From 84e6ebf57e80afe280bfc33b58e5cc78020384fe Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 9 Sep 2018 19:26:05 -0700
Subject: [PATCH] wip, gaussian surface
---
src/apps/canvas/structure-view.ts | 3 +
.../structure/representation/surface.ts | 47 ++++++
.../representation/structure/units-visual.ts | 6 +-
.../structure/visual/gaussian-surface-mesh.ts | 153 ++++++++++++++++++
.../visual/intra-unit-link-cylinder.ts | 4 +-
.../structure/visual/nucleotide-block-mesh.ts | 4 +-
.../visual/polymer-backbone-cylinder.ts | 4 +-
.../visual/polymer-direction-wedge.ts | 4 +-
.../structure/visual/polymer-gap-cylinder.ts | 4 +-
.../structure/visual/polymer-trace-mesh.ts | 4 +-
.../structure/visual/util/element.ts | 4 +-
11 files changed, 220 insertions(+), 17 deletions(-)
create mode 100644 src/mol-geo/representation/structure/representation/surface.ts
create mode 100644 src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
diff --git a/src/apps/canvas/structure-view.ts b/src/apps/canvas/structure-view.ts
index b381ab2f0..c5674578f 100644
--- a/src/apps/canvas/structure-view.ts
+++ b/src/apps/canvas/structure-view.ts
@@ -24,6 +24,7 @@ import { StructureRepresentation } from 'mol-geo/representation/structure';
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';
export interface StructureView {
readonly viewer: Viewer
@@ -66,6 +67,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const active: { [k: string]: boolean } = {
cartoon: true,
point: false,
+ surface: true,
ballAndStick: false,
carbohydrate: false,
spacefill: false,
@@ -76,6 +78,7 @@ export async function StructureView(viewer: Viewer, models: ReadonlyArray<Model>
const structureRepresentations: { [k: string]: StructureRepresentation<any> } = {
cartoon: CartoonRepresentation(),
+ surface: SurfaceRepresentation(),
point: PointRepresentation(),
ballAndStick: BallAndStickRepresentation(),
carbohydrate: CarbohydrateRepresentation(),
diff --git a/src/mol-geo/representation/structure/representation/surface.ts b/src/mol-geo/representation/structure/representation/surface.ts
new file mode 100644
index 000000000..7e95466e6
--- /dev/null
+++ b/src/mol-geo/representation/structure/representation/surface.ts
@@ -0,0 +1,47 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { UnitsRepresentation } from '..';
+import { GaussianSurfaceVisual, DefaultGaussianSurfaceProps } from '../visual/gaussian-surface-mesh';
+import { StructureRepresentation } from '../units-representation';
+import { Structure } from 'mol-model/structure';
+import { MarkerAction } from '../../../util/marker-data';
+import { Loci } from 'mol-model/loci';
+import { PickingId } from '../../../util/picking';
+
+export const DefaultSurfaceProps = {
+ ...DefaultGaussianSurfaceProps,
+}
+export type SurfaceProps = typeof DefaultSurfaceProps
+
+export type SurfaceRepresentation = StructureRepresentation<SurfaceProps>
+
+export function SurfaceRepresentation(): SurfaceRepresentation {
+ let currentProps: SurfaceProps
+ const gaussianRepr = UnitsRepresentation('Gaussian surface', GaussianSurfaceVisual)
+ return {
+ label: 'Surface',
+ get renderObjects() {
+ return [ ...gaussianRepr.renderObjects ]
+ },
+ get props() {
+ return { ...gaussianRepr.props }
+ },
+ createOrUpdate: (props: Partial<SurfaceProps> = {}, structure?: Structure) => {
+ currentProps = Object.assign({}, DefaultSurfaceProps, currentProps, props)
+ return gaussianRepr.createOrUpdate(currentProps, structure)
+ },
+ getLoci: (pickingId: PickingId) => {
+ return gaussianRepr.getLoci(pickingId)
+ },
+ mark: (loci: Loci, action: MarkerAction) => {
+ return gaussianRepr.mark(loci, action)
+ },
+ destroy() {
+ gaussianRepr.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 534764f3d..a98620a7f 100644
--- a/src/mol-geo/representation/structure/units-visual.ts
+++ b/src/mol-geo/representation/structure/units-visual.ts
@@ -32,7 +32,7 @@ export type UnitsMeshProps = typeof DefaultUnitsMeshProps
export interface UnitsMeshVisualBuilder<P extends UnitsMeshProps> {
defaultProps: P
- createMesh(ctx: RuntimeContext, unit: Unit, props: P, mesh?: Mesh): Promise<Mesh>
+ createMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: P, mesh?: Mesh): Promise<Mesh>
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
@@ -59,7 +59,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
const unit = group.units[0]
currentConformationId = Unit.conformationId(unit)
mesh = currentProps.unitKinds.includes(unit.kind)
- ? await createMesh(ctx, unit, currentProps, mesh)
+ ? await createMesh(ctx, unit, currentStructure, currentProps, mesh)
: Mesh.createEmpty(mesh)
// TODO create empty location iterator when not in unitKinds
@@ -102,7 +102,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
if (updateState.createMesh) {
mesh = newProps.unitKinds.includes(unit.kind)
- ? await createMesh(ctx, unit, newProps, mesh)
+ ? await createMesh(ctx, unit, currentStructure, newProps, mesh)
: Mesh.createEmpty(mesh)
ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
updateState.updateColor = true
diff --git a/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
new file mode 100644
index 000000000..6b894f5a5
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts
@@ -0,0 +1,153 @@
+/**
+ * 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 { UnitsVisual, MeshUpdateState } from '..';
+import { RuntimeContext } from 'mol-task'
+import { Mesh } from '../../../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 { ValueCell } from 'mol-util';
+import { smoothstep } from 'mol-math/interpolate';
+
+export interface GaussianSurfaceMeshProps {
+
+}
+
+function getDelta(box: Box3D) {
+ const extent = Vec3.sub(Vec3.zero(), box.max, box.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)
+ return delta
+}
+
+async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
+
+ const { elements } = unit;
+ const elementCount = elements.length;
+
+ const r = 2.5;
+
+ const v = Vec3.zero()
+ const p = Vec3.zero()
+ const pos = unit.conformation.invariantPosition
+ const box = unit.lookup3d.boundary.box
+ const expandedBox = Box3D.expand(Box3D.empty(), box, Vec3.create(r*3, r*3, r*3));
+ 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(r*3, r*3, r*3)))
+ 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)
+
+ for (let i = 0; i < elementCount; i++) {
+ pos(elements[i], v)
+
+ Vec3.mul(v, Vec3.sub(v, v, min), delta)
+
+ const size = r
+ const radius = size * delta[0]
+
+ const minX = Math.floor(v[0] - radius)
+ const minY = Math.floor(v[1] - radius)
+ const minZ = Math.floor(v[2] - radius)
+ const maxX = Math.floor(v[0] + radius)
+ const maxY = Math.floor(v[1] + radius)
+ const maxZ = Math.floor(v[2] + radius)
+
+ for (let x = minX; x <= maxX; ++x) {
+ for (let y = minY; y <= maxY; ++y) {
+ for (let z = minZ; z <= maxZ; ++z) {
+ const dist = Vec3.distance(Vec3.set(p, x, y, z), v)
+ if (dist <= radius) {
+ const density = 1.0 - smoothstep(0.0, radius * 1.0, dist)
+ space.set(data, x, y, z, space.get(data, x, y, z) + density)
+ }
+ }
+ }
+ }
+
+ if (i % 10000 === 0 && ctx.shouldUpdate) {
+ await ctx.update({ message: 'Gaussian surface', current: i, max: elementCount });
+ }
+ }
+
+ // console.log('data', data)
+
+ const surface = await computeMarchingCubes({
+ isoLevel: 0.1,
+ scalarField: field,
+ oldSurface: mesh
+
+ }).runAsChild(ctx);
+
+ const t = Mat4.identity()
+ Mat4.fromUniformScaling(t, 1 / delta[0])
+ Mat4.setTranslation(t, expandedBox.min)
+
+ ValueCell.update(surface.groupBuffer, new Float32Array(surface.vertexCount))
+ Mesh.transformImmediate(surface, t)
+ await Mesh.computeNormals(surface).runAsChild(ctx)
+
+ // console.log('surface', surface)
+
+ // const transform = VolumeData.getGridToCartesianTransform(volume);
+ // ctx.update({ message: 'Transforming mesh...' });
+ // Mesh.transformImmediate(surface, transform);
+
+ return surface;
+}
+
+export const DefaultGaussianSurfaceProps = {
+ ...DefaultUnitsMeshProps,
+ linearSegments: 8,
+ radialSegments: 12,
+ aspectRatio: 5,
+ arrowFactor: 1.5,
+
+ flipSided: true,
+ // flatShaded: true,
+}
+export type GaussianSurfaceProps = typeof DefaultGaussianSurfaceProps
+
+export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceProps> {
+ return UnitsMeshVisual<GaussianSurfaceProps>({
+ defaultProps: DefaultGaussianSurfaceProps,
+ createMesh: createGaussianSurfaceMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement,
+ setUpdateState: (state: MeshUpdateState, newProps: GaussianSurfaceProps, currentProps: GaussianSurfaceProps) => {}
+ })
+}
\ No newline at end of file
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 9b9452a41..a3d6dd868 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
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Unit, Link, StructureElement } from 'mol-model/structure';
+import { Unit, Link, StructureElement, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh, LinkIterator } from './util/link';
@@ -18,7 +18,7 @@ import { Interval } from 'mol-data/int';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { BitFlags } from 'mol-util';
-async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, props: LinkCylinderProps, mesh?: Mesh) {
+async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const sizeTheme = SizeTheme(props.sizeTheme)
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 8b5d893ef..dcf176ba3 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -33,7 +33,7 @@ const sVec = Vec3.zero()
const box = Box()
// TODO define props, should be scalable
-async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
+async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: {}, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
// TODO better vertex count estimate
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 d975ae940..cd9ca682c 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -23,7 +23,7 @@ export interface PolymerBackboneCylinderProps {
radialSegments: number
}
-async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
+async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
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 1e6b8e42a..bf6afd3f8 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -32,7 +32,7 @@ export interface PolymerDirectionWedgeProps {
sizeTheme: SizeThemeProps
}
-async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit, props: PolymerDirectionWedgeProps, mesh?: Mesh) {
+async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerDirectionWedgeProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
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 24038dfc3..21ebafc2d 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -24,7 +24,7 @@ export interface PolymerGapCylinderProps {
radialSegments: number
}
-async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, props: PolymerGapCylinderProps, mesh?: Mesh) {
+async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerGapCylinderProps, mesh?: Mesh) {
const polymerGapCount = unit.gapElements.length
if (!polymerGapCount) return Mesh.createEmpty(mesh)
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 1a37e4d98..685b0d3c4 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
+import { Unit, Structure } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../mesh/mesh';
@@ -26,7 +26,7 @@ export interface PolymerTraceMeshProps {
// TODO handle polymer ends properly
-async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, props: PolymerTraceMeshProps, mesh?: Mesh) {
+async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: PolymerTraceMeshProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index 0de1861ee..6887addab 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -5,7 +5,7 @@
*/
import { Vec3 } from 'mol-math/linear-algebra';
-import { Unit, StructureElement } from 'mol-model/structure';
+import { Unit, StructureElement, Structure } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task';
import { sphereVertexCount } from '../../../../primitive/sphere';
import { Mesh } from '../../../../mesh/mesh';
@@ -22,7 +22,7 @@ export interface ElementSphereMeshProps {
detail: number,
}
-export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, props: ElementSphereMeshProps, mesh?: Mesh) {
+export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: ElementSphereMeshProps, mesh?: Mesh) {
const { detail } = props
const { elements } = unit;
--
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