From be7d6cfbe1cf8323f0c9c2b21e4a0380d84e0b90 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 24 Nov 2018 19:31:15 -0800
Subject: [PATCH] wip
---
src/mol-repr/representation.ts | 2 +-
.../structure/complex-representation.ts | 2 +-
src/mol-repr/structure/complex-visual.ts | 18 +--
src/mol-repr/structure/registry.ts | 4 +-
.../representation/molecular-surface.ts | 84 +++++------
.../structure/units-representation.ts | 15 +-
src/mol-repr/structure/units-visual.ts | 18 +--
.../visual/carbohydrate-link-cylinder.ts | 2 +-
.../visual/carbohydrate-symbol-mesh.ts | 6 +-
.../carbohydrate-terminal-link-cylinder.ts | 2 +-
.../visual/cross-link-restraint-cylinder.ts | 2 +-
.../structure/visual/element-point.ts | 6 +-
.../visual/gaussian-density-point.ts | 130 +++++++++---------
.../visual/gaussian-density-volume.ts | 96 ++++++-------
.../structure/visual/gaussian-surface-mesh.ts | 102 +++++++-------
.../visual/gaussian-surface-wireframe.ts | 100 +++++++-------
.../visual/inter-unit-link-cylinder.ts | 2 +-
.../visual/intra-unit-link-cylinder.ts | 2 +-
.../structure/visual/nucleotide-block-mesh.ts | 5 +-
.../visual/polymer-backbone-cylinder.ts | 9 +-
.../visual/polymer-direction-wedge.ts | 5 +-
.../structure/visual/polymer-gap-cylinder.ts | 5 +-
.../structure/visual/polymer-trace-mesh.ts | 5 +-
src/mol-repr/structure/visual/util/element.ts | 6 +-
src/mol-repr/structure/visual/util/link.ts | 6 +-
25 files changed, 303 insertions(+), 331 deletions(-)
diff --git a/src/mol-repr/representation.ts b/src/mol-repr/representation.ts
index b990ba87a..139019a52 100644
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/representation.ts
@@ -243,7 +243,7 @@ export interface Visual<D, P extends PD.Params> {
/** Number of addressable groups in all instances of the visual */
readonly groupCount: number
readonly renderObject: RenderObject | undefined
- createOrUpdate: (ctx: VisualContext, theme: Theme, props?: Partial<PD.Values<P>>, data?: D) => Promise<void>
+ createOrUpdate: (ctx: VisualContext, theme: Theme, props?: Partial<PD.Values<P>>, data?: D) => void
getLoci: (pickingId: PickingId) => Loci
mark: (loci: Loci, action: MarkerAction) => boolean
setVisibility: (value: boolean) => void
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index 2bbfa2955..40e528521 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -38,7 +38,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
return Task.create('Creating or updating ComplexRepresentation', async runtime => {
if (!visual) visual = visualCtor()
- await visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, structure)
+ visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, structure)
updated.next(version++)
});
}
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 65086af89..5d028dd7a 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -38,7 +38,7 @@ type ComplexRenderObject = MeshRenderObject | LinesRenderObject | PointsRenderOb
interface ComplexVisualBuilder<P extends ComplexParams, G extends Geometry> {
defaultProps: PD.Values<P>
- createGeometry(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G>
+ createGeometry(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): G
createLocationIterator(structure: Structure): LocationIterator
getLoci(pickingId: PickingId, structure: Structure, id: number): Loci
mark(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean,
@@ -65,19 +65,19 @@ export function ComplexVisual<P extends ComplexParams>(builder: ComplexVisualGeo
let locationIt: LocationIterator
let conformationHash: number
- async function create(ctx: VisualContext, structure: Structure, theme: Theme, props: Partial<PD.Values<P>> = {}) {
+ function create(ctx: VisualContext, structure: Structure, theme: Theme, props: Partial<PD.Values<P>> = {}) {
currentProps = Object.assign({}, defaultProps, props)
currentTheme = theme
currentStructure = structure
conformationHash = Structure.conformationHash(currentStructure)
- geometry = await createGeometry(ctx, currentStructure, theme, currentProps, geometry)
+ geometry = createGeometry(ctx, currentStructure, theme, currentProps, geometry)
locationIt = createLocationIterator(structure)
renderObject = createRenderObject(structure, geometry, locationIt, theme, currentProps)
}
- async function update(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>>) {
+ function update(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>>) {
const newProps = Object.assign({}, currentProps, props, { structure: currentStructure })
if (!renderObject) return false
@@ -98,7 +98,7 @@ export function ComplexVisual<P extends ComplexParams>(builder: ComplexVisualGeo
//
if (updateState.createGeometry) {
- geometry = await createGeometry(ctx, currentStructure, theme, newProps, geometry)
+ geometry = createGeometry(ctx, currentStructure, theme, newProps, geometry)
ValueCell.update(renderObject.values.drawCount, Geometry.getDrawCount(geometry))
updateBoundingSphere(renderObject.values, geometry)
updateState.updateColor = true
@@ -126,18 +126,18 @@ export function ComplexVisual<P extends ComplexParams>(builder: ComplexVisualGeo
return {
get groupCount() { return locationIt ? locationIt.count : 0 },
get renderObject () { return renderObject },
- async createOrUpdate(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>> = {}, structure?: Structure) {
+ createOrUpdate(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>> = {}, structure?: Structure) {
if (!structure && !currentStructure) {
throw new Error('missing structure')
} else if (structure && (!currentStructure || !renderObject)) {
- await create(ctx, structure, theme, props)
+ create(ctx, structure, theme, props)
} else if (structure && !Structure.areEquivalent(structure, currentStructure)) {
- await create(ctx, structure, theme, props)
+ create(ctx, structure, theme, props)
} else {
if (structure && Structure.conformationHash(structure) !== Structure.conformationHash(currentStructure)) {
currentStructure = structure
}
- await update(ctx, theme, props)
+ update(ctx, theme, props)
}
},
getLoci(pickingId: PickingId) {
diff --git a/src/mol-repr/structure/registry.ts b/src/mol-repr/structure/registry.ts
index 058a9c178..16d90e630 100644
--- a/src/mol-repr/structure/registry.ts
+++ b/src/mol-repr/structure/registry.ts
@@ -8,7 +8,7 @@ import { Structure } from 'mol-model/structure';
import { RepresentationProvider, RepresentationRegistry } from '../representation';
import { CartoonRepresentationProvider } from './representation/cartoon';
import { BallAndStickRepresentationProvider } from './representation/ball-and-stick';
-import { MolecularSurfaceRepresentationProvider } from './representation/molecular-surface';
+// import { MolecularSurfaceRepresentationProvider } from './representation/molecular-surface';
import { CarbohydrateRepresentationProvider } from './representation/carbohydrate';
export class StructureRepresentationRegistry extends RepresentationRegistry<Structure> {
@@ -24,7 +24,7 @@ export class StructureRepresentationRegistry extends RepresentationRegistry<Stru
export const BuiltInStructureRepresentations = {
'cartoon': CartoonRepresentationProvider,
'ball-and-stick': BallAndStickRepresentationProvider,
- 'molecular-surface': MolecularSurfaceRepresentationProvider,
+ // 'molecular-surface': MolecularSurfaceRepresentationProvider,
'carbohydrate': CarbohydrateRepresentationProvider,
}
export type BuiltInStructureRepresentationsName = keyof typeof BuiltInStructureRepresentations
diff --git a/src/mol-repr/structure/representation/molecular-surface.ts b/src/mol-repr/structure/representation/molecular-surface.ts
index 4181217d3..02182081e 100644
--- a/src/mol-repr/structure/representation/molecular-surface.ts
+++ b/src/mol-repr/structure/representation/molecular-surface.ts
@@ -1,47 +1,47 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
+// /**
+// * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author Alexander Rose <alexander.rose@weirdbyte.de>
+// */
-import { GaussianSurfaceVisual, GaussianSurfaceParams } from '../visual/gaussian-surface-mesh';
-import { UnitsRepresentation } from '../units-representation';
-import { GaussianWireframeVisual, GaussianWireframeParams } from '../visual/gaussian-surface-wireframe';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { GaussianDensityVolumeParams, GaussianDensityVolumeVisual } from '../visual/gaussian-density-volume';
-import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
-import { Representation, RepresentationParamsGetter, RepresentationContext } from 'mol-repr/representation';
-import { ThemeRegistryContext } from 'mol-theme/theme';
-import { Structure } from 'mol-model/structure';
+// import { GaussianSurfaceVisual, GaussianSurfaceParams } from '../visual/gaussian-surface-mesh';
+// import { UnitsRepresentation } from '../units-representation';
+// import { GaussianWireframeVisual, GaussianWireframeParams } from '../visual/gaussian-surface-wireframe';
+// import { ParamDefinition as PD } from 'mol-util/param-definition';
+// import { GaussianDensityVolumeParams, GaussianDensityVolumeVisual } from '../visual/gaussian-density-volume';
+// import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
+// import { Representation, RepresentationParamsGetter, RepresentationContext } from 'mol-repr/representation';
+// import { ThemeRegistryContext } from 'mol-theme/theme';
+// import { Structure } from 'mol-model/structure';
-const MolecularSurfaceVisuals = {
- 'gaussian-surface': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianSurfaceParams>) => UnitsRepresentation('Gaussian surface', ctx, getParams, GaussianSurfaceVisual),
- 'gaussian-wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianWireframeParams>) => UnitsRepresentation('Gaussian wireframe', ctx, getParams, GaussianWireframeVisual),
- 'gaussian-volume': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianDensityVolumeParams>) => UnitsRepresentation('Gaussian volume', ctx, getParams, GaussianDensityVolumeVisual)
-}
-type MolecularSurfaceVisualName = keyof typeof MolecularSurfaceVisuals
-const MolecularSurfaceVisualOptions = Object.keys(MolecularSurfaceVisuals).map(name => [name, name] as [MolecularSurfaceVisualName, string])
+// const MolecularSurfaceVisuals = {
+// 'gaussian-surface': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianSurfaceParams>) => UnitsRepresentation('Gaussian surface', ctx, getParams, GaussianSurfaceVisual),
+// 'gaussian-wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianWireframeParams>) => UnitsRepresentation('Gaussian wireframe', ctx, getParams, GaussianWireframeVisual),
+// 'gaussian-volume': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianDensityVolumeParams>) => UnitsRepresentation('Gaussian volume', ctx, getParams, GaussianDensityVolumeVisual)
+// }
+// type MolecularSurfaceVisualName = keyof typeof MolecularSurfaceVisuals
+// const MolecularSurfaceVisualOptions = Object.keys(MolecularSurfaceVisuals).map(name => [name, name] as [MolecularSurfaceVisualName, string])
-export const MolecularSurfaceParams = {
- ...GaussianSurfaceParams,
- ...GaussianWireframeParams,
- ...GaussianDensityVolumeParams,
- visuals: PD.MultiSelect<MolecularSurfaceVisualName>(['gaussian-surface'], MolecularSurfaceVisualOptions),
-}
-export type MolecularSurfaceParams = typeof MolecularSurfaceParams
-export function getMolecularSurfaceParams(ctx: ThemeRegistryContext, structure: Structure) {
- return PD.clone(MolecularSurfaceParams)
-}
+// export const MolecularSurfaceParams = {
+// ...GaussianSurfaceParams,
+// ...GaussianWireframeParams,
+// ...GaussianDensityVolumeParams,
+// visuals: PD.MultiSelect<MolecularSurfaceVisualName>(['gaussian-surface'], MolecularSurfaceVisualOptions),
+// }
+// export type MolecularSurfaceParams = typeof MolecularSurfaceParams
+// export function getMolecularSurfaceParams(ctx: ThemeRegistryContext, structure: Structure) {
+// return PD.clone(MolecularSurfaceParams)
+// }
-export type MolecularSurfaceRepresentation = StructureRepresentation<MolecularSurfaceParams>
-export function MolecularSurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MolecularSurfaceParams>): MolecularSurfaceRepresentation {
- return Representation.createMulti('Molecular Surface', ctx, getParams, MolecularSurfaceVisuals as unknown as Representation.Def<Structure, MolecularSurfaceParams>)
-}
+// export type MolecularSurfaceRepresentation = StructureRepresentation<MolecularSurfaceParams>
+// export function MolecularSurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MolecularSurfaceParams>): MolecularSurfaceRepresentation {
+// return Representation.createMulti('Molecular Surface', ctx, getParams, MolecularSurfaceVisuals as unknown as Representation.Def<Structure, MolecularSurfaceParams>)
+// }
-export const MolecularSurfaceRepresentationProvider: StructureRepresentationProvider<MolecularSurfaceParams> = {
- label: 'Molecular Surface',
- description: 'Displays a gaussian molecular surface.',
- factory: MolecularSurfaceRepresentation,
- getParams: getMolecularSurfaceParams,
- defaultValues: PD.getDefaultValues(MolecularSurfaceParams)
-}
\ No newline at end of file
+// export const MolecularSurfaceRepresentationProvider: StructureRepresentationProvider<MolecularSurfaceParams> = {
+// label: 'Molecular Surface',
+// description: 'Displays a gaussian molecular surface.',
+// factory: MolecularSurfaceRepresentation,
+// getParams: getMolecularSurfaceParams,
+// defaultValues: PD.getDefaultValues(MolecularSurfaceParams)
+// }
\ No newline at end of file
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 01b381c9e..59ba0b2fa 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -56,8 +56,9 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
for (let i = 0; i < _groups.length; i++) {
const group = _groups[i];
const visual = visualCtor()
- await visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
+ visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
visuals.set(group.hashCode, { visual, group })
+ if (runtime.shouldUpdate) await runtime.update({ message: 'Creating or updating UnitsVisual', current: i, max: _groups.length })
}
} else if (structure && !Structure.areEquivalent(structure, _structure)) {
// console.log(label, 'structure not equivalent')
@@ -75,16 +76,17 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
// console.log('old', visualGroup.group)
// console.log('new', group)
const { visual } = visualGroup
- await visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
+ visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
visuals.set(group.hashCode, { visual, group })
oldVisuals.delete(group.hashCode)
} else {
// console.log(label, 'not found visualGroup to reuse, creating new')
// newGroups.push(group)
const visual = visualCtor()
- await visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
+ visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
visuals.set(group.hashCode, { visual, group })
}
+ if (runtime.shouldUpdate) await runtime.update({ message: 'Creating or updating UnitsVisual', current: i, max: _groups.length })
}
oldVisuals.forEach(({ visual }) => {
// console.log(label, 'removed unused visual')
@@ -113,11 +115,13 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
const group = _groups[i];
const visualGroup = visuals.get(group.hashCode)
if (visualGroup) {
- await visualGroup.visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
+ visualGroup.visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props, { group, structure })
visualGroup.group = group
+
} else {
throw new Error(`expected to find visual for hashCode ${group.hashCode}`)
}
+ if (runtime.shouldUpdate) await runtime.update({ message: 'Creating or updating UnitsVisual', current: i, max: _groups.length })
}
} else {
// console.log(label, 'no new structure')
@@ -126,7 +130,8 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
visuals.forEach(({ visual, group }) => visualsList.push([ visual, group ]))
for (let i = 0, il = visualsList.length; i < il; ++i) {
const [ visual ] = visualsList[i]
- await visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props)
+ visual.createOrUpdate({ webgl: ctx.webgl, runtime }, _theme, _props)
+ if (runtime.shouldUpdate) await runtime.update({ message: 'Creating or updating UnitsVisual', current: i, max: il })
}
}
if (structure) _structure = structure
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 6fde0097d..cc6409d48 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -38,7 +38,7 @@ type UnitsRenderObject = MeshRenderObject | LinesRenderObject | PointsRenderObje
interface UnitsVisualBuilder<P extends UnitsParams, G extends Geometry> {
defaultProps: PD.Values<P>
- createGeometry(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G>
+ createGeometry(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): G
createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
getLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Loci
mark(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean
@@ -66,7 +66,7 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
let locationIt: LocationIterator
let currentConformationId: UUID
- async function create(ctx: VisualContext, group: Unit.SymmetryGroup, theme: Theme, props: Partial<PD.Values<P>> = {}) {
+ function create(ctx: VisualContext, group: Unit.SymmetryGroup, theme: Theme, props: Partial<PD.Values<P>> = {}) {
currentProps = Object.assign({}, defaultProps, props, { structure: currentStructure })
currentTheme = theme
currentGroup = group
@@ -74,7 +74,7 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
const unit = group.units[0]
currentConformationId = Unit.conformationId(unit)
geometry = includesUnitKind(currentProps.unitKinds, unit)
- ? await createGeometry(ctx, unit, currentStructure, theme, currentProps, geometry)
+ ? createGeometry(ctx, unit, currentStructure, theme, currentProps, geometry)
: createEmptyGeometry(geometry)
// TODO create empty location iterator when not in unitKinds
@@ -82,7 +82,7 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
renderObject = createRenderObject(group, geometry, locationIt, theme, currentProps)
}
- async function update(ctx: VisualContext, group: Unit.SymmetryGroup, theme: Theme, props: Partial<PD.Values<P>> = {}) {
+ function update(ctx: VisualContext, group: Unit.SymmetryGroup, theme: Theme, props: Partial<PD.Values<P>> = {}) {
if (!renderObject) return
const newProps = Object.assign({}, currentProps, props, { structure: currentStructure })
@@ -137,7 +137,7 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
if (updateState.createGeometry) {
// console.log('update geometry')
geometry = includesUnitKind(newProps.unitKinds, unit)
- ? await createGeometry(ctx, unit, currentStructure, theme, newProps, geometry)
+ ? createGeometry(ctx, unit, currentStructure, theme, newProps, geometry)
: createEmptyGeometry(geometry)
ValueCell.update(renderObject.values.drawCount, Geometry.getDrawCount(geometry))
updateBoundingSphere(renderObject.values, geometry)
@@ -168,20 +168,20 @@ export function UnitsVisual<P extends UnitsParams>(builder: UnitsVisualGeometryB
return {
get groupCount() { return locationIt ? locationIt.count : 0 },
get renderObject () { return renderObject },
- async createOrUpdate(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<P>> = {}, structureGroup?: StructureGroup) {
+ createOrUpdate(ctx: VisualContext, theme: Theme, props: Partial<PD.Values<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, theme, props)
+ create(ctx, group, theme, props)
} else if (group && group.hashCode !== currentGroup.hashCode) {
// console.log('unit-visual group.hashCode !== currentGroup.hashCode')
- await create(ctx, group, theme, props)
+ create(ctx, group, theme, props)
} else {
// console.log('unit-visual update')
- await update(ctx, group || currentGroup, theme, props)
+ update(ctx, group || currentGroup, theme, props)
}
},
getLoci(pickingId: PickingId) {
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index f4365b289..0eebe27e7 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -21,7 +21,7 @@ import { VisualUpdateState } from '../../util';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateLinkParams>, mesh?: Mesh) {
+function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateLinkParams>, mesh?: Mesh) {
const { links, elements } = structure.carbohydrates
const { linkSizeFactor } = props
diff --git a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
index dbdf3ada0..cf9162b15 100644
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
@@ -44,7 +44,7 @@ const diamondPrism = DiamondPrism()
const pentagonalPrism = PentagonalPrism()
const hexagonalPrism = HexagonalPrism()
-async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateSymbolParams>, mesh?: Mesh) {
+function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateSymbolParams>, mesh?: Mesh) {
const builder = MeshBuilder.create(256, 128, mesh)
const { detail, sizeFactor } = props
@@ -136,10 +136,6 @@ async function createCarbohydrateSymbolMesh(ctx: VisualContext, structure: Struc
builder.add(t, hexagonalPrism)
break
}
-
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Carbohydrate symbols', current: i, max: n });
- }
}
return builder.getMesh()
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
index fe9d2414e..44231be6d 100644
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -21,7 +21,7 @@ import { VisualUpdateState } from '../../util';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateTerminalLinkParams>, mesh?: Mesh) {
+function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CarbohydrateTerminalLinkParams>, mesh?: Mesh) {
const { terminalLinks, elements } = structure.carbohydrates
const { linkSizeFactor } = props
diff --git a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
index 25303be9e..9412dd09c 100644
--- a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
@@ -21,7 +21,7 @@ import { PickingId } from 'mol-geo/geometry/picking';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CrossLinkRestraintParams>, mesh?: Mesh) {
+function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CrossLinkRestraintParams>, mesh?: Mesh) {
const crossLinks = structure.crossLinkRestraints
if (!crossLinks.count) return Mesh.createEmpty(mesh)
diff --git a/src/mol-repr/structure/visual/element-point.ts b/src/mol-repr/structure/visual/element-point.ts
index 2b146bde3..71f5d4b1f 100644
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -24,7 +24,7 @@ export type ElementPointParams = typeof ElementPointParams
// TODO size
-export async function createElementPoint(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementPointParams>, points: Points) {
+export function createElementPoint(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementPointParams>, points: Points) {
const elements = unit.elements
const n = elements.length
const builder = PointsBuilder.create(n, n / 10, points)
@@ -35,10 +35,6 @@ export async function createElementPoint(ctx: VisualContext, unit: Unit, structu
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.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Creating points', current: i, max: n });
- }
}
return builder.getPoints()
}
diff --git a/src/mol-repr/structure/visual/gaussian-density-point.ts b/src/mol-repr/structure/visual/gaussian-density-point.ts
index 6a7e20353..612bc5f01 100644
--- a/src/mol-repr/structure/visual/gaussian-density-point.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-point.ts
@@ -1,73 +1,73 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
+// /**
+// * 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 } from '../representation';
-import { VisualUpdateState } from '../../util';
-import { StructureElementIterator } from './util/element';
-import { EmptyLoci } from 'mol-model/loci';
-import { Vec3 } from 'mol-math/linear-algebra';
-import { UnitsPointsVisual, UnitsPointsParams } from '../units-visual';
-import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { Points } from 'mol-geo/geometry/points/points';
-import { PointsBuilder } from 'mol-geo/geometry/points/points-builder';
-import { VisualContext } from 'mol-repr/representation';
-import { Theme } from 'mol-theme/theme';
+// import { Unit, Structure } from 'mol-model/structure';
+// import { UnitsVisual } from '../representation';
+// import { VisualUpdateState } from '../../util';
+// import { StructureElementIterator } from './util/element';
+// import { EmptyLoci } from 'mol-model/loci';
+// import { Vec3 } from 'mol-math/linear-algebra';
+// import { UnitsPointsVisual, UnitsPointsParams } from '../units-visual';
+// import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
+// import { ParamDefinition as PD } from 'mol-util/param-definition';
+// import { Points } from 'mol-geo/geometry/points/points';
+// import { PointsBuilder } from 'mol-geo/geometry/points/points-builder';
+// import { VisualContext } from 'mol-repr/representation';
+// import { Theme } from 'mol-theme/theme';
-export const GaussianDensityPointParams = {
- ...UnitsPointsParams,
- ...GaussianDensityParams,
- pointSizeAttenuation: PD.Boolean(false),
-}
-export type GaussianDensityPointParams = typeof GaussianDensityPointParams
+// export const GaussianDensityPointParams = {
+// ...UnitsPointsParams,
+// ...GaussianDensityParams,
+// pointSizeAttenuation: PD.Boolean(false),
+// }
+// export type GaussianDensityPointParams = typeof GaussianDensityPointParams
-export async function createGaussianDensityPoint(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, points?: Points) {
- const { transform, field: { space, data } } = await unit.computeGaussianDensity(props, ctx.runtime, ctx.webgl)
+// export async function createGaussianDensityPoint(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, points?: Points) {
+// const { transform, field: { space, data } } = await unit.computeGaussianDensity(props, ctx.runtime, ctx.webgl)
- const { dimensions, get } = space
- const [ xn, yn, zn ] = dimensions
+// const { dimensions, get } = space
+// const [ xn, yn, zn ] = dimensions
- const n = xn * yn * zn * 3
- const builder = PointsBuilder.create(n, n / 10, points)
+// const n = xn * yn * zn * 3
+// const builder = PointsBuilder.create(n, n / 10, points)
- const p = Vec3.zero()
- let i = 0
+// 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.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Creating density points', current: i, max: n });
- }
- ++i
- }
- }
- }
- return builder.getPoints()
-}
+// 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.runtime.shouldUpdate) {
+// await ctx.runtime.update({ message: 'Creating density points', current: i, max: n });
+// }
+// ++i
+// }
+// }
+// }
+// return builder.getPoints()
+// }
-export function GaussianDensityPointVisual(): UnitsVisual<GaussianDensityPointParams> {
- return UnitsPointsVisual<GaussianDensityPointParams>({
- defaultProps: PD.getDefaultValues(GaussianDensityPointParams),
- createGeometry: createGaussianDensityPoint,
- createLocationIterator: StructureElementIterator.fromGroup,
- getLoci: () => EmptyLoci,
- mark: () => false,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianDensityPointParams>, currentProps: PD.Values<GaussianDensityPointParams>) => {
- if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
- if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
- if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
- if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
- if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
- }
- })
-}
\ No newline at end of file
+// export function GaussianDensityPointVisual(): UnitsVisual<GaussianDensityPointParams> {
+// return UnitsPointsVisual<GaussianDensityPointParams>({
+// defaultProps: PD.getDefaultValues(GaussianDensityPointParams),
+// createGeometry: createGaussianDensityPoint,
+// createLocationIterator: StructureElementIterator.fromGroup,
+// getLoci: () => EmptyLoci,
+// mark: () => false,
+// setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianDensityPointParams>, currentProps: PD.Values<GaussianDensityPointParams>) => {
+// if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
+// if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+// if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
+// if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
+// if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
+// }
+// })
+// }
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index 6e94b12ee..1f5c32fa1 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -1,54 +1,54 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
+// /**
+// * 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 } from '../representation';
-import { VisualUpdateState } from '../../util';
-import { UnitsDirectVolumeVisual, UnitsDirectVolumeParams } from '../units-visual';
-import { StructureElementIterator, getElementLoci, markElement } from './util/element';
-import { GaussianDensityProps, GaussianDensityParams, computeUnitGaussianDensityTexture } from 'mol-model/structure/structure/unit/gaussian-density';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { DirectVolume } from 'mol-geo/geometry/direct-volume/direct-volume';
-import { VisualContext } from 'mol-repr/representation';
-import { Theme } from 'mol-theme/theme';
+// import { Unit, Structure } from 'mol-model/structure';
+// import { UnitsVisual } from '../representation';
+// import { VisualUpdateState } from '../../util';
+// import { UnitsDirectVolumeVisual, UnitsDirectVolumeParams } from '../units-visual';
+// import { StructureElementIterator, getElementLoci, markElement } from './util/element';
+// import { GaussianDensityProps, GaussianDensityParams, computeUnitGaussianDensityTexture } from 'mol-model/structure/structure/unit/gaussian-density';
+// import { ParamDefinition as PD } from 'mol-util/param-definition';
+// import { DirectVolume } from 'mol-geo/geometry/direct-volume/direct-volume';
+// import { VisualContext } from 'mol-repr/representation';
+// import { Theme } from 'mol-theme/theme';
-async function createGaussianDensityVolume(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, directVolume?: DirectVolume): Promise<DirectVolume> {
- const { runtime, webgl } = ctx
- if (webgl === undefined) throw new Error('createGaussianDensityVolume requires `webgl` object in VisualContext')
+// async function createGaussianDensityVolume(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, directVolume?: DirectVolume): Promise<DirectVolume> {
+// const { runtime, webgl } = ctx
+// if (webgl === undefined) throw new Error('createGaussianDensityVolume requires `webgl` object in VisualContext')
- const p = { ...props, useGpu: true }
- const oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined
- const densityTextureData = await computeUnitGaussianDensityTexture(unit, p, webgl, oldTexture).runInContext(runtime)
- const { transform, texture, bbox, gridDimension } = densityTextureData
+// const p = { ...props, useGpu: true }
+// const oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined
+// const densityTextureData = await computeUnitGaussianDensityTexture(unit, p, webgl, oldTexture).runInContext(runtime)
+// const { transform, texture, bbox, gridDimension } = densityTextureData
- return DirectVolume.create(bbox, gridDimension, transform, texture, directVolume)
-}
+// return DirectVolume.create(bbox, gridDimension, transform, texture, directVolume)
+// }
-export const GaussianDensityVolumeParams = {
- ...UnitsDirectVolumeParams,
- ...GaussianDensityParams,
-}
-export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
+// export const GaussianDensityVolumeParams = {
+// ...UnitsDirectVolumeParams,
+// ...GaussianDensityParams,
+// }
+// export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
-export function GaussianDensityVolumeVisual(): UnitsVisual<GaussianDensityVolumeParams> {
- return UnitsDirectVolumeVisual<GaussianDensityVolumeParams>({
- defaultProps: PD.getDefaultValues(GaussianDensityVolumeParams),
- createGeometry: createGaussianDensityVolume,
- createLocationIterator: StructureElementIterator.fromGroup,
- getLoci: getElementLoci,
- mark: markElement,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianDensityVolumeParams>, currentProps: PD.Values<GaussianDensityVolumeParams>) => {
- if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
- if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
- if (newProps.smoothness !== currentProps.smoothness) {
- state.createGeometry = true
- newProps.isoValue = Math.exp(-newProps.smoothness)
- }
- if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
- if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
- }
- })
-}
\ No newline at end of file
+// export function GaussianDensityVolumeVisual(): UnitsVisual<GaussianDensityVolumeParams> {
+// return UnitsDirectVolumeVisual<GaussianDensityVolumeParams>({
+// defaultProps: PD.getDefaultValues(GaussianDensityVolumeParams),
+// createGeometry: createGaussianDensityVolume,
+// createLocationIterator: StructureElementIterator.fromGroup,
+// getLoci: getElementLoci,
+// mark: markElement,
+// setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianDensityVolumeParams>, currentProps: PD.Values<GaussianDensityVolumeParams>) => {
+// if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
+// if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+// if (newProps.smoothness !== currentProps.smoothness) {
+// state.createGeometry = true
+// newProps.isoValue = Math.exp(-newProps.smoothness)
+// }
+// if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
+// if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
+// }
+// })
+// }
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index 75e5550be..b4dbdce9d 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -1,58 +1,58 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
+// /**
+// * 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 } from '../representation';
-import { VisualUpdateState } from '../../util';
-import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { StructureElementIterator, getElementLoci, markElement } from './util/element';
-import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { Mesh } from 'mol-geo/geometry/mesh/mesh';
-import { computeMarchingCubesMesh } from 'mol-geo/util/marching-cubes/algorithm';
-import { VisualContext } from 'mol-repr/representation';
-import { Theme } from 'mol-theme/theme';
+// import { Unit, Structure } from 'mol-model/structure';
+// import { UnitsVisual } from '../representation';
+// import { VisualUpdateState } from '../../util';
+// import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
+// import { StructureElementIterator, getElementLoci, markElement } from './util/element';
+// import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
+// import { ParamDefinition as PD } from 'mol-util/param-definition';
+// import { Mesh } from 'mol-geo/geometry/mesh/mesh';
+// import { computeMarchingCubesMesh } from 'mol-geo/util/marching-cubes/algorithm';
+// import { VisualContext } from 'mol-repr/representation';
+// import { Theme } from 'mol-theme/theme';
-async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
- const { smoothness } = props
- const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx.runtime, ctx.webgl)
+// async function createGaussianSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
+// const { smoothness } = props
+// const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx.runtime, ctx.webgl)
- const params = {
- isoLevel: Math.exp(-smoothness),
- scalarField: field,
- idField
- }
- const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime)
+// const params = {
+// isoLevel: Math.exp(-smoothness),
+// scalarField: field,
+// idField
+// }
+// const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime)
- Mesh.transformImmediate(surface, transform)
- Mesh.computeNormalsImmediate(surface)
- Mesh.uniformTriangleGroup(surface)
+// Mesh.transformImmediate(surface, transform)
+// Mesh.computeNormalsImmediate(surface)
+// Mesh.uniformTriangleGroup(surface)
- return surface;
-}
+// return surface;
+// }
-export const GaussianSurfaceParams = {
- ...UnitsMeshParams,
- ...GaussianDensityParams,
-}
-export type GaussianSurfaceParams = typeof GaussianSurfaceParams
+// export const GaussianSurfaceParams = {
+// ...UnitsMeshParams,
+// ...GaussianDensityParams,
+// }
+// export type GaussianSurfaceParams = typeof GaussianSurfaceParams
-export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceParams> {
- return UnitsMeshVisual<GaussianSurfaceParams>({
- defaultProps: PD.getDefaultValues(GaussianSurfaceParams),
- createGeometry: createGaussianSurfaceMesh,
- createLocationIterator: StructureElementIterator.fromGroup,
- getLoci: getElementLoci,
- mark: markElement,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianSurfaceParams>, currentProps: PD.Values<GaussianSurfaceParams>) => {
- if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
- if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
- if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
- if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
- if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
- }
- })
-}
\ No newline at end of file
+// export function GaussianSurfaceVisual(): UnitsVisual<GaussianSurfaceParams> {
+// return UnitsMeshVisual<GaussianSurfaceParams>({
+// defaultProps: PD.getDefaultValues(GaussianSurfaceParams),
+// createGeometry: createGaussianSurfaceMesh,
+// createLocationIterator: StructureElementIterator.fromGroup,
+// getLoci: getElementLoci,
+// mark: markElement,
+// setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianSurfaceParams>, currentProps: PD.Values<GaussianSurfaceParams>) => {
+// if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
+// if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+// if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
+// if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
+// if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
+// }
+// })
+// }
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index dea76bc8d..c0a51d592 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -1,57 +1,57 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
+// /**
+// * 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 } from '../representation';
-import { VisualUpdateState } from '../../util';
-import { UnitsLinesVisual, UnitsLinesParams } from '../units-visual';
-import { StructureElementIterator, getElementLoci, markElement } from './util/element';
-import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
-import { ParamDefinition as PD } from 'mol-util/param-definition';
-import { Lines } from 'mol-geo/geometry/lines/lines';
-import { computeMarchingCubesLines } from 'mol-geo/util/marching-cubes/algorithm';
-import { VisualContext } from 'mol-repr/representation';
-import { Theme } from 'mol-theme/theme';
+// import { Unit, Structure } from 'mol-model/structure';
+// import { UnitsVisual } from '../representation';
+// import { VisualUpdateState } from '../../util';
+// import { UnitsLinesVisual, UnitsLinesParams } from '../units-visual';
+// import { StructureElementIterator, getElementLoci, markElement } from './util/element';
+// import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
+// import { ParamDefinition as PD } from 'mol-util/param-definition';
+// import { Lines } from 'mol-geo/geometry/lines/lines';
+// import { computeMarchingCubesLines } from 'mol-geo/util/marching-cubes/algorithm';
+// import { VisualContext } from 'mol-repr/representation';
+// import { Theme } from 'mol-theme/theme';
-async function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
- const { smoothness } = props
- const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx.runtime)
+// function createGaussianWireframe(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
+// const { smoothness } = props
+// const { transform, field, idField } = await unit.computeGaussianDensity(props, ctx.runtime)
- const params = {
- isoLevel: Math.exp(-smoothness),
- scalarField: field,
- idField
- }
- const wireframe = await computeMarchingCubesLines(params, lines).runAsChild(ctx.runtime)
+// const params = {
+// isoLevel: Math.exp(-smoothness),
+// scalarField: field,
+// idField
+// }
+// const wireframe = await computeMarchingCubesLines(params, lines).runAsChild(ctx.runtime)
- Lines.transformImmediate(wireframe, transform)
+// Lines.transformImmediate(wireframe, transform)
- return wireframe
-}
+// return wireframe
+// }
-export const GaussianWireframeParams = {
- ...UnitsLinesParams,
- ...GaussianDensityParams,
- lineSizeAttenuation: PD.Boolean(false),
-}
-export type GaussianWireframeParams = typeof GaussianWireframeParams
+// export const GaussianWireframeParams = {
+// ...UnitsLinesParams,
+// ...GaussianDensityParams,
+// lineSizeAttenuation: PD.Boolean(false),
+// }
+// export type GaussianWireframeParams = typeof GaussianWireframeParams
-export function GaussianWireframeVisual(): UnitsVisual<GaussianWireframeParams> {
- return UnitsLinesVisual<GaussianWireframeParams>({
- defaultProps: PD.getDefaultValues(GaussianWireframeParams),
- createGeometry: createGaussianWireframe,
- createLocationIterator: StructureElementIterator.fromGroup,
- getLoci: getElementLoci,
- mark: markElement,
- setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianWireframeParams>, currentProps: PD.Values<GaussianWireframeParams>) => {
- if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
- if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
- if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
- if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
- if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
- }
- })
-}
\ No newline at end of file
+// export function GaussianWireframeVisual(): UnitsVisual<GaussianWireframeParams> {
+// return UnitsLinesVisual<GaussianWireframeParams>({
+// defaultProps: PD.getDefaultValues(GaussianWireframeParams),
+// createGeometry: createGaussianWireframe,
+// createLocationIterator: StructureElementIterator.fromGroup,
+// getLoci: getElementLoci,
+// mark: markElement,
+// setUpdateState: (state: VisualUpdateState, newProps: PD.Values<GaussianWireframeParams>, currentProps: PD.Values<GaussianWireframeParams>) => {
+// if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
+// if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
+// if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
+// if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
+// if (newProps.ignoreCache !== currentProps.ignoreCache) state.createGeometry = true
+// }
+// })
+// }
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
index f9cd1c147..5f298b7d9 100644
--- a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
@@ -19,7 +19,7 @@ import { PickingId } from 'mol-geo/geometry/picking';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitLinkParams>, mesh?: Mesh) {
+function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitLinkParams>, mesh?: Mesh) {
const links = structure.links
const { bondCount, bonds } = links
const { sizeFactor, sizeAspectRatio } = props
diff --git a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
index beaa507fe..1dcfc59d4 100644
--- a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
@@ -20,7 +20,7 @@ import { PickingId } from 'mol-geo/geometry/picking';
import { VisualContext } from 'mol-repr/representation';
import { Theme } from 'mol-theme/theme';
-async function createIntraUnitLinkCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitLinkParams>, mesh?: Mesh) {
+function createIntraUnitLinkCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitLinkParams>, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const location = StructureElement.create(unit)
diff --git a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
index b3be2492c..2cf7c0b2d 100644
--- a/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-repr/structure/visual/nucleotide-block-mesh.ts
@@ -41,7 +41,7 @@ export const NucleotideBlockMeshParams = {
export const DefaultNucleotideBlockMeshProps = PD.getDefaultValues(NucleotideBlockMeshParams)
export type NucleotideBlockMeshProps = typeof DefaultNucleotideBlockMeshProps
-async function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: NucleotideBlockMeshProps, mesh?: Mesh) {
+function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: NucleotideBlockMeshProps, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const { sizeFactor } = props
@@ -109,9 +109,6 @@ async function createNucleotideBlockMesh(ctx: VisualContext, unit: Unit, structu
}
}
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Nucleotide block mesh', current: i });
- }
++i
}
}
diff --git a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
index 2e27f6e0a..f3fb52f2d 100644
--- a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
@@ -27,7 +27,8 @@ export const PolymerBackboneCylinderParams = {
export const DefaultPolymerBackboneCylinderProps = PD.getDefaultValues(PolymerBackboneCylinderParams)
export type PolymerBackboneCylinderProps = typeof DefaultPolymerBackboneCylinderProps
-async function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
+// TODO do group id based on polymer index not element index
+function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerBackboneCylinderProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
@@ -42,7 +43,6 @@ async function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit,
const pB = Vec3.zero()
const cylinderProps: CylinderProps = { radiusTop: 1, radiusBottom: 1, radialSegments }
- let i = 0
const polymerBackboneIt = PolymerBackboneIterator(unit)
while (polymerBackboneIt.hasNext) {
const { centerA, centerB } = polymerBackboneIt.move()
@@ -56,11 +56,6 @@ async function createPolymerBackboneCylinderMesh(ctx: VisualContext, unit: Unit,
cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerB) * sizeFactor
builder.setGroup(OrderedSet.indexOf(elements, centerB.element))
addCylinder(builder, pB, pA, 0.5, cylinderProps)
-
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Backbone mesh', current: i, max: polymerElementCount });
- }
- ++i
}
return builder.getMesh()
diff --git a/src/mol-repr/structure/visual/polymer-direction-wedge.ts b/src/mol-repr/structure/visual/polymer-direction-wedge.ts
index 3c9dc41c3..f0df188e9 100644
--- a/src/mol-repr/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-repr/structure/visual/polymer-direction-wedge.ts
@@ -36,7 +36,7 @@ export const PolymerDirectionWedgeParams = {
export const DefaultPolymerDirectionWedgeProps = PD.getDefaultValues(PolymerDirectionWedgeParams)
export type PolymerDirectionWedgeProps = typeof DefaultPolymerDirectionWedgeProps
-async function createPolymerDirectionWedgeMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerDirectionWedgeProps, mesh?: Mesh) {
+function createPolymerDirectionWedgeMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerDirectionWedgeProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
@@ -80,9 +80,6 @@ async function createPolymerDirectionWedgeMesh(ctx: VisualContext, unit: Unit, s
builder.add(t, wedge)
}
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Polymer direction mesh', current: i, max: polymerElementCount });
- }
++i
}
diff --git a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
index 818837ce1..0bd618b6f 100644
--- a/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-gap-cylinder.ts
@@ -29,7 +29,7 @@ export const PolymerGapCylinderParams = {
export const DefaultPolymerGapCylinderProps = PD.getDefaultValues(PolymerGapCylinderParams)
export type PolymerGapCylinderProps = typeof DefaultPolymerGapCylinderProps
-async function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerGapCylinderProps, mesh?: Mesh) {
+function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerGapCylinderProps, mesh?: Mesh) {
const polymerGapCount = unit.gapElements.length
if (!polymerGapCount) return Mesh.createEmpty(mesh)
@@ -66,9 +66,6 @@ async function createPolymerGapCylinderMesh(ctx: VisualContext, unit: Unit, stru
addFixedCountDashedCylinder(builder, pB, pA, 0.5, segmentCount, cylinderProps)
}
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Gap mesh', current: i, max: polymerGapCount });
- }
i += 2
}
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 6890b4853..0f9f4d38a 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -30,7 +30,7 @@ export type PolymerTraceMeshProps = typeof DefaultPolymerTraceMeshProps
// TODO handle polymer ends properly
-async function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerTraceMeshProps, mesh?: Mesh) {
+function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PolymerTraceMeshProps, mesh?: Mesh) {
const polymerElementCount = unit.polymerElements.length
if (!polymerElementCount) return Mesh.createEmpty(mesh)
@@ -77,9 +77,6 @@ async function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure:
addTube(builder, curvePoints, normalVectors, binormalVectors, linearSegments, radialSegments, width, height, 1, v.secStrucFirst, v.secStrucLast)
}
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Polymer trace mesh', current: i, max: polymerElementCount });
- }
++i
}
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index 38188c438..e95a606a6 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -23,7 +23,7 @@ export interface ElementSphereMeshProps {
sizeFactor: number
}
-export async function createElementSphereMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereMeshProps, mesh?: Mesh) {
+export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereMeshProps, mesh?: Mesh) {
const { detail, sizeFactor } = props
const { elements } = unit;
@@ -42,10 +42,6 @@ export async function createElementSphereMesh(ctx: VisualContext, unit: Unit, st
meshBuilder.setGroup(i)
addSphere(meshBuilder, v, theme.size.size(l) * sizeFactor, detail)
-
- if (i % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Sphere mesh', current: i, max: elementCount });
- }
}
return meshBuilder.getMesh()
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index a080395f4..5f102bdfe 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/src/mol-repr/structure/visual/util/link.ts
@@ -66,7 +66,7 @@ export interface LinkCylinderMeshBuilderProps {
* Each edge is included twice to allow for coloring/picking
* the half closer to the first vertex, i.e. vertex a.
*/
-export async function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkCylinderMeshBuilderProps, props: LinkCylinderProps, mesh?: Mesh) {
+export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkCylinderMeshBuilderProps, props: LinkCylinderProps, mesh?: Mesh) {
const { linkCount, referencePosition, position, order, flags, radius } = linkBuilder
if (!linkCount) return Mesh.createEmpty(mesh)
@@ -109,10 +109,6 @@ export async function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: Li
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius
addCylinder(meshBuilder, va, vb, 0.5, cylinderProps)
}
-
- if (edgeIndex % 10000 === 0 && ctx.runtime.shouldUpdate) {
- await ctx.runtime.update({ message: 'Cylinder mesh', current: edgeIndex, max: linkCount });
- }
}
return meshBuilder.getMesh()
--
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