VisualUpdateState.create()
let renderObject: MeshRenderObject | undefined
let currentProps: P
@@ -75,20 +76,20 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
const unit = currentGroup.units[0]
locationIt.reset()
- MeshUpdateState.reset(updateState)
+ VisualUpdateState.reset(updateState)
setUpdateState(updateState, newProps, currentProps)
const newConformationId = Unit.conformationId(unit)
if (newConformationId !== currentConformationId) {
currentConformationId = newConformationId
- updateState.createMesh = true
+ updateState.createGeometry = true
}
if (currentGroup.units.length !== locationIt.instanceCount) updateState.updateTransform = true
- if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) updateState.createMesh = true
+ if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) updateState.createGeometry = true
if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) updateState.updateColor = true
- if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createMesh = true
+ if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
//
@@ -100,7 +101,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
updateState.updateColor = true
}
- if (updateState.createMesh) {
+ if (updateState.createGeometry) {
mesh = newProps.unitKinds.includes(unit.kind)
? await createMesh(ctx, unit, currentStructure, newProps, mesh)
: Mesh.createEmpty(mesh)
@@ -112,8 +113,9 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
await createColors(ctx, locationIt, newProps.colorTheme, renderObject.values)
}
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
+ // TODO why do I need to cast here?
+ updateMeshValues(renderObject.values, newProps as UnitsMeshProps)
+ updateRenderableState(renderObject.state, newProps as UnitsMeshProps)
currentProps = newProps
}
@@ -177,4 +179,155 @@ function sameGroupConformation(groupA: Unit.SymmetryGroup, groupB: Unit.Symmetry
groupA.units.length === groupB.units.length &&
Unit.conformationId(groupA.units[0]) === Unit.conformationId(groupB.units[0])
)
+}
+
+//
+
+export const DefaultUnitsPointProps = {
+ ...DefaultStructurePointProps,
+ unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+}
+export type UnitsPointProps = typeof DefaultUnitsPointProps
+
+export interface UnitsPointVisualBuilder<P extends UnitsPointProps> {
+ defaultProps: P
+ createPoint(ctx: RuntimeContext, unit: Unit, structure: Structure, props: P, point?: Point): Promise<Point>
+ createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
+ getLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number): Loci
+ mark(loci: Loci, group: Unit.SymmetryGroup, apply: (interval: Interval) => boolean): boolean
+ setUpdateState(state: VisualUpdateState, newProps: P, currentProps: P): void
+}
+
+export function UnitsPointVisual<P extends UnitsPointProps>(builder: UnitsPointVisualBuilder<P>): UnitsVisual<P> {
+ const { defaultProps, createPoint, createLocationIterator, getLoci, mark, setUpdateState } = builder
+ const updateState = VisualUpdateState.create()
+
+ let renderObject: PointRenderObject | undefined
+ let currentProps: P
+ let point: Point
+ let currentGroup: Unit.SymmetryGroup
+ let currentStructure: Structure
+ let locationIt: LocationIterator
+ let currentConformationId: UUID
+
+ async function create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: Partial<P> = {}) {
+ currentProps = Object.assign({}, defaultProps, props)
+ currentProps.colorTheme.structure = currentStructure
+ currentGroup = group
+
+ const unit = group.units[0]
+ currentConformationId = Unit.conformationId(unit)
+ point = currentProps.unitKinds.includes(unit.kind)
+ ? await createPoint(ctx, unit, currentStructure, currentProps, point)
+ : Point.createEmpty(point)
+
+ // TODO create empty location iterator when not in unitKinds
+ locationIt = createLocationIterator(group)
+ renderObject = await createUnitsPointRenderObject(ctx, group, point, locationIt, currentProps)
+ }
+
+ async function update(ctx: RuntimeContext, props: Partial<P> = {}) {
+ if (!renderObject) return
+
+ const newProps = Object.assign({}, currentProps, props)
+ newProps.colorTheme.structure = currentStructure
+ const unit = currentGroup.units[0]
+
+ locationIt.reset()
+ VisualUpdateState.reset(updateState)
+ setUpdateState(updateState, newProps, currentProps)
+
+ const newConformationId = Unit.conformationId(unit)
+ if (newConformationId !== currentConformationId) {
+ currentConformationId = newConformationId
+ updateState.createGeometry = true
+ }
+
+ if (currentGroup.units.length !== locationIt.instanceCount) updateState.updateTransform = true
+
+ if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) updateState.createGeometry = true
+ if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) updateState.updateColor = true
+ if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) updateState.createGeometry = true
+
+ //
+
+ if (updateState.updateTransform) {
+ locationIt = createLocationIterator(currentGroup)
+ const { instanceCount, groupCount } = locationIt
+ createTransforms(currentGroup, renderObject.values)
+ createMarkers(instanceCount * groupCount, renderObject.values)
+ updateState.updateColor = true
+ }
+
+ if (updateState.createGeometry) {
+ point = newProps.unitKinds.includes(unit.kind)
+ ? await createPoint(ctx, unit, currentStructure, newProps, point)
+ : Point.createEmpty(point)
+ ValueCell.update(renderObject.values.drawCount, point.vertexCount)
+ updateState.updateColor = true
+ }
+
+ if (updateState.updateColor) {
+ await createColors(ctx, locationIt, newProps.colorTheme, renderObject.values)
+ }
+
+ // TODO why do I need to cast here?
+ updatePointValues(renderObject.values, newProps as UnitsPointProps)
+ updateRenderableState(renderObject.state, newProps as UnitsPointProps)
+
+ currentProps = newProps
+ }
+
+ return {
+ get renderObject () { return renderObject },
+ async createOrUpdate(ctx: RuntimeContext, props: Partial<P> = {}, structureGroup?: StructureGroup) {
+ if (structureGroup) currentStructure = structureGroup.structure
+ const group = structureGroup ? structureGroup.group : undefined
+ if (!group && !currentGroup) {
+ throw new Error('missing group')
+ } else if (group && (!currentGroup || !renderObject)) {
+ // console.log('unit-visual first create')
+ await create(ctx, group, props)
+ } else if (group && group.hashCode !== currentGroup.hashCode) {
+ // console.log('unit-visual group.hashCode !== currentGroup.hashCode')
+ await create(ctx, group, props)
+ } else {
+ // console.log('unit-visual update')
+ if (group && !sameGroupConformation(group, currentGroup)) {
+ // console.log('unit-visual new conformation')
+ currentGroup = group
+ }
+ await update(ctx, props)
+ }
+ },
+ getLoci(pickingId: PickingId) {
+ return renderObject ? getLoci(pickingId, currentGroup, renderObject.id) : EmptyLoci
+ },
+ mark(loci: Loci, action: MarkerAction) {
+ if (!renderObject) return false
+ const { tMarker } = renderObject.values
+ const { groupCount, instanceCount } = locationIt
+
+ function apply(interval: Interval) {
+ const start = Interval.start(interval)
+ const end = Interval.end(interval)
+ return applyMarkerAction(tMarker.ref.value.array, start, end, action)
+ }
+
+ let changed = false
+ if (isEveryLoci(loci)) {
+ changed = apply(Interval.ofBounds(0, groupCount * instanceCount))
+ } else {
+ changed = mark(loci, currentGroup, apply)
+ }
+ if (changed) {
+ ValueCell.update(tMarker, tMarker.ref.value)
+ }
+ return changed
+ },
+ destroy() {
+ // TODO
+ renderObject = undefined
+ }
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
index 185835c629e4bcca92a85f02008992f9466199df..d4270f02ebad1f6632c44d65ea24c91c1a2ddfa2 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -5,12 +5,11 @@
*/
import { Unit, Structure, Link, StructureElement } from 'mol-model/structure';
-import { DefaultStructureProps, ComplexVisual, MeshUpdateState } from '..';
+import { DefaultStructureProps, ComplexVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
+import { Mesh } from '../../../geometry/mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { DefaultMeshProps } from '../../util';
import { Vec3 } from 'mol-math/linear-algebra';
import { LocationIterator } from '../../../util/location-iterator';
import { createLinkCylinderMesh, DefaultLinkCylinderProps, LinkCylinderProps } from './util/link';
@@ -19,6 +18,7 @@ import { ComplexMeshVisual } from '../complex-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { LinkType } from 'mol-model/structure/model/types';
import { BitFlags } from 'mol-util';
+import { DefaultMeshProps } from '../../../geometry/geometry';
// TODO create seperate visual
// for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {
@@ -77,8 +77,8 @@ export function CarbohydrateLinkVisual(): ComplexVisual<CarbohydrateLinkProps> {
createLocationIterator: CarbohydrateLinkIterator,
getLoci: getLinkLoci,
mark: markLink,
- setUpdateState: (state: MeshUpdateState, newProps: CarbohydrateLinkProps, currentProps: CarbohydrateLinkProps) => {
- state.createMesh = newProps.radialSegments !== currentProps.radialSegments
+ setUpdateState: (state: VisualUpdateState, newProps: CarbohydrateLinkProps, currentProps: CarbohydrateLinkProps) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
}
})
}
diff --git a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
index 13d568ccb73cd097c659a36a8281c9e600b4aa85..fd6603b25e7caf6683e571e98638fc56141cbd52 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -5,19 +5,19 @@
*/
import { Unit, Structure, StructureElement } from 'mol-model/structure';
-import { ComplexVisual, MeshUpdateState } from '..';
+import { ComplexVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
+import { Mesh } from '../../../geometry/mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants';
import { LocationIterator } from '../../../util/location-iterator';
import { OrderedSet, Interval } from 'mol-data/int';
import { ComplexMeshVisual, DefaultComplexMeshProps } from '../complex-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
-import { addSphere } from '../../../mesh/builder/sphere';
+import { addSphere } from '../../../geometry/mesh/builder/sphere';
import { Box, PerforatedBox } from '../../../primitive/box';
import { OctagonalPyramid, PerforatedOctagonalPyramid } from '../../../primitive/pyramid';
import { Star } from '../../../primitive/star';
@@ -154,8 +154,8 @@ export function CarbohydrateSymbolVisual(): ComplexVisual<CarbohydrateSymbolProp
createLocationIterator: CarbohydrateElementIterator,
getLoci: getCarbohydrateLoci,
mark: markCarbohydrate,
- setUpdateState: (state: MeshUpdateState, newProps: CarbohydrateSymbolProps, currentProps: CarbohydrateSymbolProps) => {
- state.createMesh = newProps.detail !== currentProps.detail
+ setUpdateState: (state: VisualUpdateState, newProps: CarbohydrateSymbolProps, currentProps: CarbohydrateSymbolProps) => {
+ state.createGeometry = newProps.detail !== currentProps.detail
}
})
}
diff --git a/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts
index 735499fd290cee6d58f5213079613c20aed9d75b..f36e157eb43682d86e44021bb2ac3d658db7056c 100644
--- a/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts
@@ -5,10 +5,10 @@
*/
import { Link, Structure, StructureElement } from 'mol-model/structure';
-import { ComplexVisual, MeshUpdateState } from '..';
+import { ComplexVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh } from './util/link';
-import { Mesh } from '../../../mesh/mesh';
+import { Mesh } from '../../../geometry/mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
@@ -65,8 +65,8 @@ export function CrossLinkRestraintVisual(): ComplexVisual<CrossLinkRestraintProp
createLocationIterator: CrossLinkRestraintIterator,
getLoci: getLinkLoci,
mark: markLink,
- setUpdateState: (state: MeshUpdateState, newProps: CrossLinkRestraintProps, currentProps: CrossLinkRestraintProps) => {
- state.createMesh = newProps.radialSegments !== currentProps.radialSegments
+ setUpdateState: (state: VisualUpdateState, newProps: CrossLinkRestraintProps, currentProps: CrossLinkRestraintProps) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
}
})
}
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index eac5fb80226aad8dc30f67570d11f9c7469cdfe2..f624d11f10d49c0d3ec3b3009b3e24f421882e12 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -2,169 +2,56 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ValueCell } from 'mol-util/value-cell'
-import { PointRenderObject } from 'mol-gl/render-object'
import { Unit, Structure } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task'
-import { UnitsVisual, DefaultStructureProps } from '..';
+import { UnitsVisual, VisualUpdateState } from '..';
import { getElementLoci, StructureElementIterator, markElement } from './util/element';
-import { createColors, createSizes, createUnitsPointRenderObject } from './util/common';
-import { deepEqual, UUID } from 'mol-util';
-import { Interval } from 'mol-data/int';
-import { PickingId } from '../../../util/picking';
-import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
-import { MarkerAction, createMarkers, applyMarkerAction } from '../../../util/marker-data';
import { Vec3 } from 'mol-math/linear-algebra';
-import { fillSerial } from 'mol-util/array';
import { SizeThemeProps } from 'mol-view/theme/size';
-import { LocationIterator } from '../../../util/location-iterator';
-import { createTransforms } from '../../../util/transform-data';
-import { StructureGroup } from '../units-visual';
-import { updateRenderableState, updateBaseValues } from '../../util';
+import { UnitsPointVisual, DefaultUnitsPointProps } from '../units-visual';
+import { Point } from '../../../geometry/point/point';
+import { PointBuilder } from '../../../geometry/point/point-builder';
export const DefaultElementPointProps = {
- ...DefaultStructureProps,
+ ...DefaultUnitsPointProps,
sizeTheme: { name: 'uniform', value: 0.2 } as SizeThemeProps,
pointSizeAttenuation: true,
}
-export type ElementPointProps = Partial<typeof DefaultElementPointProps>
+export type ElementPointProps = typeof DefaultElementPointProps
-export async function createElementPointVertices(ctx: RuntimeContext, unit: Unit, vertices?: ValueCell<Float32Array>) {
+// TODO size
+
+export async function createElementPoint(ctx: RuntimeContext, unit: Unit, structure: Structure, props: ElementPointProps, point: Point) {
const elements = unit.elements
- const n = elements.length * 3
- const array = vertices && vertices.ref.value.length >= n ? vertices.ref.value : new Float32Array(n)
+ const n = elements.length
+ const builder = PointBuilder.create(n, n / 10, point)
const pos = unit.conformation.invariantPosition
-
const p = Vec3.zero()
- for (let i = 0; i < n; i += 3) {
- pos(elements[i / 3], p)
- array[i] = p[0]
- array[i + 1] = p[1]
- array[i + 2] = p[2]
+
+ for (let i = 0; i < n; ++i) {
+ pos(elements[i], p)
+ builder.add(p[0], p[1], p[2], i)
if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Creating points', current: i / 3, max: elements.length });
+ await ctx.update({ message: 'Creating points', current: i, max: n });
}
- ++i
}
- return vertices ? ValueCell.update(vertices, array) : ValueCell.create(array)
+ return builder.getPoint()
}
export function ElementPointVisual(): UnitsVisual<ElementPointProps> {
- let renderObject: PointRenderObject | undefined
- let currentProps = DefaultElementPointProps
- let currentGroup: Unit.SymmetryGroup
- let currentStructure: Structure
- let locationIt: LocationIterator
- let vertices: ValueCell<Float32Array>
- let currentConformationId: UUID
-
- return {
- get renderObject () { return renderObject },
- async createOrUpdate(ctx: RuntimeContext, props: ElementPointProps = {}, structureGroup?: StructureGroup) {
- if (structureGroup) currentStructure = structureGroup.structure
- const group = structureGroup ? structureGroup.group : undefined
- if (!group && !currentGroup) {
- throw new Error('missing group')
- } else if (group && !currentGroup) {
- currentProps = Object.assign({}, DefaultElementPointProps, props)
- currentProps.colorTheme.structure = currentStructure
- currentGroup = group
- locationIt = StructureElementIterator.fromGroup(group)
-
- const unit = group.units[0]
- currentConformationId = Unit.conformationId(unit)
- vertices = await createElementPointVertices(ctx, unit, vertices)
-
- renderObject = await createUnitsPointRenderObject(ctx, group, vertices, locationIt, currentProps)
- } else if (renderObject) {
- if (group) currentGroup = group
-
- const newProps = { ...currentProps, ...props }
- const unit = currentGroup.units[0]
-
- let updateTransform = false
- let createVertices = false
- let updateColor = false
- let updateSize = false
-
- const newConformationId = Unit.conformationId(unit)
- if (newConformationId !== currentConformationId) {
- currentConformationId = newConformationId
- createVertices = true
- }
-
- if (currentGroup.units.length !== locationIt.instanceCount) updateTransform = true
+ return UnitsPointVisual<ElementPointProps>({
+ defaultProps: DefaultElementPointProps,
+ createPoint: createElementPoint,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement,
+ setUpdateState: (state: VisualUpdateState, newProps: ElementPointProps, currentProps: ElementPointProps) => {
- if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) createVertices = true
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) updateColor = true
- if (!deepEqual(newProps.sizeTheme, currentProps.sizeTheme)) updateSize = true
-
- if (updateTransform) {
- locationIt = StructureElementIterator.fromGroup(currentGroup)
- const { instanceCount, groupCount } = locationIt
- createTransforms(currentGroup, renderObject.values)
- createMarkers(instanceCount * groupCount, renderObject.values)
- updateColor = true
- updateSize = true
- }
-
- if (createVertices) {
- await createElementPointVertices(ctx, unit, vertices)
- ValueCell.update(renderObject.values.aGroup, fillSerial(new Float32Array(locationIt.groupCount))) // TODO reuse array
- ValueCell.update(renderObject.values.drawCount, locationIt.groupCount)
- updateColor = true
- updateSize = true
- }
-
- if (updateColor) {
- await createColors(ctx, locationIt, newProps.colorTheme, renderObject.values)
- }
-
- if (updateSize) {
- await createSizes(ctx, locationIt, newProps.sizeTheme, renderObject.values)
- }
-
- updateBaseValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- }
- },
- getLoci(pickingId: PickingId) {
- return renderObject ? getElementLoci(pickingId, currentGroup, renderObject.id) : EmptyLoci
- },
- mark(loci: Loci, action: MarkerAction) {
- if (!renderObject) return false
- const { tMarker } = renderObject.values
- const { groupCount, instanceCount } = locationIt
-
- function apply(interval: Interval) {
- const start = Interval.start(interval)
- const end = Interval.end(interval)
- return applyMarkerAction(tMarker.ref.value.array, start, end, action)
- }
-
- let changed = false
- if (isEveryLoci(loci)) {
- apply(Interval.ofBounds(0, groupCount * instanceCount))
- changed = true
- } else {
- changed = markElement(loci, currentGroup, apply)
- }
- if (changed) {
- ValueCell.update(tMarker, tMarker.ref.value)
- }
- return changed
- },
- destroy() {
- // TODO
- renderObject = undefined
}
- }
-}
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/element-sphere.ts b/src/mol-geo/representation/structure/visual/element-sphere.ts
index 523e19e1e3d62d8cc1a0c0ce6c3d1fdc4b699c14..62a59004bb7393a0220bfc8d46c1b5e2e213242f 100644
--- a/src/mol-geo/representation/structure/visual/element-sphere.ts
+++ b/src/mol-geo/representation/structure/visual/element-sphere.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { UnitsVisual, MeshUpdateState } from '..';
+import { UnitsVisual, VisualUpdateState } from '..';
import { createElementSphereMesh, markElement, getElementLoci, StructureElementIterator } from './util/element';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
@@ -22,8 +22,8 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
- setUpdateState: (state: MeshUpdateState, newProps: ElementSphereProps, currentProps: ElementSphereProps) => {
- state.createMesh = newProps.detail !== currentProps.detail
+ setUpdateState: (state: VisualUpdateState, newProps: ElementSphereProps, currentProps: ElementSphereProps) => {
+ state.createGeometry = newProps.detail !== currentProps.detail
}
})
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/gaussian-density-point.ts b/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7bc2d1c9d671bad4c69321708b4b25ea99af4621
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/gaussian-density-point.ts
@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, Structure } from 'mol-model/structure';
+import { RuntimeContext } from 'mol-task'
+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 { Point } from '../../../geometry/point/point';
+import { PointBuilder } from '../../../geometry/point/point-builder';
+
+export const DefaultGaussianDensityPointProps = {
+ ...DefaultUnitsPointProps,
+
+ sizeTheme: { name: 'uniform', value: 1.5 } as SizeThemeProps,
+ colorTheme: { name: 'uniform', value: Color(0xAAAAAA) } as ColorThemeProps,
+ 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) {
+ const { transform, field: { space, data } } = await computeGaussianDensity(unit, structure, props).runAsChild(ctx)
+
+ const { dimensions, get } = space
+ const [ xn, yn, zn ] = dimensions
+
+ const n = xn * yn * zn * 3
+ const builder = PointBuilder.create(n, n / 10, point)
+
+ const p = Vec3.zero()
+ let i = 0
+
+ for (let x = 0; x < xn; ++x) {
+ for (let y = 0; y < yn; ++y) {
+ for (let z = 0; z < zn; ++z) {
+ if (get(data, x, y, z) > 0.001) {
+ Vec3.set(p, x, y, z)
+ Vec3.transformMat4(p, p, transform)
+ builder.add(p[0], p[1], p[2], i)
+ }
+ if (i % 100000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Creating density points', current: i, max: n });
+ }
+ ++i
+ }
+ }
+ }
+ return builder.getPoint()
+}
+
+export function GaussianDensityPointVisual(): UnitsVisual<GaussianDensityPointProps> {
+ return UnitsPointVisual<GaussianDensityPointProps>({
+ defaultProps: DefaultGaussianDensityPointProps,
+ createPoint: createGaussianDensityPoint,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: () => EmptyLoci,
+ mark: () => false,
+ setUpdateState: (state: VisualUpdateState, newProps: GaussianDensityPointProps, currentProps: GaussianDensityPointProps) => {
+
+ }
+ })
+}
\ 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 f966d5076ce7949b6309f33eea7095e8302b7da6..8966ca864a445e4ae546d338d66a73f151c231af 100644
--- a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -4,17 +4,17 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, Structure, StructureElement } from 'mol-model/structure';
-import { UnitsVisual, MeshUpdateState } from '..';
+import { Unit, Structure } from 'mol-model/structure';
+import { UnitsVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
+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 { Tensor, Vec3, Mat4 } from 'mol-math/linear-algebra';
-import { Box3D } from 'mol-math/geometry';
-import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
+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';
export interface GaussianSurfaceMeshProps {
sizeTheme: SizeThemeProps
@@ -24,116 +24,22 @@ export interface GaussianSurfaceMeshProps {
isoValue: number
}
-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
-}
-
async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
- const { resolutionFactor, probeRadius, isoValue } = props
-
- const { elements } = unit;
- const elementCount = elements.length;
- const sizeTheme = SizeTheme(props.sizeTheme)
-
- const v = Vec3.zero()
- const p = Vec3.zero()
- const pos = unit.conformation.invariantPosition
- const l = StructureElement.create()
- l.unit = unit
-
- const pad = (probeRadius + 2) * 2 // 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)
- const min = expandedBox.min
-
- // const n = Math.pow(128, 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)
-
- // console.log('extent', extent)
- // console.log('n', n)
- // console.log('f', f)
- // console.log('s', s)
- // console.log('size', size)
- // console.log('delta', delta)
- const delta = getDelta(Box3D.expand(Box3D.empty(), structure.boundary.box, Vec3.create(pad, pad, pad)), resolutionFactor)
- const dim = Vec3.zero()
- Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
- // console.log('dim', dim, dim[0] * dim[1] * dim[2])
-
- const space = Tensor.Space(dim, [0, 1, 2], Float32Array)
- const data = space.create()
- const field = Tensor.create(space, data)
-
- const c = Vec3.zero()
-
- const radius2 = Vec3.scale(Vec3.zero(), delta, 2)
- const alpha = 1.5 // smoothness
+ const { isoValue } = props
console.time('surface density')
- for (let i = 0; i < elementCount; i++) {
- l.element = elements[i]
- pos(elements[i], v)
-
- Vec3.sub(v, v, min)
- Vec3.mul(c, v, delta)
-
- const radius = sizeTheme.size(l) // + probeRadius
-
- const minX = Math.floor(c[0] - radius2[0]) - 1
- const minY = Math.floor(c[1] - radius2[1]) - 1
- const minZ = Math.floor(c[2] - radius2[2]) - 1
- const maxX = Math.ceil(c[0] + radius2[0]) + 1
- const maxY = Math.ceil(c[1] + radius2[1]) + 1
- const maxZ = Math.ceil(c[2] + radius2[2]) + 1
-
- for (let x = minX; x < maxX; ++x) {
- for (let y = minY; y < maxY; ++y) {
- for (let z = minZ; z < maxZ; ++z) {
- Vec3.set(p, x, y, z)
- Vec3.div(p, p, delta)
- const dist = Vec3.distance(p, v)
- const density = Math.exp(-alpha * Math.pow((dist) / radius, 2))
- space.set(data, x, y, z, space.get(data, x, y, z) + density)
- }
- }
- }
-
- if (i % 100 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Gaussian surface', current: i, max: elementCount });
- }
- }
+ const { transform, field } = await computeGaussianDensity(unit, structure, props).runAsChild(ctx)
console.timeEnd('surface density')
- // console.log('data', data)
-
console.time('surface mc')
const surface = await computeMarchingCubes({
- isoLevel: isoValue * Math.exp(-alpha),
+ isoLevel: Math.exp(-isoValue),
scalarField: field,
oldSurface: mesh
}).runAsChild(ctx)
console.timeEnd('surface mc')
- const t = Mat4.identity()
- Mat4.fromScaling(t, Vec3.inverse(Vec3.zero(), delta))
- Mat4.setTranslation(t, expandedBox.min)
-
- Mesh.transformImmediate(surface, t)
+ Mesh.transformImmediate(surface, transform)
Mesh.computeNormalsImmediate(surface)
return surface;
@@ -149,11 +55,11 @@ export const DefaultGaussianSurfaceProps = {
flipSided: true,
// flatShaded: true,
alpha: 0.7,
- colorTheme: { name: 'uniform' as 'uniform', value: Color(0xDDDDDD) },
+ colorTheme: { name: 'uniform' as 'uniform', value: Color(0xDDDDDD) } as ColorThemeProps,
resolutionFactor: 7,
- probeRadius: 1.4,
- isoValue: 1,
+ probeRadius: 0,
+ isoValue: 1.5,
}
export type GaussianSurfaceProps = typeof DefaultGaussianSurfaceProps
@@ -164,10 +70,10 @@ export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
- setUpdateState: (state: MeshUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {
- if (newProps.resolutionFactor !== currentProps.resolutionFactor) state.createMesh = true
- if (newProps.probeRadius !== currentProps.probeRadius) state.createMesh = true
- if (newProps.isoValue !== currentProps.isoValue) state.createMesh = true
+ 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
}
})
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
index 44469dacff2b8bc4587e8cdb89ce9da3a15b4bff..91fac0b244bbbe0d56cfe65f1abbb20deacd925d 100644
--- a/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts
@@ -5,10 +5,10 @@
*/
import { Link, Structure, StructureElement } from 'mol-model/structure';
-import { ComplexVisual, MeshUpdateState } from '..';
+import { ComplexVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh, LinkIterator } from './util/link';
-import { Mesh } from '../../../mesh/mesh';
+import { Mesh } from '../../../geometry/mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
@@ -63,8 +63,8 @@ export function InterUnitLinkVisual(): ComplexVisual<InterUnitLinkProps> {
createLocationIterator: LinkIterator.fromStructure,
getLoci: getLinkLoci,
mark: markLink,
- setUpdateState: (state: MeshUpdateState, newProps: InterUnitLinkProps, currentProps: InterUnitLinkProps) => {
- state.createMesh = newProps.radialSegments !== currentProps.radialSegments
+ setUpdateState: (state: VisualUpdateState, newProps: InterUnitLinkProps, currentProps: InterUnitLinkProps) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
}
})
}
diff --git a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
index a3d6dd8687bc1624fd75fb2b45c2a96e383af1c8..8ec45a83d67947576d6647137b871bcf71471d00 100644
--- a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
@@ -6,10 +6,10 @@
*/
import { Unit, Link, StructureElement, Structure } from 'mol-model/structure';
-import { UnitsVisual, MeshUpdateState } from '..';
+import { UnitsVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh, LinkIterator } from './util/link';
-import { Mesh } from '../../../mesh/mesh';
+import { Mesh } from '../../../geometry/mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
@@ -77,8 +77,8 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
createLocationIterator: LinkIterator.fromGroup,
getLoci: getLinkLoci,
mark: markLink,
- setUpdateState: (state: MeshUpdateState, newProps: LinkCylinderProps, currentProps: LinkCylinderProps) => {
- state.createMesh = newProps.radialSegments !== currentProps.radialSegments
+ setUpdateState: (state: VisualUpdateState, newProps: LinkCylinderProps, currentProps: LinkCylinderProps) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
}
})
}
diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index 82387af83fe0a284eebadd7a38b129219606807e..48733329c73d40cc64bb6eb23416b73826b69375 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -7,14 +7,14 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
-import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { Mesh } from '../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { Segmentation } from 'mol-data/int';
import { MoleculeType, isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
import { getElementIndexForAtomId, getElementIndexForAtomRole } from 'mol-model/structure/util';
import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
-import { addCylinder } from '../../../mesh/builder/cylinder';
+import { addCylinder } from '../../../geometry/mesh/builder/cylinder';
import { Box } from '../../../primitive/box';
import { NucleotideLocationIterator, markNucleotideElement, getNucleotideElementLoci } from './util/nucleotide';
diff --git a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
index cd9ca682c0cab90544d44ab88e7958a4858ef956..db7428205695bdcc41335eb12be0c7123fe235d6 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -5,10 +5,10 @@
*/
import { Unit, Structure } from 'mol-model/structure';
-import { UnitsVisual, MeshUpdateState } from '..';
+import { UnitsVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
-import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { Mesh } from '../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
import { PolymerBackboneIterator } from './util/polymer';
import { getElementLoci, markElement, StructureElementIterator } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
@@ -16,7 +16,7 @@ import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { CylinderProps } from '../../../primitive/cylinder';
import { OrderedSet } from 'mol-data/int';
-import { addCylinder } from '../../../mesh/builder/cylinder';
+import { addCylinder } from '../../../geometry/mesh/builder/cylinder';
export interface PolymerBackboneCylinderProps {
sizeTheme: SizeThemeProps
@@ -77,8 +77,8 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
createLocationIterator: StructureElementIterator.fromGroup,
getLoci: getElementLoci,
mark: markElement,
- setUpdateState: (state: MeshUpdateState, newProps: PolymerBackboneProps, currentProps: PolymerBackboneProps) => {
- state.createMesh = newProps.radialSegments !== currentProps.radialSegments
+ setUpdateState: (state: VisualUpdateState, newProps: PolymerBackboneProps, currentProps: PolymerBackboneProps) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
}
})
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
index ddd31a67d6970f1b0e00416461a4a57fd7d79d40..0b6f96f8844ee94c01e37a7ab5efad3df5fbf4f0 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -7,8 +7,8 @@
import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
-import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { Mesh } from '../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement } from './util/polymer';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
diff --git a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
index 21ebafc2d3ffd91d4160defa3e9412568df14d86..cab4cd3940e72cad0ea9b5394c1c95435b47aad4 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -5,17 +5,17 @@
*/
import { Unit, Structure } from 'mol-model/structure';
-import { UnitsVisual, MeshUpdateState } from '..';
+import { UnitsVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
-import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { Mesh } from '../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
import { PolymerGapIterator, PolymerGapLocationIterator, markPolymerGapElement, getPolymerGapElementLoci } from './util/polymer';
import { Vec3 } from 'mol-math/linear-algebra';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { CylinderProps } from '../../../primitive/cylinder';
-import { addSphere } from '../../../mesh/builder/sphere';
-import { addFixedCountDashedCylinder } from '../../../mesh/builder/cylinder';
+import { addSphere } from '../../../geometry/mesh/builder/sphere';
+import { addFixedCountDashedCylinder } from '../../../geometry/mesh/builder/cylinder';
const segmentCount = 10
@@ -84,8 +84,8 @@ export function PolymerGapVisual(): UnitsVisual<PolymerGapProps> {
createLocationIterator: PolymerGapLocationIterator.fromGroup,
getLoci: getPolymerGapElementLoci,
mark: markPolymerGapElement,
- setUpdateState: (state: MeshUpdateState, newProps: PolymerGapProps, currentProps: PolymerGapProps) => {
- state.createMesh = newProps.radialSegments !== currentProps.radialSegments
+ setUpdateState: (state: VisualUpdateState, newProps: PolymerGapProps, currentProps: PolymerGapProps) => {
+ state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
}
})
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
index 186f374e1ad71d661731431b3e9f100b6f690e63..6ecfa05d443b4bd7e725898ad697ca32b0f287be 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -5,16 +5,16 @@
*/
import { Unit, Structure } from 'mol-model/structure';
-import { UnitsVisual, MeshUpdateState } from '..';
+import { UnitsVisual, VisualUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../mesh/mesh';
-import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { Mesh } from '../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement } from './util/polymer';
import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
-import { addSheet } from '../../../mesh/builder/sheet';
-import { addTube } from '../../../mesh/builder/tube';
+import { addSheet } from '../../../geometry/mesh/builder/sheet';
+import { addTube } from '../../../geometry/mesh/builder/tube';
export interface PolymerTraceMeshProps {
sizeTheme: SizeThemeProps
@@ -97,8 +97,8 @@ export function PolymerTraceVisual(): UnitsVisual<PolymerTraceProps> {
createLocationIterator: PolymerLocationIterator.fromGroup,
getLoci: getPolymerElementLoci,
mark: markPolymerElement,
- setUpdateState: (state: MeshUpdateState, newProps: PolymerTraceProps, currentProps: PolymerTraceProps) => {
- state.createMesh = (
+ setUpdateState: (state: VisualUpdateState, newProps: PolymerTraceProps, currentProps: PolymerTraceProps) => {
+ state.createGeometry = (
newProps.linearSegments !== currentProps.linearSegments ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.aspectRatio !== currentProps.aspectRatio ||
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index 0dfb1317bd369f48ba0ec9f8590f0811f3cdba6b..1377c9cd97ed38a41c676cf841cac568e5a36463 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -8,12 +8,10 @@
import { Unit, Structure } from 'mol-model/structure';
import { createUniformColor, ColorData, createGroupColor, createGroupInstanceColor, createInstanceColor, ColorType } from '../../../../util/color-data';
import { createUniformSize, SizeData, createGroupSize, createGroupInstanceSize, createInstanceSize, SizeType } from '../../../../util/size-data';
-import { ValueCell } from 'mol-util';
import { LocationIterator } from '../../../../util/location-iterator';
-import { Mesh } from '../../../../mesh/mesh';
+import { Mesh } from '../../../../geometry/mesh/mesh';
import { MeshValues, PointValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../../util/mesh-data';
-import { MeshProps, createMeshValues, createRenderableState, createPointValues } from '../../../util';
import { StructureProps } from '../..';
import { createMarkers } from '../../../../util/marker-data';
import { createMeshRenderObject, createPointRenderObject } from 'mol-gl/render-object';
@@ -21,8 +19,10 @@ import { ColorThemeProps, ColorTheme } from 'mol-view/theme/color';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { RuntimeContext } from 'mol-task';
import { PointProps } from 'mol-geo/representation/structure/representation/point';
-import { fillSerial } from 'mol-util/array';
import { TransformData, createIdentityTransform, createTransforms } from '../../../../util/transform-data';
+import { Point } from '../../../../geometry/point/point';
+import { getPointData } from '../../../../util/point-data';
+import { MeshProps, createMeshValues, createRenderableState, createPointValues } from '../../../../geometry/geometry';
function getGranularity(locationIt: LocationIterator, granularity: ColorType | SizeType) {
// Always use 'group' granularity for 'complex' location iterators,
@@ -52,7 +52,7 @@ export async function createSizes(ctx: RuntimeContext, locationIt: LocationItera
// mesh
-type StructureMeshProps = Required<MeshProps & StructureProps>
+type StructureMeshProps = MeshProps & StructureProps
async function _createMeshValues(ctx: RuntimeContext, transforms: TransformData, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps): Promise<MeshValues> {
const { instanceCount, groupCount } = locationIt
@@ -100,19 +100,18 @@ export async function updateComplexMeshRenderObject(ctx: RuntimeContext, structu
// point
-type StructurePointProps = Required<PointProps & StructureProps>
+type StructurePointProps = PointProps & StructureProps
-async function _createPointValues(ctx: RuntimeContext, transforms: TransformData, vertices: ValueCell<Float32Array>, locationIt: LocationIterator, props: StructurePointProps): Promise<PointValues> {
+async function _createPointValues(ctx: RuntimeContext, transforms: TransformData, point: Point, locationIt: LocationIterator, props: StructurePointProps): Promise<PointValues> {
const { instanceCount, groupCount } = locationIt
const color = await createColors(ctx, locationIt, props.colorTheme)
const size = await createSizes(ctx, locationIt, props.sizeTheme)
const marker = createMarkers(instanceCount * groupCount)
- const counts = { drawCount: groupCount, groupCount, instanceCount }
+ const counts = { drawCount: point.vertexCount, groupCount, instanceCount }
return {
- aPosition: vertices,
- aGroup: ValueCell.create(fillSerial(new Float32Array(groupCount))),
+ ...getPointData(point),
...color,
...size,
...marker,
@@ -121,13 +120,13 @@ async function _createPointValues(ctx: RuntimeContext, transforms: TransformData
}
}
-export async function createUnitsPointValues(ctx: RuntimeContext, group: Unit.SymmetryGroup, vertices: ValueCell<Float32Array>, locationIt: LocationIterator, props: StructurePointProps): Promise<PointValues> {
+export async function createUnitsPointValues(ctx: RuntimeContext, group: Unit.SymmetryGroup, point: Point, locationIt: LocationIterator, props: StructurePointProps): Promise<PointValues> {
const transforms = createTransforms(group)
- return _createPointValues(ctx, transforms, vertices, locationIt, props)
+ return _createPointValues(ctx, transforms, point, locationIt, props)
}
-export async function createUnitsPointRenderObject(ctx: RuntimeContext, group: Unit.SymmetryGroup, vertices: ValueCell<Float32Array>, locationIt: LocationIterator, props: StructurePointProps) {
- const values = await createUnitsPointValues(ctx, group, vertices, locationIt, props)
+export async function createUnitsPointRenderObject(ctx: RuntimeContext, group: Unit.SymmetryGroup, point: Point, locationIt: LocationIterator, props: StructurePointProps) {
+ const values = await createUnitsPointValues(ctx, group, point, locationIt, props)
const state = createRenderableState(props)
return createPointRenderObject(values, state)
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index 6887addab337f1956adcb4c1645e2586c9bbd4ab..28d4f1add33e11152269038cf6aedc4052ba5851 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -8,14 +8,14 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { Unit, StructureElement, Structure } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task';
import { sphereVertexCount } from '../../../../primitive/sphere';
-import { Mesh } from '../../../../mesh/mesh';
-import { MeshBuilder } from '../../../../mesh/mesh-builder';
+import { Mesh } from '../../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../../geometry/mesh/mesh-builder';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { Interval, OrderedSet } from 'mol-data/int';
import { PickingId } from '../../../../util/picking';
import { SizeTheme, SizeThemeProps } from 'mol-view/theme/size';
import { LocationIterator } from '../../../../util/location-iterator';
-import { addSphere } from '../../../../mesh/builder/sphere';
+import { addSphere } from '../../../../geometry/mesh/builder/sphere';
export interface ElementSphereMeshProps {
sizeTheme: SizeThemeProps,
diff --git a/src/mol-geo/representation/structure/visual/util/gaussian.ts b/src/mol-geo/representation/structure/visual/util/gaussian.ts
new file mode 100644
index 0000000000000000000000000000000000000000..1607bbb7fb3f71ce0a4e5d0998da9fa1c05289de
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/util/gaussian.ts
@@ -0,0 +1,124 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+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';
+
+export interface GaussianDensityProps {
+ sizeTheme: SizeThemeProps
+
+ resolutionFactor: number
+ probeRadius: number
+ isoValue: number
+}
+
+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
+}
+
+type Density = { transform: Mat4, field: Tensor }
+
+export function computeGaussianDensity(unit: Unit, structure: Structure, props: GaussianDensityProps) {
+ return Task.create('Gaussian Density', async ctx => {
+ return await GaussianDensity(ctx, unit, structure, props);
+ });
+}
+
+export async function GaussianDensity(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps): Promise<Density> {
+ const { resolutionFactor, probeRadius, isoValue } = props
+
+ const { elements } = unit;
+ const elementCount = elements.length;
+ const sizeTheme = SizeTheme(props.sizeTheme)
+
+ 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 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)
+ const min = expandedBox.min
+
+ const delta = getDelta(Box3D.expand(Box3D.empty(), structure.boundary.box, Vec3.create(pad, pad, pad)), resolutionFactor)
+ const dim = Vec3.zero()
+ Vec3.ceil(dim, Vec3.mul(dim, extent, delta))
+
+ const space = Tensor.Space(dim, [0, 1, 2], Float32Array)
+ const data = space.create()
+ const field = Tensor.create(space, data)
+
+ const c = Vec3.zero()
+
+ const alpha = isoValue // smoothness
+
+ const _r2 = (probeRadius + 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]))
+
+ const beg = Vec3.zero()
+ const end = Vec3.zero()
+
+ for (let i = 0; i < elementCount; i++) {
+ l.element = elements[i]
+ pos(elements[i], v)
+
+ Vec3.sub(v, v, min)
+ Vec3.mul(c, v, delta)
+
+ const radius = sizeTheme.size(l) + probeRadius
+ const rSq = radius * radius
+
+ const r2 = (probeRadius + radius * 2)
+ const radius2 = Vec3.create(r2, r2, r2)
+ Vec3.mul(radius2, radius2, delta)
+ const r2sq = r2 * r2
+
+ const [ begX, begY, begZ ] = Vec3.floor(beg, Vec3.sub(beg, c, radius2))
+ const [ endX, endY, endZ ] = Vec3.ceil(end, Vec3.add(end, c, radius2))
+
+ for (let x = begX; x < endX; ++x) {
+ for (let y = begY; y < endY; ++y) {
+ for (let z = begZ; z < endZ; ++z) {
+ Vec3.set(p, x, y, z)
+ Vec3.div(p, p, delta)
+ const distSq = Vec3.squaredDistance(p, v)
+ if (distSq <= r2sq) {
+ space.add(data, x, y, z, Math.exp(-alpha * (distSq / rSq)))
+ }
+ }
+ }
+ }
+
+ if (i % updateChunk === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'filling density grid', current: i, max: elementCount });
+ }
+ }
+
+ const t = Mat4.identity()
+ Mat4.fromScaling(t, Vec3.inverse(Vec3.zero(), delta))
+ Mat4.setTranslation(t, expandedBox.min)
+
+ return {
+ field,
+ transform: t
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/link.ts b/src/mol-geo/representation/structure/visual/util/link.ts
index ca73e55b9cb017173c7cb9af15701e7aff21a1fc..b218c9cf2420e8da986886068bb0bb6349e22d50 100644
--- a/src/mol-geo/representation/structure/visual/util/link.ts
+++ b/src/mol-geo/representation/structure/visual/util/link.ts
@@ -6,15 +6,15 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { RuntimeContext } from 'mol-task';
-import { Mesh } from '../../../../mesh/mesh';
-import { MeshBuilder } from '../../../../mesh/mesh-builder';
+import { Mesh } from '../../../../geometry/mesh/mesh';
+import { MeshBuilder } from '../../../../geometry/mesh/mesh-builder';
import { LinkType } from 'mol-model/structure/model/types';
-import { DefaultMeshProps } from '../../../util';
import { SizeThemeProps } from 'mol-view/theme/size';
import { CylinderProps } from '../../../../primitive/cylinder';
import { LocationIterator } from '../../../../util/location-iterator';
import { Unit, StructureElement, Structure, Link } from 'mol-model/structure';
-import { addFixedCountDashedCylinder, addCylinder, addDoubleCylinder } from '../../../../mesh/builder/cylinder';
+import { addFixedCountDashedCylinder, addCylinder, addDoubleCylinder } from '../../../../geometry/mesh/builder/cylinder';
+import { DefaultMeshProps } from '../../../../geometry/geometry';
export const DefaultLinkCylinderProps = {
...DefaultMeshProps,
diff --git a/src/mol-geo/representation/util.ts b/src/mol-geo/representation/util.ts
index 48df84aa75bcdbd5b215c031c7144a7f7b4a330d..407ade0f2311b0472fd15688a57b63b555251444 100644
--- a/src/mol-geo/representation/util.ts
+++ b/src/mol-geo/representation/util.ts
@@ -4,97 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ValueCell } from 'mol-util/value-cell'
-import { BaseValues } from 'mol-gl/renderable/schema';
-import { MeshValues, RenderableState } from 'mol-gl/renderable';
import { defaults } from 'mol-util';
import { Structure } from 'mol-model/structure';
-
-export const DefaultBaseProps = {
- alpha: 1,
- visible: true,
- depthMask: true,
- useFog: false,
- quality: 'auto' as VisualQuality
-}
-export type BaseProps = typeof DefaultBaseProps
-
-export const DefaultMeshProps = {
- ...DefaultBaseProps,
- doubleSided: false,
- flipSided: false,
- flatShaded: false,
-}
-export type MeshProps = typeof DefaultMeshProps
-
-export const DefaultPointProps = {
- ...DefaultBaseProps,
- pointSizeAttenuation: true
-}
-export type PointProps = typeof DefaultPointProps
-
-type Counts = { drawCount: number, groupCount: number, instanceCount: number }
-
-export function createBaseValues(props: Required<BaseProps>, counts: Counts) {
- return {
- uAlpha: ValueCell.create(props.alpha),
- uGroupCount: ValueCell.create(counts.groupCount),
- drawCount: ValueCell.create(counts.drawCount),
- dUseFog: ValueCell.create(props.useFog),
- }
-}
-
-export function createMeshValues(props: Required<MeshProps>, counts: Counts) {
- return {
- ...createBaseValues(props, counts),
- dDoubleSided: ValueCell.create(props.doubleSided),
- dFlatShaded: ValueCell.create(props.flatShaded),
- dFlipSided: ValueCell.create(props.flipSided),
- }
-}
-
-export function createPointValues(props: Required<PointProps>, counts: Counts) {
- return {
- ...createBaseValues(props, counts),
- dPointSizeAttenuation: ValueCell.create(props.pointSizeAttenuation),
- }
-}
-
-export function createRenderableState(props: Required<BaseProps>): RenderableState {
- return {
- visible: props.visible,
- depthMask: props.depthMask
- }
-}
-
-export function updateBaseValues(values: BaseValues, props: Required<BaseProps>) {
- ValueCell.updateIfChanged(values.uAlpha, props.alpha)
- ValueCell.updateIfChanged(values.dUseFog, props.useFog)
-}
-
-export function updateMeshValues(values: MeshValues, props: Required<MeshProps>) {
- updateBaseValues(values, props)
- ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided)
- ValueCell.updateIfChanged(values.dFlatShaded, props.flatShaded)
- ValueCell.updateIfChanged(values.dFlipSided, props.flipSided)
-}
-
-export function updateRenderableState(state: RenderableState, props: Required<BaseProps>) {
- state.visible = props.visible
- state.depthMask = props.depthMask
-}
-
-export const VisualQualityInfo = {
- 'custom': {},
- 'auto': {},
- 'highest': {},
- 'high': {},
- 'medium': {},
- 'low': {},
- 'lowest': {},
-}
-export type VisualQuality = keyof typeof VisualQualityInfo
-export const VisualQualityNames = Object.keys(VisualQualityInfo)
+import { VisualQuality } from '../geometry/geometry';
export interface QualityProps {
quality: VisualQuality
diff --git a/src/mol-geo/representation/volume/index.ts b/src/mol-geo/representation/volume/index.ts
index 9197885d3c9cebb758d2cd37218437ec3164f561..0ddad3eeaba9ca880578380152e0bf4126026687 100644
--- a/src/mol-geo/representation/volume/index.ts
+++ b/src/mol-geo/representation/volume/index.ts
@@ -11,7 +11,7 @@ import { VolumeData } from 'mol-model/volume';
import { PickingId } from '../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction } from '../../util/marker-data';
-import { DefaultBaseProps } from '../util';
+import { DefaultBaseProps } from '../../geometry/geometry';
export interface VolumeVisual<P extends RepresentationProps = {}> extends Visual<VolumeData, P> { }
diff --git a/src/mol-geo/representation/volume/surface.ts b/src/mol-geo/representation/volume/surface.ts
index 46671107fcfff72a825598c02692718e6c1953b7..c621e43ebb6ea16b8a9260f8ac382bc7dfa1309a 100644
--- a/src/mol-geo/representation/volume/surface.ts
+++ b/src/mol-geo/representation/volume/surface.ts
@@ -8,7 +8,7 @@
import { VolumeData, VolumeIsoValue } from 'mol-model/volume'
import { Task, RuntimeContext } from 'mol-task'
import { computeMarchingCubes } from '../../util/marching-cubes/algorithm';
-import { Mesh } from '../../mesh/mesh';
+import { Mesh } from '../../geometry/mesh/mesh';
import { VolumeVisual } from '.';
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object';
import { ValueCell, defaults } from 'mol-util';
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 6ac77a8ffdb2e3411223ec1f4f0729bcb386547c..19393af7888be054c874c82d37949b5ecf24596e 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -7,7 +7,7 @@
import { Task, RuntimeContext } from 'mol-task'
import { ChunkedArray } from 'mol-data/util'
import { Tensor } from 'mol-math/linear-algebra'
-import { Mesh } from '../../mesh/mesh'
+import { Mesh } from '../../geometry/mesh/mesh'
import { Index, EdgeIdInfo, CubeEdges, EdgeTable, TriTable } from './tables'
import { ValueCell } from 'mol-util'
@@ -76,6 +76,7 @@ class MarchingCubesComputation {
const os = this.parameters.oldSurface
return {
+ kind: 'mesh',
vertexCount: this.state.vertexCount,
triangleCount: this.state.triangleCount,
vertexBuffer: os ? ValueCell.update(os.vertexBuffer, vb) : ValueCell.create(vb),
diff --git a/src/mol-geo/util/mesh-data.ts b/src/mol-geo/util/mesh-data.ts
index 0451ee98a8bfee2d7e2790c69a40a3144ca6ba69..37ed0291ce8843e72ac7068ddc8c4d23f6f7454d 100644
--- a/src/mol-geo/util/mesh-data.ts
+++ b/src/mol-geo/util/mesh-data.ts
@@ -5,7 +5,7 @@
*/
import { ValueCell } from 'mol-util/value-cell'
-import { Mesh } from '../mesh/mesh';
+import { Mesh } from '../geometry/mesh/mesh';
type MeshData = {
aPosition: ValueCell<Float32Array>,
diff --git a/src/mol-geo/util/point-data.ts b/src/mol-geo/util/point-data.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ce070cf7e9d34fb6bc418f3efa91b95af428d3e5
--- /dev/null
+++ b/src/mol-geo/util/point-data.ts
@@ -0,0 +1,20 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ValueCell } from 'mol-util/value-cell'
+import { Point } from '../geometry/point/point';
+
+type PointData = {
+ aPosition: ValueCell<Float32Array>,
+ aGroup: ValueCell<Float32Array>,
+}
+
+export function getPointData(point: Point): PointData {
+ return {
+ aPosition: point.vertexBuffer,
+ aGroup: point.groupBuffer,
+ }
+}
\ No newline at end of file
diff --git a/src/mol-io/reader/obj/parser.ts b/src/mol-io/reader/obj/parser.ts
index 46cd16ccb151b1fb0ab69afa873c83f33a09e0b8..046143b305b51530b1e8d0e1cad7f8cb097fa50c 100644
--- a/src/mol-io/reader/obj/parser.ts
+++ b/src/mol-io/reader/obj/parser.ts
@@ -6,7 +6,7 @@
import Result from '../result'
import { Task, RuntimeContext } from 'mol-task'
-import { Mesh } from 'mol-geo/mesh/mesh';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<Mesh>> {
// TODO
diff --git a/src/mol-math/linear-algebra/tensor.ts b/src/mol-math/linear-algebra/tensor.ts
index 4bcae46f7bd0db8987d0036ed8590ba804cd1d9c..0909730c58111245e1c2cf33ef46c49f648b31f7 100644
--- a/src/mol-math/linear-algebra/tensor.ts
+++ b/src/mol-math/linear-algebra/tensor.ts
@@ -20,6 +20,7 @@ export namespace Tensor {
create(array?: ArrayCtor): Tensor.Data,
get(data: Tensor.Data, ...coords: number[]): number
set(data: Tensor.Data, ...coordsAndValue: number[]): number
+ add(data: Tensor.Data, ...coordsAndValue: number[]): number
}
interface Layout {
@@ -45,8 +46,8 @@ export namespace Tensor {
export function Space(dimensions: number[], axisOrderSlowToFast: number[], ctor?: ArrayCtor): Space {
const layout = Layout(dimensions, axisOrderSlowToFast, ctor);
- const { get, set } = accessors(layout);
- return { rank: dimensions.length, dimensions, axisOrderSlowToFast, create: creator(layout), get, set };
+ const { get, set, add } = accessors(layout);
+ return { rank: dimensions.length, dimensions, axisOrderSlowToFast, create: creator(layout), get, set, add };
}
export function Data1(values: ArrayLike<number>): Data { return values as Data; }
@@ -98,52 +99,89 @@ export namespace Tensor {
return true;
}
- function accessors(layout: Layout): { get: Space['get'], set: Space['set'] } {
+ function accessors(layout: Layout): { get: Space['get'], set: Space['set'], add: Space['add'] } {
const { dimensions, axisOrderFastToSlow: ao } = layout;
switch (dimensions.length) {
- case 1: return { get: (t, d) => t[d], set: (t, d, x) => t[d] = x };
+ case 1: return {
+ get: (t, d) => t[d],
+ set: (t, d, x) => t[d] = x,
+ add: (t, d, x) => t[d] += x
+ };
case 2: {
// column major
if (ao[0] === 0 && ao[1] === 1) {
const rows = dimensions[0];
- return { get: (t, i, j) => t[j * rows + i], set: (t, i, j, x) => t[j * rows + i] = x };
+ return {
+ get: (t, i, j) => t[j * rows + i],
+ set: (t, i, j, x) => t[j * rows + i] = x,
+ add: (t, i, j, x) => t[j * rows + i] += x
+ };
}
if (ao[0] === 1 && ao[1] === 0) {
const cols = dimensions[1];
- return { get: (t, i, j) => t[i * cols + j], set: (t, i, j, x) => t[i * cols + j] = x };
+ return {
+ get: (t, i, j) => t[i * cols + j],
+ set: (t, i, j, x) => t[i * cols + j] = x,
+ add: (t, i, j, x) => t[i * cols + j] += x
+ };
}
throw new Error('bad axis order')
}
case 3: {
if (ao[0] === 0 && ao[1] === 1 && ao[2] === 2) { // 012 ijk
const u = dimensions[0], v = dimensions[1], uv = u * v;
- return { get: (t, i, j, k) => t[i + j * u + k * uv], set: (t, i, j, k, x ) => t[i + j * u + k * uv] = x };
+ return {
+ get: (t, i, j, k) => t[i + j * u + k * uv],
+ set: (t, i, j, k, x ) => t[i + j * u + k * uv] = x,
+ add: (t, i, j, k, x ) => t[i + j * u + k * uv] += x
+ };
}
if (ao[0] === 0 && ao[1] === 2 && ao[2] === 1) { // 021 ikj
const u = dimensions[0], v = dimensions[2], uv = u * v;
- return { get: (t, i, j, k) => t[i + k * u + j * uv], set: (t, i, j, k, x ) => t[i + k * u + j * uv] = x };
+ return {
+ get: (t, i, j, k) => t[i + k * u + j * uv],
+ set: (t, i, j, k, x ) => t[i + k * u + j * uv] = x,
+ add: (t, i, j, k, x ) => t[i + k * u + j * uv] += x
+ };
}
if (ao[0] === 1 && ao[1] === 0 && ao[2] === 2) { // 102 jik
const u = dimensions[1], v = dimensions[0], uv = u * v;
- return { get: (t, i, j, k) => t[j + i * u + k * uv], set: (t, i, j, k, x ) => t[j + i * u + k * uv] = x };
+ return {
+ get: (t, i, j, k) => t[j + i * u + k * uv],
+ set: (t, i, j, k, x ) => t[j + i * u + k * uv] = x,
+ add: (t, i, j, k, x ) => t[j + i * u + k * uv] += x
+ };
}
if (ao[0] === 1 && ao[1] === 2 && ao[2] === 0) { // 120 jki
const u = dimensions[1], v = dimensions[2], uv = u * v;
- return { get: (t, i, j, k) => t[j + k * u + i * uv], set: (t, i, j, k, x ) => t[j + k * u + i * uv] = x };
+ return {
+ get: (t, i, j, k) => t[j + k * u + i * uv],
+ set: (t, i, j, k, x ) => t[j + k * u + i * uv] = x,
+ add: (t, i, j, k, x ) => t[j + k * u + i * uv] += x
+ };
}
if (ao[0] === 2 && ao[1] === 0 && ao[2] === 1) { // 201 kij
const u = dimensions[2], v = dimensions[0], uv = u * v;
- return { get: (t, i, j, k) => t[k + i * u + j * uv], set: (t, i, j, k, x ) => t[k + i * u + j * uv] = x };
+ return {
+ get: (t, i, j, k) => t[k + i * u + j * uv],
+ set: (t, i, j, k, x ) => t[k + i * u + j * uv] = x,
+ add: (t, i, j, k, x ) => t[k + i * u + j * uv] += x
+ };
}
if (ao[0] === 2 && ao[1] === 1 && ao[2] === 0) { // 210 kji
const u = dimensions[2], v = dimensions[1], uv = u * v;
- return { get: (t, i, j, k) => t[k + j * u + i * uv], set: (t, i, j, k, x ) => t[k + j * u + i * uv] = x };
+ return {
+ get: (t, i, j, k) => t[k + j * u + i * uv],
+ set: (t, i, j, k, x ) => t[k + j * u + i * uv] = x,
+ add: (t, i, j, k, x ) => t[k + j * u + i * uv] += x
+ };
}
throw new Error('bad axis order')
}
default: return {
get: (t, ...c) => t[dataOffset(layout, c)],
- set: (t, ...c) => t[dataOffset(layout, c)] = c[c.length - 1]
+ set: (t, ...c) => t[dataOffset(layout, c)] = c[c.length - 1],
+ add: (t, ...c) => t[dataOffset(layout, c)] += c[c.length - 1]
};
}
}
diff --git a/src/mol-model/shape/shape.ts b/src/mol-model/shape/shape.ts
index ffc602342db05a6419dd471d38b755ff41c51fa3..b911bd340fa8432444d4253b4fbcbed3608a592e 100644
--- a/src/mol-model/shape/shape.ts
+++ b/src/mol-model/shape/shape.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Mesh } from 'mol-geo/mesh/mesh';
+import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { Color } from 'mol-util/color';
import { UUID, ValueCell } from 'mol-util';
import { OrderedSet } from 'mol-data/int';