From 8d4e760856c6df2ada985a27f155f984892f20f3 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 10 Aug 2018 17:46:58 -0700
Subject: [PATCH] wip, refactoring of representations and visuals
---
src/mol-app/ui/transform/file-loader.tsx | 8 +-
src/mol-app/ui/transform/url-loader.tsx | 10 +-
src/mol-geo/representation/index.ts | 8 +-
.../structure/complex-representation.ts | 6 +-
.../structure/complex-visual.ts | 79 +++++++++++++-
src/mol-geo/representation/structure/index.ts | 10 +-
.../structure/representation/backbone.ts | 15 +--
.../representation/ball-and-stick.ts | 23 ++--
.../structure/representation/carbohydrate.ts | 19 ++--
.../structure/representation/cartoon.ts | 27 ++---
.../representation/distance-restraint.ts | 16 +--
.../structure/representation/spacefill.ts | 4 +-
.../structure/units-representation.ts | 6 +-
.../representation/structure/units-visual.ts | 95 +++++++++++++++-
.../visual/carbohydrate-link-cylinder.ts | 62 ++---------
.../visual/carbohydrate-symbol-mesh.ts | 64 ++---------
.../visual/cross-link-restraint-cylinder.ts | 92 +++++-----------
.../structure/visual/element-point.ts | 4 +-
.../structure/visual/element-sphere.ts | 97 +++--------------
.../visual/inter-unit-link-cylinder.ts | 64 ++---------
.../visual/intra-unit-link-cylinder.ts | 71 ++----------
.../structure/visual/nucleotide-block-mesh.ts | 92 +++-------------
.../visual/polymer-backbone-cylinder.ts | 92 +++-------------
.../visual/polymer-direction-wedge.ts | 103 +++---------------
.../structure/visual/polymer-gap-cylinder.ts | 92 +++-------------
.../structure/visual/polymer-trace-mesh.ts | 103 +++---------------
.../structure/visual/util/common.ts | 11 +-
.../structure/visual/util/element.ts | 22 +++-
src/mol-geo/representation/util.ts | 4 +-
src/mol-geo/representation/volume/index.ts | 14 ++-
.../structure/unit/pair-restraints/data.ts | 11 +-
.../pair-restraints/extract-cross-links.ts | 13 ++-
src/mol-view/stage.ts | 12 +-
src/mol-view/state/entity.ts | 12 +-
src/mol-view/state/transform.ts | 60 +++++-----
35 files changed, 495 insertions(+), 926 deletions(-)
diff --git a/src/mol-app/ui/transform/file-loader.tsx b/src/mol-app/ui/transform/file-loader.tsx
index 02f76c55c..32712dfa0 100644
--- a/src/mol-app/ui/transform/file-loader.tsx
+++ b/src/mol-app/ui/transform/file-loader.tsx
@@ -16,14 +16,14 @@ import { BallAndStickProps } from 'mol-geo/representation/structure/representati
import { DistanceRestraintProps } from 'mol-geo/representation/structure/representation/distance-restraint';
import { BackboneProps } from 'mol-geo/representation/structure/representation/backbone';
-const spacefillProps: SpacefillProps = {
+const spacefillProps: Partial<SpacefillProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
quality: 'auto',
useFog: false
}
-const ballAndStickProps: BallAndStickProps = {
+const ballAndStickProps: Partial<BallAndStickProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
sizeTheme: { name: 'uniform', value: 0.05 },
@@ -32,7 +32,7 @@ const ballAndStickProps: BallAndStickProps = {
useFog: false
}
-const distanceRestraintProps: DistanceRestraintProps = {
+const distanceRestraintProps: Partial<DistanceRestraintProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
linkRadius: 0.5,
@@ -40,7 +40,7 @@ const distanceRestraintProps: DistanceRestraintProps = {
useFog: false
}
-const backboneProps: BackboneProps = {
+const backboneProps: Partial<BackboneProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
quality: 'auto',
diff --git a/src/mol-app/ui/transform/url-loader.tsx b/src/mol-app/ui/transform/url-loader.tsx
index ed0b8ef8b..58667e93d 100644
--- a/src/mol-app/ui/transform/url-loader.tsx
+++ b/src/mol-app/ui/transform/url-loader.tsx
@@ -16,14 +16,14 @@ import { DistanceRestraintProps } from 'mol-geo/representation/structure/represe
import { BackboneProps } from 'mol-geo/representation/structure/representation/backbone';
import { CartoonProps } from 'mol-geo/representation/structure/representation/cartoon';
-const spacefillProps: SpacefillProps = {
+const spacefillProps: Partial<SpacefillProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
quality: 'auto',
useFog: false
}
-const ballAndStickProps: BallAndStickProps = {
+const ballAndStickProps: Partial<BallAndStickProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
sizeTheme: { name: 'uniform', value: 0.05 },
@@ -32,7 +32,7 @@ const ballAndStickProps: BallAndStickProps = {
useFog: false
}
-const distanceRestraintProps: DistanceRestraintProps = {
+const distanceRestraintProps: Partial<DistanceRestraintProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
linkRadius: 0.5,
@@ -40,14 +40,14 @@ const distanceRestraintProps: DistanceRestraintProps = {
useFog: false
}
-const backboneProps: BackboneProps = {
+const backboneProps: Partial<BackboneProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
quality: 'auto',
useFog: false
}
-const cartoonProps: CartoonProps = {
+const cartoonProps: Partial<CartoonProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
quality: 'auto',
diff --git a/src/mol-geo/representation/index.ts b/src/mol-geo/representation/index.ts
index ab18c4cdf..a444545fe 100644
--- a/src/mol-geo/representation/index.ts
+++ b/src/mol-geo/representation/index.ts
@@ -15,8 +15,8 @@ export interface RepresentationProps {}
export interface Representation<D, P extends RepresentationProps = {}> {
readonly renderObjects: ReadonlyArray<RenderObject>
readonly props: Readonly<P>
- create: (data: D, props?: P) => Task<void>
- update: (props: P) => Task<void>
+ create: (data: D, props?: Partial<P>) => Task<void>
+ update: (props: Partial<P>) => Task<void>
getLoci: (pickingId: PickingId) => Loci
mark: (loci: Loci, action: MarkerAction) => void
destroy: () => void
@@ -24,8 +24,8 @@ export interface Representation<D, P extends RepresentationProps = {}> {
export interface Visual<D, P extends RepresentationProps = {}> {
readonly renderObject: RenderObject
- create: (ctx: RuntimeContext, data: D, props: P) => Promise<void>
- update: (ctx: RuntimeContext, props: P) => Promise<boolean>
+ create: (ctx: RuntimeContext, data: D, props?: Partial<P>) => Promise<void>
+ update: (ctx: RuntimeContext, props: Partial<P>) => Promise<boolean>
getLoci: (pickingId: PickingId) => Loci
mark: (loci: Loci, action: MarkerAction) => void
destroy: () => void
diff --git a/src/mol-geo/representation/structure/complex-representation.ts b/src/mol-geo/representation/structure/complex-representation.ts
index 2ddb9d8cb..5bc2b81a2 100644
--- a/src/mol-geo/representation/structure/complex-representation.ts
+++ b/src/mol-geo/representation/structure/complex-representation.ts
@@ -17,10 +17,10 @@ import { ComplexVisual } from './complex-visual';
export function ComplexRepresentation<P extends StructureProps>(visualCtor: () => ComplexVisual<P>): StructureRepresentation<P> {
let visual: ComplexVisual<P>
- let _props: Required<P>
+ let _props: P
let _structure: Structure
- function create(structure: Structure, props: P = {} as P) {
+ function create(structure: Structure, props: Partial<P> = {}) {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, structure))
_props.colorTheme!.structure = structure
@@ -41,7 +41,7 @@ export function ComplexRepresentation<P extends StructureProps>(visualCtor: () =
});
}
- function update(props: P) {
+ function update(props: Partial<P>) {
return Task.create('Updating StructureRepresentation', async ctx => {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, _structure))
_props.colorTheme!.structure = _structure
diff --git a/src/mol-geo/representation/structure/complex-visual.ts b/src/mol-geo/representation/structure/complex-visual.ts
index 8c193d515..9c02d9861 100644
--- a/src/mol-geo/representation/structure/complex-visual.ts
+++ b/src/mol-geo/representation/structure/complex-visual.ts
@@ -2,10 +2,83 @@
* 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 { Structure } from 'mol-model/structure';
-import { RepresentationProps, Visual } from '..';
+import { Visual } from '..';
+import { MeshRenderObject } from 'mol-gl/render-object';
+import { Mesh } from '../../shape/mesh';
+import { RuntimeContext } from 'mol-task';
+import { LocationIterator } from './visual/util/location-iterator';
+import { createComplexMeshRenderObject, createColors } from './visual/util/common';
+import { StructureMeshProps, StructureProps } from '.';
+import { deepEqual } from 'mol-util';
+import { updateMeshValues, updateRenderableState } from '../util';
+import { PickingId } from '../../util/picking';
+import { Loci } from 'mol-model/loci';
+import { MarkerAction, MarkerData } from '../../util/marker-data';
-export interface ComplexVisual<P extends RepresentationProps = {}> extends Visual<Structure, P> { }
\ No newline at end of file
+export interface ComplexVisual<P extends StructureProps> extends Visual<Structure, P> { }
+
+export interface ComplexMeshVisualBuilder<P extends StructureMeshProps> {
+ defaultProps: P
+ createMesh(ctx: RuntimeContext, structure: Structure, props: P, mesh?: Mesh): Promise<Mesh>
+ createLocationIterator(structure: Structure): LocationIterator
+ getLoci(pickingId: PickingId, structure: Structure, id: number): Loci
+ mark(loci: Loci, action: MarkerAction, structure: Structure, values: MarkerData): void
+}
+
+export function ComplexMeshVisual<P extends StructureMeshProps>(builder: ComplexMeshVisualBuilder<P>): ComplexVisual<P> {
+ const { defaultProps, createMesh, createLocationIterator, getLoci, mark } = builder
+
+ let renderObject: MeshRenderObject
+ let currentProps: P
+ let mesh: Mesh
+ let currentStructure: Structure
+
+ return {
+ get renderObject () { return renderObject },
+ async create(ctx: RuntimeContext, structure: Structure, props: Partial<P> = {}) {
+ currentProps = Object.assign({}, defaultProps, props)
+ currentStructure = structure
+
+ mesh = await createMesh(ctx, currentStructure, currentProps, mesh)
+
+ const locationIt = createLocationIterator(structure)
+ renderObject = createComplexMeshRenderObject(structure, mesh, locationIt, currentProps)
+ },
+ async update(ctx: RuntimeContext, props: Partial<P>) {
+ const newProps = Object.assign({}, currentProps, props)
+
+ if (!renderObject) return false
+
+ let updateColor = false
+
+ // TODO create in-place
+ // if (currentProps.radialSegments !== newProps.radialSegments) return false
+
+ if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
+ updateColor = true
+ }
+
+ if (updateColor) {
+ createColors(createLocationIterator(currentStructure), newProps.colorTheme, renderObject.values)
+ }
+
+ updateMeshValues(renderObject.values, newProps)
+ updateRenderableState(renderObject.state, newProps)
+
+ currentProps = newProps
+ return false
+ },
+ getLoci(pickingId: PickingId) {
+ return getLoci(pickingId, currentStructure, renderObject.id)
+ },
+ mark(loci: Loci, action: MarkerAction) {
+ mark(loci, action, currentStructure, renderObject.values)
+ },
+ destroy() {
+ // TODO
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 2b0b0da9c..951d43369 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -8,7 +8,7 @@
import { Structure } from 'mol-model/structure';
import { Representation, RepresentationProps } from '..';
import { ColorTheme, SizeTheme } from '../../theme';
-import { DefaultBaseProps } from '../util';
+import { DefaultBaseProps, DefaultMeshProps } from '../util';
export interface StructureRepresentation<P extends RepresentationProps = {}> extends Representation<Structure, P> { }
@@ -17,7 +17,13 @@ export const DefaultStructureProps = {
colorTheme: { name: 'instance-index' } as ColorTheme,
sizeTheme: { name: 'physical' } as SizeTheme,
}
-export type StructureProps = Partial<typeof DefaultStructureProps>
+export type StructureProps = typeof DefaultStructureProps
+
+export const DefaultStructureMeshProps = {
+ ...DefaultStructureProps,
+ ...DefaultMeshProps
+}
+export type StructureMeshProps = typeof DefaultStructureMeshProps
export { ComplexRepresentation } from './complex-representation'
export { UnitsRepresentation } from './units-representation'
diff --git a/src/mol-geo/representation/structure/representation/backbone.ts b/src/mol-geo/representation/structure/representation/backbone.ts
index 4930d9775..2afb0c8cf 100644
--- a/src/mol-geo/representation/structure/representation/backbone.ts
+++ b/src/mol-geo/representation/structure/representation/backbone.ts
@@ -15,11 +15,12 @@ import { PolymerBackboneVisual, DefaultPolymerBackboneProps } from '../visual/po
export const DefaultBackboneProps = {
...DefaultPolymerBackboneProps
}
-export type BackboneProps = Partial<typeof DefaultBackboneProps>
+export type BackboneProps = typeof DefaultBackboneProps
export function BackboneRepresentation(): StructureRepresentation<BackboneProps> {
const traceRepr = UnitsRepresentation(PolymerBackboneVisual)
+ let currentProps: BackboneProps
return {
get renderObjects() {
return [ ...traceRepr.renderObjects ]
@@ -27,16 +28,16 @@ export function BackboneRepresentation(): StructureRepresentation<BackboneProps>
get props() {
return { ...traceRepr.props }
},
- create: (structure: Structure, props: BackboneProps = {} as BackboneProps) => {
- const p = Object.assign({}, DefaultBackboneProps, props)
+ create: (structure: Structure, props: Partial<BackboneProps> = {}) => {
+ currentProps = Object.assign({}, DefaultBackboneProps, props)
return Task.create('BackboneRepresentation', async ctx => {
- await traceRepr.create(structure, p).runInContext(ctx)
+ await traceRepr.create(structure, currentProps).runInContext(ctx)
})
},
- update: (props: BackboneProps) => {
- const p = Object.assign({}, props)
+ update: (props: Partial<BackboneProps>) => {
+ currentProps = Object.assign(currentProps, props)
return Task.create('Updating BackboneRepresentation', async ctx => {
- await traceRepr.update(p).runInContext(ctx)
+ await traceRepr.update(currentProps).runInContext(ctx)
})
},
getLoci: (pickingId: PickingId) => {
diff --git a/src/mol-geo/representation/structure/representation/ball-and-stick.ts b/src/mol-geo/representation/structure/representation/ball-and-stick.ts
index 094eb1fcb..b32faf0ce 100644
--- a/src/mol-geo/representation/structure/representation/ball-and-stick.ts
+++ b/src/mol-geo/representation/structure/representation/ball-and-stick.ts
@@ -22,13 +22,14 @@ export const DefaultBallAndStickProps = {
sizeTheme: { name: 'uniform', value: 0.25 } as SizeTheme,
unitKinds: [ Unit.Kind.Atomic ] as Unit.Kind[]
}
-export type BallAndStickProps = Partial<typeof DefaultBallAndStickProps>
+export type BallAndStickProps = typeof DefaultBallAndStickProps
export function BallAndStickRepresentation(): StructureRepresentation<BallAndStickProps> {
const elmementRepr = UnitsRepresentation(ElementSphereVisual)
const intraLinkRepr = UnitsRepresentation(IntraUnitLinkVisual)
const interLinkRepr = ComplexRepresentation(InterUnitLinkVisual)
+ let currentProps: BallAndStickProps
return {
get renderObjects() {
return [ ...elmementRepr.renderObjects, ...intraLinkRepr.renderObjects, ...interLinkRepr.renderObjects ]
@@ -36,20 +37,20 @@ export function BallAndStickRepresentation(): StructureRepresentation<BallAndSti
get props() {
return { ...elmementRepr.props, ...intraLinkRepr.props, ...interLinkRepr.props }
},
- create: (structure: Structure, props: BallAndStickProps = {} as BallAndStickProps) => {
- const p = Object.assign({}, DefaultBallAndStickProps, props)
+ create: (structure: Structure, props: Partial<BallAndStickProps> = {}) => {
+ currentProps = Object.assign({}, DefaultBallAndStickProps, props)
return Task.create('DistanceRestraintRepresentation', async ctx => {
- await elmementRepr.create(structure, p).runInContext(ctx)
- await intraLinkRepr.create(structure, p).runInContext(ctx)
- await interLinkRepr.create(structure, p).runInContext(ctx)
+ await elmementRepr.create(structure, currentProps).runInContext(ctx)
+ await intraLinkRepr.create(structure, currentProps).runInContext(ctx)
+ await interLinkRepr.create(structure, currentProps).runInContext(ctx)
})
},
- update: (props: BallAndStickProps) => {
- const p = Object.assign({}, props)
+ update: (props: Partial<BallAndStickProps>) => {
+ currentProps = Object.assign(currentProps, props)
return Task.create('Updating BallAndStickRepresentation', async ctx => {
- await elmementRepr.update(p).runInContext(ctx)
- await intraLinkRepr.update(p).runInContext(ctx)
- await interLinkRepr.update(p).runInContext(ctx)
+ await elmementRepr.update(currentProps).runInContext(ctx)
+ await intraLinkRepr.update(currentProps).runInContext(ctx)
+ await interLinkRepr.update(currentProps).runInContext(ctx)
})
},
getLoci: (pickingId: PickingId) => {
diff --git a/src/mol-geo/representation/structure/representation/carbohydrate.ts b/src/mol-geo/representation/structure/representation/carbohydrate.ts
index 75e63d930..bc877da0f 100644
--- a/src/mol-geo/representation/structure/representation/carbohydrate.ts
+++ b/src/mol-geo/representation/structure/representation/carbohydrate.ts
@@ -17,12 +17,13 @@ export const DefaultCartoonProps = {
...DefaultCarbohydrateSymbolProps,
...DefaultCarbohydrateLinkProps
}
-export type CarbohydrateProps = Partial<typeof DefaultCartoonProps>
+export type CarbohydrateProps = typeof DefaultCartoonProps
export function CarbohydrateRepresentation(): StructureRepresentation<CarbohydrateProps> {
const carbohydrateSymbolRepr = ComplexRepresentation(CarbohydrateSymbolVisual)
const carbohydrateLinkRepr = ComplexRepresentation(CarbohydrateLinkVisual)
+ let currentProps: CarbohydrateProps
return {
get renderObjects() {
return [ ...carbohydrateSymbolRepr.renderObjects, ...carbohydrateLinkRepr.renderObjects ]
@@ -30,18 +31,18 @@ export function CarbohydrateRepresentation(): StructureRepresentation<Carbohydra
get props() {
return { ...carbohydrateSymbolRepr.props, ...carbohydrateLinkRepr.props }
},
- create: (structure: Structure, props: CarbohydrateProps = {} as CarbohydrateProps) => {
- const p = Object.assign({}, DefaultCartoonProps, props)
+ create: (structure: Structure, props: Partial<CarbohydrateProps> = {} as CarbohydrateProps) => {
+ currentProps = Object.assign({}, DefaultCartoonProps, props)
return Task.create('Creating CarbohydrateRepresentation', async ctx => {
- await carbohydrateSymbolRepr.create(structure, p).runInContext(ctx)
- await carbohydrateLinkRepr.create(structure, p).runInContext(ctx)
+ await carbohydrateSymbolRepr.create(structure, currentProps).runInContext(ctx)
+ await carbohydrateLinkRepr.create(structure, currentProps).runInContext(ctx)
})
},
- update: (props: CarbohydrateProps) => {
- const p = Object.assign({}, props)
+ update: (props: Partial<CarbohydrateProps>) => {
+ currentProps = Object.assign(currentProps, props)
return Task.create('Updating CarbohydrateRepresentation', async ctx => {
- await carbohydrateSymbolRepr.update(p).runInContext(ctx)
- await carbohydrateLinkRepr.update(p).runInContext(ctx)
+ await carbohydrateSymbolRepr.update(currentProps).runInContext(ctx)
+ await carbohydrateLinkRepr.update(currentProps).runInContext(ctx)
})
},
getLoci: (pickingId: PickingId) => {
diff --git a/src/mol-geo/representation/structure/representation/cartoon.ts b/src/mol-geo/representation/structure/representation/cartoon.ts
index 498c0f30b..904b43360 100644
--- a/src/mol-geo/representation/structure/representation/cartoon.ts
+++ b/src/mol-geo/representation/structure/representation/cartoon.ts
@@ -21,7 +21,7 @@ export const DefaultCartoonProps = {
...DefaultNucleotideBlockProps,
...DefaultPolymerDirectionProps
}
-export type CartoonProps = Partial<typeof DefaultCartoonProps>
+export type CartoonProps = typeof DefaultCartoonProps
export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const traceRepr = UnitsRepresentation(PolymerTraceVisual)
@@ -29,6 +29,7 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
const blockRepr = UnitsRepresentation(NucleotideBlockVisual)
const directionRepr = UnitsRepresentation(PolymerDirectionVisual)
+ let currentProps: CartoonProps
return {
get renderObjects() {
return [ ...traceRepr.renderObjects, ...gapRepr.renderObjects,
@@ -37,22 +38,22 @@ export function CartoonRepresentation(): StructureRepresentation<CartoonProps> {
get props() {
return { ...traceRepr.props, ...gapRepr.props, ...blockRepr.props }
},
- create: (structure: Structure, props: CartoonProps = {} as CartoonProps) => {
- const p = Object.assign({}, DefaultCartoonProps, props)
+ create: (structure: Structure, props: Partial<CartoonProps> = {}) => {
+ currentProps = Object.assign({}, DefaultCartoonProps, props)
return Task.create('Creating CartoonRepresentation', async ctx => {
- await traceRepr.create(structure, p).runInContext(ctx)
- await gapRepr.create(structure, p).runInContext(ctx)
- await blockRepr.create(structure, p).runInContext(ctx)
- await directionRepr.create(structure, p).runInContext(ctx)
+ await traceRepr.create(structure, currentProps).runInContext(ctx)
+ await gapRepr.create(structure, currentProps).runInContext(ctx)
+ await blockRepr.create(structure, currentProps).runInContext(ctx)
+ await directionRepr.create(structure, currentProps).runInContext(ctx)
})
},
- update: (props: CartoonProps) => {
- const p = Object.assign({}, props)
+ update: (props: Partial<CartoonProps>) => {
+ currentProps = Object.assign(currentProps, props)
return Task.create('Updating CartoonRepresentation', async ctx => {
- await traceRepr.update(p).runInContext(ctx)
- await gapRepr.update(p).runInContext(ctx)
- await blockRepr.update(p).runInContext(ctx)
- await directionRepr.update(p).runInContext(ctx)
+ await traceRepr.update(currentProps).runInContext(ctx)
+ await gapRepr.update(currentProps).runInContext(ctx)
+ await blockRepr.update(currentProps).runInContext(ctx)
+ await directionRepr.update(currentProps).runInContext(ctx)
})
},
getLoci: (pickingId: PickingId) => {
diff --git a/src/mol-geo/representation/structure/representation/distance-restraint.ts b/src/mol-geo/representation/structure/representation/distance-restraint.ts
index 68d2d994c..6618ce311 100644
--- a/src/mol-geo/representation/structure/representation/distance-restraint.ts
+++ b/src/mol-geo/representation/structure/representation/distance-restraint.ts
@@ -15,14 +15,14 @@ import { CrossLinkRestraintVisual, DefaultCrossLinkRestraintProps } from '../vis
export const DefaultDistanceRestraintProps = {
...DefaultCrossLinkRestraintProps,
-
sizeTheme: { name: 'uniform', value: 0.25 } as SizeTheme,
}
-export type DistanceRestraintProps = Partial<typeof DefaultDistanceRestraintProps>
+export type DistanceRestraintProps = typeof DefaultDistanceRestraintProps
export function DistanceRestraintRepresentation(): StructureRepresentation<DistanceRestraintProps> {
const crossLinkRepr = ComplexRepresentation(CrossLinkRestraintVisual)
+ let currentProps: DistanceRestraintProps
return {
get renderObjects() {
return [ ...crossLinkRepr.renderObjects ]
@@ -30,16 +30,16 @@ export function DistanceRestraintRepresentation(): StructureRepresentation<Dista
get props() {
return { ...crossLinkRepr.props }
},
- create: (structure: Structure, props: DistanceRestraintProps = {} as DistanceRestraintProps) => {
- const p = Object.assign({}, DefaultDistanceRestraintProps, props)
+ create: (structure: Structure, props: Partial<DistanceRestraintProps> = {}) => {
+ currentProps = Object.assign({}, DefaultDistanceRestraintProps, props)
return Task.create('DistanceRestraintRepresentation', async ctx => {
- await crossLinkRepr.create(structure, p).runInContext(ctx)
+ await crossLinkRepr.create(structure, currentProps).runInContext(ctx)
})
},
- update: (props: DistanceRestraintProps) => {
- const p = Object.assign({}, props)
+ update: (props: Partial<DistanceRestraintProps>) => {
+ currentProps = Object.assign(currentProps, props)
return Task.create('Updating DistanceRestraintRepresentation', async ctx => {
- await crossLinkRepr.update(p).runInContext(ctx)
+ await crossLinkRepr.update(currentProps).runInContext(ctx)
})
},
getLoci: (pickingId: PickingId) => {
diff --git a/src/mol-geo/representation/structure/representation/spacefill.ts b/src/mol-geo/representation/structure/representation/spacefill.ts
index 0fab7f5a9..d2062b297 100644
--- a/src/mol-geo/representation/structure/representation/spacefill.ts
+++ b/src/mol-geo/representation/structure/representation/spacefill.ts
@@ -8,9 +8,9 @@ import { UnitsRepresentation } from '..';
import { ElementSphereVisual, DefaultElementSphereProps } from '../visual/element-sphere';
export const DefaultSpacefillProps = {
- ...DefaultElementSphereProps,
+ ...DefaultElementSphereProps
}
-export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
+export type SpacefillProps = typeof DefaultSpacefillProps
export function SpacefillRepresentation() {
return UnitsRepresentation(ElementSphereVisual)
diff --git a/src/mol-geo/representation/structure/units-representation.ts b/src/mol-geo/representation/structure/units-representation.ts
index eb9a9efdb..78c3a5795 100644
--- a/src/mol-geo/representation/structure/units-representation.ts
+++ b/src/mol-geo/representation/structure/units-representation.ts
@@ -23,11 +23,11 @@ export interface StructureRepresentation<P extends RepresentationProps = {}> ext
export function UnitsRepresentation<P extends StructureProps>(visualCtor: () => UnitsVisual<P>): StructureRepresentation<P> {
let visuals = new Map<number, { group: Unit.SymmetryGroup, visual: UnitsVisual<P> }>()
- let _props: Required<P>
+ let _props: P
let _structure: Structure
let _groups: ReadonlyArray<Unit.SymmetryGroup>
- function create(structure: Structure, props: P = {} as P) {
+ function create(structure: Structure, props: Partial<P> = {}) {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, structure))
_props.colorTheme!.structure = structure
@@ -80,7 +80,7 @@ export function UnitsRepresentation<P extends StructureProps>(visualCtor: () =>
});
}
- function update(props: P) {
+ function update(props: Partial<P>) {
return Task.create('Updating StructureRepresentation', async ctx => {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, _structure))
_props.colorTheme!.structure = _structure
diff --git a/src/mol-geo/representation/structure/units-visual.ts b/src/mol-geo/representation/structure/units-visual.ts
index 540aa7fec..f91783253 100644
--- a/src/mol-geo/representation/structure/units-visual.ts
+++ b/src/mol-geo/representation/structure/units-visual.ts
@@ -2,10 +2,101 @@
* 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 { RepresentationProps, Visual } from '..';
import { Unit } from 'mol-model/structure';
+import { RepresentationProps, Visual } from '..';
+import { DefaultStructureMeshProps } from '.';
+import { RuntimeContext } from 'mol-task';
+import { PickingId } from '../../util/picking';
+import { LocationIterator } from './visual/util/location-iterator';
+import { Mesh } from '../../shape/mesh';
+import { MarkerData, MarkerAction } from '../../util/marker-data';
+import { Loci } from 'mol-model/loci';
+import { MeshRenderObject } from 'mol-gl/render-object';
+import { createUnitsMeshRenderObject, createColors } from './visual/util/common';
+import { deepEqual } from 'mol-util';
+import { updateMeshValues, updateRenderableState } from '../util';
export interface UnitsVisual<P extends RepresentationProps = {}> extends Visual<Unit.SymmetryGroup, P> { }
+
+export const DefaultUnitsMeshProps = {
+ ...DefaultStructureMeshProps,
+ unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+}
+export type UnitsMeshProps = typeof DefaultUnitsMeshProps
+
+export interface UnitsMeshVisualBuilder<P extends UnitsMeshProps> {
+ defaultProps: P
+ createMesh(ctx: RuntimeContext, unit: Unit, props: P, mesh?: Mesh): Promise<Mesh>
+ createLocationIterator(group: Unit.SymmetryGroup): LocationIterator
+ getLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number): Loci
+ mark(loci: Loci, action: MarkerAction, group: Unit.SymmetryGroup, values: MarkerData): void
+}
+
+export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisualBuilder<P>): UnitsVisual<P> {
+ const { defaultProps, createMesh, createLocationIterator, getLoci, mark } = builder
+
+ let renderObject: MeshRenderObject
+ let currentProps: P
+ let mesh: Mesh
+ let currentGroup: Unit.SymmetryGroup
+
+ return {
+ get renderObject () { return renderObject },
+ async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: Partial<P> = {}) {
+ currentProps = Object.assign({}, defaultProps, props)
+ currentGroup = group
+
+ const unit = group.units[0]
+ mesh = currentProps.unitKinds.includes(unit.kind)
+ ? await createMesh(ctx, unit, currentProps, mesh)
+ : Mesh.createEmpty(mesh)
+
+ const locationIt = createLocationIterator(group)
+ renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
+ },
+ async update(ctx: RuntimeContext, props: Partial<P>) {
+ const newProps = Object.assign({}, currentProps, props)
+
+ if (!renderObject) return false
+
+ let updateColor = false
+
+ // TODO create in-place
+ // if (currentProps.radialSegments !== newProps.radialSegments) return false
+
+ // TODO
+ // if (newProps.detail !== currentProps.detail) {
+ // const unit = currentGroup.units[0]
+ // const radius = getElementRadius(unit, newProps.sizeTheme)
+ // mesh = await createElementSphereMesh(ctx, unit, radius, newProps.detail, mesh)
+ // ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
+ // updateColor = true
+ // }
+
+ if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
+ updateColor = true
+ }
+
+ if (updateColor) {
+ createColors(createLocationIterator(currentGroup), newProps.colorTheme, renderObject.values)
+ }
+
+ updateMeshValues(renderObject.values, newProps)
+ updateRenderableState(renderObject.state, newProps)
+
+ currentProps = newProps
+ return true
+ },
+ getLoci(pickingId: PickingId) {
+ return getLoci(pickingId, currentGroup, renderObject.id)
+ },
+ mark(loci: Loci, action: MarkerAction) {
+ mark(loci, action, currentGroup, renderObject.values)
+ },
+ destroy() {
+ // TODO
+ }
+ }
+}
\ 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 1792cf586..73ba9d65e 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -6,22 +6,20 @@
import { ValueCell } from 'mol-util/value-cell'
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Unit, Structure, Link, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, ComplexVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createStructureMeshRenderObject } from './util/common';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { MarkerAction, MarkerData, applyMarkerAction } from '../../../util/marker-data';
import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
+import { DefaultMeshProps } from '../../util';
import { Vec3 } from 'mol-math/linear-algebra';
-import { deepEqual } from 'mol-util';
import { LocationIterator } from './util/location-iterator';
import { createLinkCylinderMesh, DefaultLinkCylinderProps, LinkCylinderProps } from './util/link';
import { OrderedSet } from 'mol-data/int';
+import { ComplexMeshVisual } from '../complex-visual';
// TODO create seperate visual
// for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {
@@ -61,56 +59,16 @@ export const DefaultCarbohydrateLinkProps = {
detail: 0,
unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
}
-export type CarbohydrateLinkProps = Partial<typeof DefaultCarbohydrateLinkProps>
+export type CarbohydrateLinkProps = typeof DefaultCarbohydrateLinkProps
export function CarbohydrateLinkVisual(): ComplexVisual<CarbohydrateLinkProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultCarbohydrateLinkProps
- let mesh: Mesh
- let currentStructure: Structure
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, structure: Structure, props: CarbohydrateLinkProps = {}) {
- currentProps = Object.assign({}, DefaultCarbohydrateLinkProps, props)
- currentStructure = structure
-
- mesh = await createCarbohydrateLinkCylinderMesh(ctx, currentStructure, currentProps, mesh)
-
- const locationIt = CarbohydrateLinkIterator(structure)
- renderObject = createStructureMeshRenderObject(structure, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: CarbohydrateLinkProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- createColors(CarbohydrateLinkIterator(currentStructure), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return false
- },
- getLoci(pickingId: PickingId) {
- return getLinkLoci(pickingId, currentStructure, renderObject.id)
- },
- mark(loci: Loci, action: MarkerAction) {
- markLink(loci, action, currentStructure, renderObject.values)
- },
- destroy() {
- // TODO
- }
- }
+ return ComplexMeshVisual<CarbohydrateLinkProps>({
+ defaultProps: DefaultCarbohydrateLinkProps,
+ createMesh: createCarbohydrateLinkCylinderMesh,
+ createLocationIterator: CarbohydrateLinkIterator,
+ getLoci: getLinkLoci,
+ mark: markLink
+ })
}
function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
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 f84782fff..5afee10ec 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -6,29 +6,27 @@
import { ValueCell } from 'mol-util/value-cell'
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Unit, Structure, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, ComplexVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createStructureMeshRenderObject } from './util/common';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { MarkerAction, MarkerData, applyMarkerAction } from '../../../util/marker-data';
import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
+import { DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants';
-import { deepEqual } from 'mol-util';
import { LocationIterator } from './util/location-iterator';
import { OrderedSet } from 'mol-data/int';
+import { ComplexMeshVisual } from '../complex-visual';
const t = Mat4.identity()
const sVec = Vec3.zero()
const pd = Vec3.zero()
-async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Structure, mesh?: Mesh) {
+async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Structure, props: CarbohydrateSymbolProps, mesh?: Mesh) {
const builder = MeshBuilder.create(256, 128, mesh)
const carbohydrates = structure.carbohydrates
@@ -124,56 +122,16 @@ export const DefaultCarbohydrateSymbolProps = {
detail: 0,
unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
}
-export type CarbohydrateSymbolProps = Partial<typeof DefaultCarbohydrateSymbolProps>
+export type CarbohydrateSymbolProps = typeof DefaultCarbohydrateSymbolProps
export function CarbohydrateSymbolVisual(): ComplexVisual<CarbohydrateSymbolProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultCarbohydrateSymbolProps
- let mesh: Mesh
- let currentStructure: Structure
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, structure: Structure, props: CarbohydrateSymbolProps = {}) {
- currentProps = Object.assign({}, DefaultCarbohydrateSymbolProps, props)
- currentStructure = structure
-
- mesh = await createCarbohydrateSymbolMesh(ctx, currentStructure, mesh)
-
- const locationIt = CarbohydrateElementIterator(structure)
- renderObject = createStructureMeshRenderObject(structure, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: CarbohydrateSymbolProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- createColors(CarbohydrateElementIterator(currentStructure), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return false
- },
- getLoci(pickingId: PickingId) {
- return getCarbohydrateLoci(pickingId, currentStructure, renderObject.id)
- },
- mark(loci: Loci, action: MarkerAction) {
- markCarbohydrate(loci, action, currentStructure, renderObject.values)
- },
- destroy() {
- // TODO
- }
- }
+ return ComplexMeshVisual<CarbohydrateSymbolProps>({
+ defaultProps: DefaultCarbohydrateSymbolProps,
+ createMesh: createCarbohydrateSymbolMesh,
+ createLocationIterator: CarbohydrateElementIterator,
+ getLoci: getCarbohydrateLoci,
+ mark: markCarbohydrate
+ })
}
function CarbohydrateElementIterator(structure: Structure): LocationIterator {
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 7a2435546..2942d1d70 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
@@ -6,23 +6,18 @@
import { ValueCell } from 'mol-util/value-cell'
-import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
import { Link, Structure, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, ComplexVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh } from './util/link';
-import { MeshValues } from 'mol-gl/renderable';
-import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
-import { createValueColor } from '../../../util/color-data';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
-import { MarkerAction, applyMarkerAction, createMarkers, MarkerData } from '../../../util/marker-data';
+import { MarkerAction, applyMarkerAction, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
-import { createIdentityTransform } from './util/common';
-import { updateMeshValues, updateRenderableState, createMeshValues, createRenderableState } from '../../util';
-// import { chainIdLinkColorData } from '../../../theme/structure/color/chain-id';
+import { ComplexMeshVisual } from '../complex-visual';
+import { LocationIterator } from './util/location-iterator';
async function createCrossLinkRestraintCylinderMesh(ctx: RuntimeContext, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
@@ -54,66 +49,35 @@ export const DefaultCrossLinkRestraintProps = {
flipSided: false,
flatShaded: false,
}
-export type CrossLinkRestraintProps = Partial<typeof DefaultCrossLinkRestraintProps>
+export type CrossLinkRestraintProps = typeof DefaultCrossLinkRestraintProps
-export function CrossLinkRestraintVisual(): ComplexVisual<CrossLinkRestraintProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultCrossLinkRestraintProps
- let mesh: Mesh
- let currentStructure: Structure
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, structure: Structure, props: CrossLinkRestraintProps = {}) {
- currentProps = Object.assign({}, DefaultCrossLinkRestraintProps, props)
- currentStructure = structure
-
- const elementCount = structure.crossLinkRestraints.count
- const instanceCount = 1
-
- mesh = await createCrossLinkRestraintCylinderMesh(ctx, structure, currentProps)
-
- const transforms = createIdentityTransform()
- const color = createValueColor(0x119911) // TODO
- const marker = createMarkers(instanceCount * elementCount)
-
- const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
-
- const values: MeshValues = {
- ...getMeshData(mesh),
- ...color,
- ...marker,
- aTransform: transforms,
- elements: mesh.indexBuffer,
- ...createMeshValues(currentProps, counts),
- }
- const state = createRenderableState(currentProps)
-
- renderObject = createMeshRenderObject(values, state)
- },
- async update(ctx: RuntimeContext, props: CrossLinkRestraintProps) {
- const newProps = Object.assign({}, currentProps, props)
+// TODO update & create in-place
+// if (currentProps.radialSegments !== newProps.radialSegments) return false
- if (!renderObject) return false
-
- // TODO create in-place
- if (currentProps.radialSegments !== newProps.radialSegments) return false
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
+export function CrossLinkRestraintVisual(): ComplexVisual<CrossLinkRestraintProps> {
+ return ComplexMeshVisual<CrossLinkRestraintProps>({
+ defaultProps: DefaultCrossLinkRestraintProps,
+ createMesh: createCrossLinkRestraintCylinderMesh,
+ createLocationIterator: CrossLinkRestraintIterator,
+ getLoci: getLinkLoci,
+ mark: markLink
+ })
+}
- return false
- },
- getLoci(pickingId: PickingId) {
- return getLinkLoci(pickingId, currentStructure, renderObject.id)
- },
- mark(loci: Loci, action: MarkerAction) {
- markLink(loci, action, currentStructure, renderObject.values)
- },
- destroy() {
- // TODO
- }
+function CrossLinkRestraintIterator(structure: Structure): LocationIterator {
+ const { pairs } = structure.crossLinkRestraints
+ const elementCount = pairs.length
+ const instanceCount = 1
+ const location = Link.Location()
+ const getLocation = (elementIndex: number, instanceIndex: number) => {
+ const pair = pairs[elementIndex]
+ location.aUnit = pair.unitA
+ location.aIndex = pair.indexA
+ location.bUnit = pair.unitB
+ location.bIndex = pair.indexB
+ return location
}
+ return LocationIterator(elementCount, instanceCount, getLocation)
}
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index 55a4b30eb..d512c3048 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -130,10 +130,10 @@ export default function PointVisual(): UnitsVisual<PointProps> {
return false
},
getLoci(pickingId: PickingId) {
- return getElementLoci(renderObject.id, currentGroup, pickingId)
+ return getElementLoci(pickingId, currentGroup, renderObject.id)
},
mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
+ markElement(loci, action, currentGroup, renderObject.values)
},
destroy() {
// TODO
diff --git a/src/mol-geo/representation/structure/visual/element-sphere.ts b/src/mol-geo/representation/structure/visual/element-sphere.ts
index 48735943b..6b5c78cc1 100644
--- a/src/mol-geo/representation/structure/visual/element-sphere.ts
+++ b/src/mol-geo/representation/structure/visual/element-sphere.ts
@@ -5,92 +5,23 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ValueCell } from 'mol-util/value-cell'
-
-import { MeshRenderObject } from 'mol-gl/render-object'
-import { Unit } from 'mol-model/structure';
-import { DefaultStructureProps, UnitsVisual } from '..';
-import { RuntimeContext } from 'mol-task'
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { createElementSphereMesh, markElement, getElementRadius, getElementLoci } from './util/element';
-import { deepEqual } from 'mol-util';
-import { Mesh } from '../../../shape/mesh';
-import { PickingId } from '../../../util/picking';
-import { MarkerAction } from '../../../util/marker-data';
-import { Loci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
+import { UnitsVisual } from '..';
+import { createElementSphereMesh, markElement, getElementLoci } from './util/element';
import { StructureElementIterator } from './util/location-iterator';
+import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
export const DefaultElementSphereProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
- detail: 0,
- unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+ ...DefaultUnitsMeshProps,
+ detail: 0
}
-export type ElementSphereProps = Partial<typeof DefaultElementSphereProps>
+export type ElementSphereProps = typeof DefaultElementSphereProps
export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultElementSphereProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: ElementSphereProps = {}) {
- currentProps = Object.assign({}, DefaultElementSphereProps, props)
- currentGroup = group
-
- const { detail, sizeTheme, unitKinds } = { ...DefaultElementSphereProps, ...props }
- const unit = group.units[0]
-
- const radius = getElementRadius(unit, sizeTheme)
- mesh = unitKinds.includes(unit.kind)
- ? await createElementSphereMesh(ctx, unit, radius, detail, mesh)
- : Mesh.createEmpty(mesh)
-
- const locationIt = StructureElementIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: ElementSphereProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (newProps.detail !== currentProps.detail) {
- const unit = currentGroup.units[0]
- const radius = getElementRadius(unit, newProps.sizeTheme)
- mesh = await createElementSphereMesh(ctx, unit, radius, newProps.detail, mesh)
- ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
- updateColor = true
- }
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- return getElementLoci(renderObject.id, currentGroup, pickingId)
- },
- mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
- },
- destroy() {
- // TODO
- }
- }
-}
+ return UnitsMeshVisual<ElementSphereProps>({
+ defaultProps: DefaultElementSphereProps,
+ createMesh: createElementSphereMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement
+ })
+}
\ 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 7587b44fa..0285609bf 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
@@ -6,7 +6,6 @@
import { ValueCell } from 'mol-util/value-cell'
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Link, Structure, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, ComplexVisual } from '..';
import { RuntimeContext } from 'mol-task'
@@ -17,10 +16,8 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
-import { createColors, createStructureMeshRenderObject } from './util/common';
-import { updateMeshValues, updateRenderableState } from '../../util';
import { LinkIterator } from './util/location-iterator';
-import { deepEqual } from 'mol-util';
+import { ComplexMeshVisual } from '../complex-visual';
async function createInterUnitLinkCylinderMesh(ctx: RuntimeContext, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
const links = structure.links
@@ -49,59 +46,16 @@ export const DefaultInterUnitLinkProps = {
...DefaultLinkCylinderProps,
sizeTheme: { name: 'physical', factor: 0.3 } as SizeTheme,
}
-export type InterUnitLinkProps = Partial<typeof DefaultInterUnitLinkProps>
+export type InterUnitLinkProps = typeof DefaultInterUnitLinkProps
export function InterUnitLinkVisual(): ComplexVisual<InterUnitLinkProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultInterUnitLinkProps
- let mesh: Mesh
- let currentStructure: Structure
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, structure: Structure, props: InterUnitLinkProps = {}) {
- currentProps = Object.assign({}, DefaultInterUnitLinkProps, props)
- currentStructure = structure
-
- mesh = await createInterUnitLinkCylinderMesh(ctx, structure, currentProps)
-
- const locationIt = LinkIterator.fromStructure(structure)
- renderObject = createStructureMeshRenderObject(structure, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: InterUnitLinkProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- // TODO create in-place
- if (currentProps.radialSegments !== newProps.radialSegments) return false
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- createColors(LinkIterator.fromStructure(currentStructure), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return false
- },
- getLoci(pickingId: PickingId) {
- return getLinkLoci(pickingId, currentStructure, renderObject.id)
- },
- mark(loci: Loci, action: MarkerAction) {
- markLink(loci, action, currentStructure, renderObject.values)
- },
- destroy() {
- // TODO
- }
- }
+ return ComplexMeshVisual<InterUnitLinkProps>({
+ defaultProps: DefaultInterUnitLinkProps,
+ createMesh: createInterUnitLinkCylinderMesh,
+ createLocationIterator: LinkIterator.fromStructure,
+ getLoci: getLinkLoci,
+ mark: markLink
+ })
}
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
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 34db658a1..d9c66bd1b 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
@@ -7,22 +7,18 @@
import { ValueCell } from 'mol-util/value-cell'
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Unit, Link, StructureElement } from 'mol-model/structure';
-import { UnitsVisual, DefaultStructureProps } from '..';
+import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh } from './util/link';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
-// import { createUniformColor } from '../../../util/color-data';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
import { LinkIterator } from './util/location-iterator';
-import { deepEqual } from 'mol-util';
+import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, props: LinkCylinderProps, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -62,65 +58,20 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
}
export const DefaultIntraUnitLinkProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
+ ...DefaultUnitsMeshProps,
...DefaultLinkCylinderProps,
sizeTheme: { name: 'physical', factor: 0.3 } as SizeTheme,
}
-export type IntraUnitLinkProps = Partial<typeof DefaultIntraUnitLinkProps>
+export type IntraUnitLinkProps = typeof DefaultIntraUnitLinkProps
export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultIntraUnitLinkProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: IntraUnitLinkProps = {}) {
- currentProps = Object.assign({}, DefaultIntraUnitLinkProps, props)
- currentGroup = group
-
- const unit = group.units[0]
- mesh = await createIntraUnitLinkCylinderMesh(ctx, unit, currentProps)
-
- const locationIt = LinkIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: IntraUnitLinkProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- // TODO create in-place
- if (currentProps.radialSegments !== newProps.radialSegments) return false
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- createColors(LinkIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- return getLinkLoci(pickingId, currentGroup, renderObject.id)
- },
- mark(loci: Loci, action: MarkerAction) {
- markLink(loci, action, currentGroup, renderObject.values)
- },
- destroy() {
- // TODO
- }
- }
+ return UnitsMeshVisual<IntraUnitLinkProps>({
+ defaultProps: DefaultIntraUnitLinkProps,
+ createMesh: createIntraUnitLinkCylinderMesh,
+ createLocationIterator: LinkIterator.fromGroup,
+ getLoci: getLinkLoci,
+ mark: markLink
+ })
}
function getLinkLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number) {
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 7f76cf611..3bd6af749 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -4,20 +4,10 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ValueCell } from 'mol-util/value-cell'
-
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Unit } from 'mol-model/structure';
-import { DefaultStructureProps, UnitsVisual } from '..';
+import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { deepEqual } from 'mol-util';
import { Mesh } from '../../../shape/mesh';
-import { PickingId } from '../../../util/picking';
-import { MarkerAction } from '../../../util/marker-data';
-import { Loci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getElementLoci, markElement } from './util/element';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
@@ -25,6 +15,7 @@ import { Segmentation, SortedArray } from 'mol-data/int';
import { MoleculeType, isNucleic, isPurinBase, isPyrimidineBase } from 'mol-model/structure/model/types';
import { getElementIndexForAtomId, getElementIndexForAtomRole } from 'mol-model/structure/util';
import { StructureElementIterator } from './util/location-iterator';
+import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
const p1 = Vec3.zero()
const p2 = Vec3.zero()
@@ -39,7 +30,7 @@ const center = Vec3.zero()
const t = Mat4.identity()
const sVec = Vec3.zero()
-async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
+async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
const builder = MeshBuilder.create(256, 128, mesh)
@@ -113,73 +104,16 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, mesh?:
}
export const DefaultNucleotideBlockProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
- detail: 0,
- unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+ ...DefaultUnitsMeshProps
}
-export type NucleotideBlockProps = Partial<typeof DefaultNucleotideBlockProps>
+export type NucleotideBlockProps = typeof DefaultNucleotideBlockProps
export function NucleotideBlockVisual(): UnitsVisual<NucleotideBlockProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultNucleotideBlockProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: NucleotideBlockProps = {}) {
- currentProps = Object.assign({}, DefaultNucleotideBlockProps, props)
- currentGroup = group
-
- const { unitKinds } = { ...DefaultNucleotideBlockProps, ...props }
- const unit = group.units[0]
-
- mesh = unitKinds.includes(unit.kind)
- ? await createNucleotideBlockMesh(ctx, unit, mesh)
- : Mesh.createEmpty(mesh)
-
- const locationIt = StructureElementIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: NucleotideBlockProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (newProps.detail !== currentProps.detail) {
- const unit = currentGroup.units[0]
- mesh = await createNucleotideBlockMesh(ctx, unit, mesh)
- ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
- updateColor = true
- }
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- if (ctx.shouldUpdate) await ctx.update('Computing nucleotide block colors');
- createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- return getElementLoci(renderObject.id, currentGroup, pickingId)
- },
- mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
- },
- destroy() {
- // TODO
- }
- }
-}
+ return UnitsMeshVisual<NucleotideBlockProps>({
+ defaultProps: DefaultNucleotideBlockProps,
+ createMesh: createNucleotideBlockMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement
+ })
+}
\ No newline at end of file
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 2956a9d8e..1cf481582 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -4,27 +4,18 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ValueCell } from 'mol-util/value-cell'
-
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Unit } from 'mol-model/structure';
-import { DefaultStructureProps, UnitsVisual } from '..';
+import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { deepEqual } from 'mol-util';
import { Mesh } from '../../../shape/mesh';
-import { PickingId } from '../../../util/picking';
-import { MarkerAction } from '../../../util/marker-data';
-import { Loci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
import { getElementLoci, markElement } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
import { StructureElementIterator } from './util/location-iterator';
+import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
-async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
+async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
if (!polymerElementCount) return Mesh.createEmpty(mesh)
console.log('polymerElementCount backbone', polymerElementCount)
@@ -59,73 +50,16 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
}
export const DefaultPolymerBackboneProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
- detail: 0,
- unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+ ...DefaultUnitsMeshProps
}
-export type PolymerBackboneProps = Partial<typeof DefaultPolymerBackboneProps>
+export type PolymerBackboneProps = typeof DefaultPolymerBackboneProps
export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultPolymerBackboneProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: PolymerBackboneProps = {}) {
- currentProps = Object.assign({}, DefaultPolymerBackboneProps, props)
- currentGroup = group
-
- const { unitKinds } = { ...DefaultPolymerBackboneProps, ...props }
- const unit = group.units[0]
-
- mesh = unitKinds.includes(unit.kind)
- ? await createPolymerBackboneCylinderMesh(ctx, unit, mesh)
- : Mesh.createEmpty(mesh)
-
- const locationIt = StructureElementIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: PolymerBackboneProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (newProps.detail !== currentProps.detail) {
- const unit = currentGroup.units[0]
- mesh = await createPolymerBackboneCylinderMesh(ctx, unit, mesh)
- ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
- updateColor = true
- }
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
- createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- return getElementLoci(renderObject.id, currentGroup, pickingId)
- },
- mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
- },
- destroy() {
- // TODO
- }
- }
-}
+ return UnitsMeshVisual<PolymerBackboneProps>({
+ defaultProps: DefaultPolymerBackboneProps,
+ createMesh: createPolymerBackboneCylinderMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement
+ })
+}
\ 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 926d76775..3ac265684 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -4,27 +4,17 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ValueCell } from 'mol-util/value-cell'
-
-import { MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, StructureElement } from 'mol-model/structure';
-import { DefaultStructureProps, UnitsVisual } from '..';
+import { Unit } from 'mol-model/structure';
+import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { markElement } from './util/element';
-import { deepEqual } from 'mol-util';
+import { markElement, getElementLoci } from './util/element';
import { Mesh } from '../../../shape/mesh';
-import { PickingId } from '../../../util/picking';
-import { OrderedSet } from 'mol-data/int';
-import { MarkerAction } from '../../../util/marker-data';
-import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment } from './util/polymer';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
import { StructureElementIterator } from './util/location-iterator';
+import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
const t = Mat4.identity()
const sVec = Vec3.zero()
@@ -32,7 +22,7 @@ const n0 = Vec3.zero()
const n1 = Vec3.zero()
const upVec = Vec3.zero()
-async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
+async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
console.log('polymerElementCount direction', polymerElementCount)
if (!polymerElementCount) return Mesh.createEmpty(mesh)
@@ -87,79 +77,16 @@ async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit,
}
export const DefaultPolymerDirectionProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
- detail: 0,
- unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+ ...DefaultUnitsMeshProps
}
-export type PolymerDirectionProps = Partial<typeof DefaultPolymerDirectionProps>
+export type PolymerDirectionProps = typeof DefaultPolymerDirectionProps
export function PolymerDirectionVisual(): UnitsVisual<PolymerDirectionProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultPolymerDirectionProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: PolymerDirectionProps = {}) {
- currentProps = Object.assign({}, DefaultPolymerDirectionProps, props)
- currentGroup = group
-
- const { unitKinds } = { ...DefaultPolymerDirectionProps, ...props }
- const unit = group.units[0]
-
- mesh = unitKinds.includes(unit.kind)
- ? await createPolymerDirectionWedgeMesh(ctx, unit, mesh)
- : Mesh.createEmpty(mesh)
-
- const locationIt = StructureElementIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: PolymerDirectionProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (newProps.detail !== currentProps.detail) {
- const unit = currentGroup.units[0]
- mesh = await createPolymerDirectionWedgeMesh(ctx, unit, mesh)
- ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
- updateColor = true
- }
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- if (ctx.shouldUpdate) await ctx.update('Computing direction colors');
- createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- const { objectId, instanceId, elementId } = pickingId
- if (renderObject.id === objectId) {
- const unit = currentGroup.units[instanceId]
- const indices = OrderedSet.ofSingleton(elementId as StructureElement.UnitIndex);
- return StructureElement.Loci([{ unit, indices }])
- }
- return EmptyLoci
- },
- mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
- },
- destroy() {
- // TODO
- }
- }
-}
+ return UnitsMeshVisual<PolymerDirectionProps>({
+ defaultProps: DefaultPolymerDirectionProps,
+ createMesh: createPolymerDirectionWedgeMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement
+ })
+}
\ No newline at end of file
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 5c9dc9668..172b2b52f 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -4,27 +4,18 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ValueCell } from 'mol-util/value-cell'
-
-import { MeshRenderObject } from 'mol-gl/render-object'
import { Unit } from 'mol-model/structure';
-import { DefaultStructureProps, UnitsVisual } from '..';
+import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { deepEqual } from 'mol-util';
import { Mesh } from '../../../shape/mesh';
-import { PickingId } from '../../../util/picking';
-import { MarkerAction } from '../../../util/marker-data';
-import { Loci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerGapCount, PolymerGapIterator } from './util/polymer';
import { getElementLoci, markElement } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
import { StructureElementIterator } from './util/location-iterator';
+import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
-async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
+async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
const polymerGapCount = getPolymerGapCount(unit)
if (!polymerGapCount) return Mesh.createEmpty(mesh)
console.log('polymerGapCount', polymerGapCount)
@@ -65,73 +56,16 @@ async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, mes
}
export const DefaultPolymerGapProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
- detail: 0,
- unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+ ...DefaultUnitsMeshProps
}
-export type PolymerGapProps = Partial<typeof DefaultPolymerGapProps>
+export type PolymerGapProps = typeof DefaultPolymerGapProps
export function PolymerGapVisual(): UnitsVisual<PolymerGapProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultPolymerGapProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: PolymerGapProps = {}) {
- currentProps = Object.assign({}, DefaultPolymerGapProps, props)
- currentGroup = group
-
- const { unitKinds } = { ...DefaultPolymerGapProps, ...props }
- const unit = group.units[0]
-
- mesh = unitKinds.includes(unit.kind)
- ? await createPolymerGapCylinderMesh(ctx, unit, mesh)
- : Mesh.createEmpty(mesh)
-
- const locationIt = StructureElementIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: PolymerGapProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (newProps.detail !== currentProps.detail) {
- const unit = currentGroup.units[0]
- mesh = await createPolymerGapCylinderMesh(ctx, unit, mesh)
- ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
- updateColor = true
- }
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
- createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- return getElementLoci(renderObject.id, currentGroup, pickingId)
- },
- mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
- },
- destroy() {
- // TODO
- }
- }
-}
+ return UnitsMeshVisual<PolymerGapProps>({
+ defaultProps: DefaultPolymerGapProps,
+ createMesh: createPolymerGapCylinderMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement
+ })
+}
\ 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 472f4366e..91b25ffe0 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -4,30 +4,20 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ValueCell } from 'mol-util/value-cell'
-
-import { MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, StructureElement } from 'mol-model/structure';
-import { DefaultStructureProps, UnitsVisual } from '..';
+import { Unit } from 'mol-model/structure';
+import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { createColors, createUnitsMeshRenderObject } from './util/common';
-import { markElement } from './util/element';
-import { deepEqual } from 'mol-util';
+import { markElement, getElementLoci } from './util/element';
import { Mesh } from '../../../shape/mesh';
-import { PickingId } from '../../../util/picking';
-import { OrderedSet } from 'mol-data/int';
-import { MarkerAction } from '../../../util/marker-data';
-import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
-import { updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment } from './util/polymer';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
import { StructureElementIterator } from './util/location-iterator';
+import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
// TODO handle polymer ends properly
-async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
+async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
console.log('polymerElementCount trace', polymerElementCount)
if (!polymerElementCount) return Mesh.createEmpty(mesh)
@@ -80,79 +70,16 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, mesh?: Me
}
export const DefaultPolymerTraceProps = {
- ...DefaultMeshProps,
- ...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
- detail: 0,
- unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
+ ...DefaultUnitsMeshProps
}
-export type PolymerTraceProps = Partial<typeof DefaultPolymerTraceProps>
+export type PolymerTraceProps = typeof DefaultPolymerTraceProps
export function PolymerTraceVisual(): UnitsVisual<PolymerTraceProps> {
- let renderObject: MeshRenderObject
- let currentProps: typeof DefaultPolymerTraceProps
- let mesh: Mesh
- let currentGroup: Unit.SymmetryGroup
-
- return {
- get renderObject () { return renderObject },
- async create(ctx: RuntimeContext, group: Unit.SymmetryGroup, props: PolymerTraceProps = {}) {
- currentProps = Object.assign({}, DefaultPolymerTraceProps, props)
- currentGroup = group
-
- const { unitKinds } = { ...DefaultPolymerTraceProps, ...props }
- const unit = group.units[0]
-
- mesh = unitKinds.includes(unit.kind)
- ? await createPolymerTraceMesh(ctx, unit, mesh)
- : Mesh.createEmpty(mesh)
-
- const locationIt = StructureElementIterator.fromGroup(group)
- renderObject = createUnitsMeshRenderObject(group, mesh, locationIt, currentProps)
- },
- async update(ctx: RuntimeContext, props: PolymerTraceProps) {
- const newProps = Object.assign({}, currentProps, props)
-
- if (!renderObject) return false
-
- let updateColor = false
-
- if (newProps.detail !== currentProps.detail) {
- const unit = currentGroup.units[0]
- mesh = await createPolymerTraceMesh(ctx, unit, mesh)
- ValueCell.update(renderObject.values.drawCount, mesh.triangleCount * 3)
- updateColor = true
- }
-
- if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
- updateColor = true
- }
-
- if (updateColor) {
- if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
- createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
- }
-
- updateMeshValues(renderObject.values, newProps)
- updateRenderableState(renderObject.state, newProps)
-
- currentProps = newProps
- return true
- },
- getLoci(pickingId: PickingId) {
- const { objectId, instanceId, elementId } = pickingId
- if (renderObject.id === objectId) {
- const unit = currentGroup.units[instanceId]
- const indices = OrderedSet.ofSingleton(elementId as StructureElement.UnitIndex);
- return StructureElement.Loci([{ unit, indices }])
- }
- return EmptyLoci
- },
- mark(loci: Loci, action: MarkerAction) {
- markElement(renderObject.values.tMarker, currentGroup, loci, action)
- },
- destroy() {
- // TODO
- }
- }
-}
+ return UnitsMeshVisual<PolymerTraceProps>({
+ defaultProps: DefaultPolymerTraceProps,
+ createMesh: createPolymerTraceMesh,
+ createLocationIterator: StructureElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ mark: markElement
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index 25fd7d104..e07b033c5 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -86,7 +86,7 @@ function _createMeshValues(transforms: ValueCell<Float32Array>, mesh: Mesh, loca
}
}
-export function createStructureMeshValues(structure: Structure, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps): MeshValues {
+export function createComplexMeshValues(structure: Structure, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps): MeshValues {
const transforms = createIdentityTransform()
return _createMeshValues(transforms, mesh, locationIt, props)
}
@@ -96,8 +96,8 @@ export function createUnitsMeshValues(group: Unit.SymmetryGroup, mesh: Mesh, loc
return _createMeshValues(transforms, mesh, locationIt, props)
}
-export function createStructureMeshRenderObject(structure: Structure, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps) {
- const values = createStructureMeshValues(structure, mesh, locationIt, props)
+export function createComplexMeshRenderObject(structure: Structure, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps) {
+ const values = createComplexMeshValues(structure, mesh, locationIt, props)
const state = createRenderableState(props)
return createMeshRenderObject(values, state)
}
@@ -106,4 +106,9 @@ export function createUnitsMeshRenderObject(group: Unit.SymmetryGroup, mesh: Mes
const values = createUnitsMeshValues(group, mesh, locationIt, props)
const state = createRenderableState(props)
return createMeshRenderObject(values, state)
+}
+
+export function updateComplexMeshRenderObject(structure: Structure, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps): MeshValues {
+ const transforms = createIdentityTransform()
+ return _createMeshValues(transforms, mesh, locationIt, props)
}
\ 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 885b96aec..b23bc8010 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -12,9 +12,8 @@ import { sphereVertexCount } from '../../../../primitive/sphere';
import { Mesh } from '../../../../shape/mesh';
import { MeshBuilder } from '../../../../shape/mesh-builder';
import { ValueCell, defaults } from 'mol-util';
-import { TextureImage } from 'mol-gl/renderable/util';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
-import { MarkerAction, applyMarkerAction } from '../../../../util/marker-data';
+import { MarkerAction, applyMarkerAction, MarkerData } from '../../../../util/marker-data';
import { Interval, OrderedSet } from 'mol-data/int';
import { getPhysicalRadius } from '../../../../theme/structure/size/physical';
import { PickingId } from '../../../../util/picking';
@@ -30,8 +29,16 @@ export function getElementRadius(unit: Unit, props: SizeTheme): StructureElement
}
}
-export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, radius: StructureElement.Property<number>, detail: number, mesh?: Mesh) {
+export interface ElementSphereMeshProps {
+ sizeTheme: SizeTheme,
+ detail: number,
+}
+
+export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, props: ElementSphereMeshProps, mesh?: Mesh) {
+ const { detail, sizeTheme } = props
+
const { elements } = unit;
+ const radius = getElementRadius(unit, sizeTheme)
const elementCount = elements.length;
const vertexCount = elementCount * sphereVertexCount(detail)
const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
@@ -56,10 +63,13 @@ export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, r
return meshBuilder.getMesh()
}
-export function markElement(tMarker: ValueCell<TextureImage>, group: Unit.SymmetryGroup, loci: Loci, action: MarkerAction) {
- let changed = false
+export function markElement(loci: Loci, action: MarkerAction, group: Unit.SymmetryGroup, values: MarkerData) {
+ const tMarker = values.tMarker
+
const elementCount = group.elements.length
const instanceCount = group.units.length
+
+ let changed = false
const array = tMarker.ref.value.array
if (isEveryLoci(loci)) {
applyMarkerAction(array, 0, elementCount * instanceCount, action)
@@ -92,7 +102,7 @@ export function markElement(tMarker: ValueCell<TextureImage>, group: Unit.Symmet
}
}
-export function getElementLoci(id: number, group: Unit.SymmetryGroup, pickingId: PickingId) {
+export function getElementLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number) {
const { objectId, instanceId, elementId } = pickingId
if (id === objectId) {
const unit = group.units[instanceId]
diff --git a/src/mol-geo/representation/util.ts b/src/mol-geo/representation/util.ts
index c76ad36b1..13d34ebec 100644
--- a/src/mol-geo/representation/util.ts
+++ b/src/mol-geo/representation/util.ts
@@ -18,7 +18,7 @@ export const DefaultBaseProps = {
useFog: true,
quality: 'auto' as VisualQuality
}
-export type BaseProps = Partial<typeof DefaultBaseProps>
+export type BaseProps = typeof DefaultBaseProps
export const DefaultMeshProps = {
...DefaultBaseProps,
@@ -26,7 +26,7 @@ export const DefaultMeshProps = {
flipSided: false,
flatShaded: false,
}
-export type MeshProps = Partial<typeof DefaultMeshProps>
+export type MeshProps = typeof DefaultMeshProps
type Counts = { drawCount: number, elementCount: number, instanceCount: number }
diff --git a/src/mol-geo/representation/volume/index.ts b/src/mol-geo/representation/volume/index.ts
index c1f0706af..75555e2ca 100644
--- a/src/mol-geo/representation/volume/index.ts
+++ b/src/mol-geo/representation/volume/index.ts
@@ -11,18 +11,24 @@ 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';
export interface VolumeVisual<P extends RepresentationProps = {}> extends Visual<VolumeData, P> { }
export interface VolumeRepresentation<P extends RepresentationProps = {}> extends Representation<VolumeData, P> { }
-export function VolumeRepresentation<P>(visualCtor: (volumeData: VolumeData) => VolumeVisual<P>): VolumeRepresentation<P> {
+export const DefaultVolumeProps = {
+ ...DefaultBaseProps
+}
+export type VolumeProps = typeof DefaultVolumeProps
+
+export function VolumeRepresentation<P extends VolumeProps>(visualCtor: (volumeData: VolumeData) => VolumeVisual<P>): VolumeRepresentation<P> {
const renderObjects: RenderObject[] = []
let _volumeData: VolumeData
let _props: P
- function create(volumeData: VolumeData, props: P = {} as P) {
- _props = props
+ function create(volumeData: VolumeData, props: Partial<P> = {}) {
+ _props = Object.assign({}, DefaultVolumeProps, _props, props)
return Task.create('VolumeRepresentation.create', async ctx => {
_volumeData = volumeData
const visual = visualCtor(_volumeData)
@@ -31,7 +37,7 @@ export function VolumeRepresentation<P>(visualCtor: (volumeData: VolumeData) =>
});
}
- function update(props: P) {
+ function update(props: Partial<P>) {
return Task.create('VolumeRepresentation.update', async ctx => {})
}
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/data.ts b/src/mol-model/structure/structure/unit/pair-restraints/data.ts
index 0fdd3ce75..7b0d01e86 100644
--- a/src/mol-model/structure/structure/unit/pair-restraints/data.ts
+++ b/src/mol-model/structure/structure/unit/pair-restraints/data.ts
@@ -5,6 +5,7 @@
*/
import Unit from '../../unit';
+import { StructureElement } from '../../../structure';
const emptyArray: number[] = []
@@ -13,13 +14,13 @@ class CrossLinkRestraints {
private readonly pairKeyIndices: Map<string, number[]>
/** Indices into this.pairs */
- getPairIndices(indexA: number, unitA: Unit, indexB: number, unitB: Unit): ReadonlyArray<number> {
+ getPairIndices(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): ReadonlyArray<number> {
const key = CrossLinkRestraints.getPairKey(indexA, unitA, indexB, unitB)
const indices = this.pairKeyIndices.get(key)
return indices !== undefined ? indices : emptyArray
}
- getPairs(indexA: number, unitA: Unit, indexB: number, unitB: Unit): CrossLinkRestraints.Pair[] | undefined {
+ getPairs(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit): CrossLinkRestraints.Pair[] | undefined {
const indices = this.getPairIndices(indexA, unitA, indexB, unitB)
return indices.length ? indices.map(idx => this.pairs[idx]) : undefined
}
@@ -42,8 +43,8 @@ namespace CrossLinkRestraints {
export interface Pair {
readonly unitA: Unit,
readonly unitB: Unit,
- readonly indexA: number,
- readonly indexB: number,
+ readonly indexA: StructureElement.UnitIndex,
+ readonly indexB: StructureElement.UnitIndex,
readonly restraintType: 'harmonic' | 'upper bound' | 'lower bound',
readonly distanceThreshold: number,
@@ -52,7 +53,7 @@ namespace CrossLinkRestraints {
readonly sigma2: number,
}
- export function getPairKey(indexA: number, unitA: Unit, indexB: number, unitB: Unit) {
+ export function getPairKey(indexA: StructureElement.UnitIndex, unitA: Unit, indexB: StructureElement.UnitIndex, unitB: Unit) {
return `${indexA}|${unitA.id}|${indexB}|${unitB.id}`
}
}
diff --git a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts b/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
index a69307757..cfe6aaa23 100644
--- a/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
+++ b/src/mol-model/structure/structure/unit/pair-restraints/extract-cross-links.ts
@@ -8,6 +8,7 @@ import Unit from '../../unit';
import Structure from '../../structure';
import { IHMCrossLinkRestraint } from '../../../model/formats/mmcif/pair-restraint';
import { CrossLinkRestraints } from './data';
+import { StructureElement } from '../../../structure';
function _addRestraints(map: Map<number, number>, unit: Unit, restraints: IHMCrossLinkRestraint) {
const { elements } = unit;
@@ -27,8 +28,8 @@ function extractInter(pairs: CrossLinkRestraints.Pair[], unitA: Unit, unitB: Uni
const restraints = IHMCrossLinkRestraint.fromModel(unitA.model)
if (!restraints) return
- const rA = new Map<number, number>();
- const rB = new Map<number, number>();
+ const rA = new Map<number, StructureElement.UnitIndex>();
+ const rB = new Map<number, StructureElement.UnitIndex>();
_addRestraints(rA, unitA, restraints)
_addRestraints(rB, unitB, restraints)
@@ -53,14 +54,14 @@ function extractIntra(pairs: CrossLinkRestraints.Pair[], unit: Unit) {
const elementCount = elements.length;
const kind = unit.kind
- const r = new Map<number, number[]>();
+ const r = new Map<number, StructureElement.UnitIndex[]>();
for (let i = 0; i < elementCount; i++) {
const e = elements[i];
restraints.getIndicesByElement(e, kind).forEach(ri => {
const il = r.get(ri)
- if (il) il.push(i)
- else r.set(ri, [i])
+ if (il) il.push(i as StructureElement.UnitIndex)
+ else r.set(ri, [i as StructureElement.UnitIndex])
})
}
@@ -74,7 +75,7 @@ function extractIntra(pairs: CrossLinkRestraints.Pair[], unit: Unit) {
})
}
-function createCrossLinkRestraint(unitA: Unit, indexA: number, unitB: Unit, indexB: number, restraints: IHMCrossLinkRestraint, row: number): CrossLinkRestraints.Pair {
+function createCrossLinkRestraint(unitA: Unit, indexA: StructureElement.UnitIndex, unitB: Unit, indexB: StructureElement.UnitIndex, restraints: IHMCrossLinkRestraint, row: number): CrossLinkRestraints.Pair {
return {
unitA, indexA, unitB, indexB,
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 06c561e74..f490b055a 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -17,14 +17,14 @@ import { DistanceRestraintProps } from 'mol-geo/representation/structure/represe
import { BackboneProps } from 'mol-geo/representation/structure/representation/backbone';
// import { Queries as Q, StructureProperties as SP, Query, Selection } from 'mol-model/structure';
-const spacefillProps: SpacefillProps = {
+const spacefillProps: Partial<SpacefillProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
quality: 'auto',
useFog: false
}
-const ballAndStickProps: BallAndStickProps = {
+const ballAndStickProps: Partial<BallAndStickProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
sizeTheme: { name: 'uniform', value: 0.15 },
@@ -33,7 +33,7 @@ const ballAndStickProps: BallAndStickProps = {
useFog: false
}
-const distanceRestraintProps: DistanceRestraintProps = {
+const distanceRestraintProps: Partial<DistanceRestraintProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
linkRadius: 0.5,
@@ -41,7 +41,7 @@ const distanceRestraintProps: DistanceRestraintProps = {
useFog: false
}
-const backboneProps: BackboneProps = {
+const backboneProps: Partial<BackboneProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
// colorTheme: { name: 'uniform', value: 0xFF0000 },
@@ -50,7 +50,7 @@ const backboneProps: BackboneProps = {
alpha: 0.5
}
-const cartoonProps: CartoonProps = {
+const cartoonProps: Partial<CartoonProps> = {
doubleSided: true,
colorTheme: { name: 'chain-id' },
// colorTheme: { name: 'uniform', value: 0x2200CC },
@@ -58,7 +58,7 @@ const cartoonProps: CartoonProps = {
useFog: false
}
-const carbohydrateProps: CartoonProps = {
+const carbohydrateProps: Partial<CartoonProps> = {
doubleSided: true,
colorTheme: { name: 'carbohydrate-symbol' },
// colorTheme: { name: 'uniform', value: 0x2200CC },
diff --git a/src/mol-view/state/entity.ts b/src/mol-view/state/entity.ts
index 22c94076f..60ba57af0 100644
--- a/src/mol-view/state/entity.ts
+++ b/src/mol-view/state/entity.ts
@@ -122,41 +122,41 @@ export namespace StructureEntity {
export type SpacefillEntity = StateEntity<StructureRepresentation<SpacefillProps>, 'spacefill'>
export namespace SpacefillEntity {
export function ofRepr(ctx: StateContext, repr: StructureRepresentation<SpacefillProps>): SpacefillEntity {
- return StateEntity.create(ctx, 'spacefill', repr )
+ return StateEntity.create(ctx, 'spacefill', repr)
}
}
export type BallAndStickEntity = StateEntity<StructureRepresentation<BallAndStickProps>, 'ballandstick'>
export namespace BallAndStickEntity {
export function ofRepr(ctx: StateContext, repr: StructureRepresentation<BallAndStickProps>): BallAndStickEntity {
- return StateEntity.create(ctx, 'ballandstick', repr )
+ return StateEntity.create(ctx, 'ballandstick', repr)
}
}
export type DistanceRestraintEntity = StateEntity<StructureRepresentation<DistanceRestraintProps>, 'distancerestraint'>
export namespace DistanceRestraintEntity {
export function ofRepr(ctx: StateContext, repr: StructureRepresentation<DistanceRestraintProps>): DistanceRestraintEntity {
- return StateEntity.create(ctx, 'distancerestraint', repr )
+ return StateEntity.create(ctx, 'distancerestraint', repr)
}
}
export type BackboneEntity = StateEntity<StructureRepresentation<BackboneProps>, 'backbone'>
export namespace BackboneEntity {
export function ofRepr(ctx: StateContext, repr: StructureRepresentation<BackboneProps>): BackboneEntity {
- return StateEntity.create(ctx, 'backbone', repr )
+ return StateEntity.create(ctx, 'backbone', repr)
}
}
export type CartoonEntity = StateEntity<StructureRepresentation<CartoonProps>, 'cartoon'>
export namespace CartoonEntity {
export function ofRepr(ctx: StateContext, repr: StructureRepresentation<CartoonProps>): CartoonEntity {
- return StateEntity.create(ctx, 'cartoon', repr )
+ return StateEntity.create(ctx, 'cartoon', repr)
}
}
export type CarbohydrateEntity = StateEntity<StructureRepresentation<CarbohydrateProps>, 'carbohydrate'>
export namespace CarbohydrateEntity {
export function ofRepr(ctx: StateContext, repr: StructureRepresentation<CarbohydrateProps>): CarbohydrateEntity {
- return StateEntity.create(ctx, 'carbohydrate', repr )
+ return StateEntity.create(ctx, 'carbohydrate', repr)
}
}
\ No newline at end of file
diff --git a/src/mol-view/state/transform.ts b/src/mol-view/state/transform.ts
index b4381c8b3..bda97a320 100644
--- a/src/mol-view/state/transform.ts
+++ b/src/mol-view/state/transform.ts
@@ -95,9 +95,9 @@ export const StructureCenter: StructureCenter = StateTransform.create('structure
return NullEntity
})
-export type StructureToSpacefill = StateTransform<StructureEntity, SpacefillEntity, SpacefillProps>
+export type StructureToSpacefill = StateTransform<StructureEntity, SpacefillEntity, Partial<SpacefillProps>>
export const StructureToSpacefill: StructureToSpacefill = StateTransform.create('structure', 'spacefill', 'structure-to-spacefill',
- async function (ctx: StateContext, structureEntity: StructureEntity, props: SpacefillProps = {}) {
+ async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<SpacefillProps> = {}) {
const spacefillRepr = SpacefillRepresentation()
await spacefillRepr.create(structureEntity.value, props).run(ctx.log)
ctx.viewer.add(spacefillRepr)
@@ -106,9 +106,9 @@ export const StructureToSpacefill: StructureToSpacefill = StateTransform.create(
return SpacefillEntity.ofRepr(ctx, spacefillRepr)
})
-export type StructureToBallAndStick = StateTransform<StructureEntity, BallAndStickEntity, BallAndStickProps>
+export type StructureToBallAndStick = StateTransform<StructureEntity, BallAndStickEntity, Partial<BallAndStickProps>>
export const StructureToBallAndStick: StructureToBallAndStick = StateTransform.create('structure', 'ballandstick', 'structure-to-ballandstick',
- async function (ctx: StateContext, structureEntity: StructureEntity, props: BallAndStickProps = {}) {
+ async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<BallAndStickProps> = {}) {
const ballAndStickRepr = BallAndStickRepresentation()
await ballAndStickRepr.create(structureEntity.value, props).run(ctx.log)
ctx.viewer.add(ballAndStickRepr)
@@ -117,9 +117,9 @@ export const StructureToBallAndStick: StructureToBallAndStick = StateTransform.c
return BallAndStickEntity.ofRepr(ctx, ballAndStickRepr)
})
-export type StructureToDistanceRestraint = StateTransform<StructureEntity, DistanceRestraintEntity, DistanceRestraintProps>
+export type StructureToDistanceRestraint = StateTransform<StructureEntity, DistanceRestraintEntity, Partial<DistanceRestraintProps>>
export const StructureToDistanceRestraint: StructureToDistanceRestraint = StateTransform.create('structure', 'distancerestraint', 'structure-to-distancerestraint',
- async function (ctx: StateContext, structureEntity: StructureEntity, props: DistanceRestraintProps = {}) {
+ async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<DistanceRestraintProps> = {}) {
const distanceRestraintRepr = DistanceRestraintRepresentation()
await distanceRestraintRepr.create(structureEntity.value, props).run(ctx.log)
ctx.viewer.add(distanceRestraintRepr)
@@ -128,9 +128,9 @@ export const StructureToDistanceRestraint: StructureToDistanceRestraint = StateT
return DistanceRestraintEntity.ofRepr(ctx, distanceRestraintRepr)
})
-export type StructureToBackbone = StateTransform<StructureEntity, BackboneEntity, BackboneProps>
+export type StructureToBackbone = StateTransform<StructureEntity, BackboneEntity, Partial<BackboneProps>>
export const StructureToBackbone: StructureToBackbone = StateTransform.create('structure', 'backbone', 'structure-to-backbone',
- async function (ctx: StateContext, structureEntity: StructureEntity, props: BackboneProps = {}) {
+ async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<BackboneProps> = {}) {
const backboneRepr = BackboneRepresentation()
await backboneRepr.create(structureEntity.value, props).run(ctx.log)
ctx.viewer.add(backboneRepr)
@@ -139,9 +139,9 @@ export const StructureToBackbone: StructureToBackbone = StateTransform.create('s
return BackboneEntity.ofRepr(ctx, backboneRepr)
})
-export type StructureToCartoon = StateTransform<StructureEntity, CartoonEntity, CartoonProps>
+export type StructureToCartoon = StateTransform<StructureEntity, CartoonEntity, Partial<CartoonProps>>
export const StructureToCartoon: StructureToCartoon = StateTransform.create('structure', 'cartoon', 'structure-to-cartoon',
- async function (ctx: StateContext, structureEntity: StructureEntity, props: CartoonProps = {}) {
+ async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<CartoonProps> = {}) {
const cartoonRepr = CartoonRepresentation()
await cartoonRepr.create(structureEntity.value, props).run(ctx.log)
ctx.viewer.add(cartoonRepr)
@@ -150,9 +150,9 @@ export const StructureToCartoon: StructureToCartoon = StateTransform.create('str
return CartoonEntity.ofRepr(ctx, cartoonRepr)
})
-export type StructureToCarbohydrate = StateTransform<StructureEntity, CarbohydrateEntity, CarbohydrateProps>
+export type StructureToCarbohydrate = StateTransform<StructureEntity, CarbohydrateEntity, Partial<CarbohydrateProps>>
export const StructureToCarbohydrate: StructureToCarbohydrate = StateTransform.create('structure', 'carbohydrate', 'structure-to-cartoon',
- async function (ctx: StateContext, structureEntity: StructureEntity, props: CarbohydrateProps = {}) {
+ async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<CarbohydrateProps> = {}) {
const carbohydrateRepr = CarbohydrateRepresentation()
await carbohydrateRepr.create(structureEntity.value, props).run(ctx.log)
ctx.viewer.add(carbohydrateRepr)
@@ -161,9 +161,9 @@ export const StructureToCarbohydrate: StructureToCarbohydrate = StateTransform.c
return CarbohydrateEntity.ofRepr(ctx, carbohydrateRepr)
})
-export type SpacefillUpdate = StateTransform<SpacefillEntity, NullEntity, SpacefillProps>
+export type SpacefillUpdate = StateTransform<SpacefillEntity, NullEntity, Partial<SpacefillProps>>
export const SpacefillUpdate: SpacefillUpdate = StateTransform.create('spacefill', 'null', 'spacefill-update',
- async function (ctx: StateContext, spacefillEntity: SpacefillEntity, props: SpacefillProps = {}) {
+ async function (ctx: StateContext, spacefillEntity: SpacefillEntity, props: Partial<SpacefillProps> = {}) {
const spacefillRepr = spacefillEntity.value
await spacefillRepr.update(props).run(ctx.log)
ctx.viewer.add(spacefillRepr)
@@ -172,9 +172,9 @@ export const SpacefillUpdate: SpacefillUpdate = StateTransform.create('spacefill
return NullEntity
})
-export type BallAndStickUpdate = StateTransform<BallAndStickEntity, NullEntity, BallAndStickProps>
+export type BallAndStickUpdate = StateTransform<BallAndStickEntity, NullEntity, Partial<BallAndStickProps>>
export const BallAndStickUpdate: BallAndStickUpdate = StateTransform.create('ballandstick', 'null', 'ballandstick-update',
- async function (ctx: StateContext, ballAndStickEntity: BallAndStickEntity, props: BallAndStickProps = {}) {
+ async function (ctx: StateContext, ballAndStickEntity: BallAndStickEntity, props: Partial<BallAndStickProps> = {}) {
const ballAndStickRepr = ballAndStickEntity.value
await ballAndStickRepr.update(props).run(ctx.log)
ctx.viewer.add(ballAndStickRepr)
@@ -183,9 +183,9 @@ export const BallAndStickUpdate: BallAndStickUpdate = StateTransform.create('bal
return NullEntity
})
-export type DistanceRestraintUpdate = StateTransform<DistanceRestraintEntity, NullEntity, DistanceRestraintProps>
+export type DistanceRestraintUpdate = StateTransform<DistanceRestraintEntity, NullEntity, Partial<DistanceRestraintProps>>
export const DistanceRestraintUpdate: DistanceRestraintUpdate = StateTransform.create('distancerestraint', 'null', 'distancerestraint-update',
- async function (ctx: StateContext, distanceRestraintEntity: DistanceRestraintEntity, props: DistanceRestraintProps = {}) {
+ async function (ctx: StateContext, distanceRestraintEntity: DistanceRestraintEntity, props: Partial<DistanceRestraintProps> = {}) {
const distanceRestraintRepr = distanceRestraintEntity.value
await distanceRestraintRepr.update(props).run(ctx.log)
ctx.viewer.add(distanceRestraintRepr)
@@ -194,9 +194,9 @@ export const DistanceRestraintUpdate: DistanceRestraintUpdate = StateTransform.c
return NullEntity
})
-export type BackboneUpdate = StateTransform<BackboneEntity, NullEntity, BackboneProps>
+export type BackboneUpdate = StateTransform<BackboneEntity, NullEntity, Partial<BackboneProps>>
export const BackboneUpdate: BackboneUpdate = StateTransform.create('backbone', 'null', 'backbone-update',
- async function (ctx: StateContext, backboneEntity: BackboneEntity, props: BackboneProps = {}) {
+ async function (ctx: StateContext, backboneEntity: BackboneEntity, props: Partial<BackboneProps> = {}) {
const backboneRepr = backboneEntity.value
await backboneRepr.update(props).run(ctx.log)
ctx.viewer.add(backboneRepr)
@@ -205,9 +205,9 @@ export const BackboneUpdate: BackboneUpdate = StateTransform.create('backbone',
return NullEntity
})
-export type CartoonUpdate = StateTransform<CartoonEntity, NullEntity, CartoonProps>
+export type CartoonUpdate = StateTransform<CartoonEntity, NullEntity, Partial<CartoonProps>>
export const CartoonUpdate: CartoonUpdate = StateTransform.create('cartoon', 'null', 'cartoon-update',
- async function (ctx: StateContext, cartoonEntity: CartoonEntity, props: CartoonProps = {}) {
+ async function (ctx: StateContext, cartoonEntity: CartoonEntity, props: Partial<CartoonProps> = {}) {
const cartoonRepr = cartoonEntity.value
await cartoonRepr.update(props).run(ctx.log)
ctx.viewer.add(cartoonRepr)
@@ -216,9 +216,9 @@ export const CartoonUpdate: CartoonUpdate = StateTransform.create('cartoon', 'nu
return NullEntity
})
-export type CarbohydrateUpdate = StateTransform<CarbohydrateEntity, NullEntity, CarbohydrateProps>
+export type CarbohydrateUpdate = StateTransform<CarbohydrateEntity, NullEntity, Partial<CarbohydrateProps>>
export const CarbohydrateUpdate: CarbohydrateUpdate = StateTransform.create('carbohydrate', 'null', 'carbohydrate-update',
- async function (ctx: StateContext, carbohydrateEntity: CarbohydrateEntity, props: CarbohydrateProps = {}) {
+ async function (ctx: StateContext, carbohydrateEntity: CarbohydrateEntity, props: Partial<CarbohydrateProps> = {}) {
const carbohydrateRepr = carbohydrateEntity.value
await carbohydrateRepr.update(props).run(ctx.log)
ctx.viewer.add(carbohydrateRepr)
@@ -251,24 +251,24 @@ export const DataToModel: DataToModel = StateTransform.create('data', 'model', '
return MmcifToModel.apply(ctx, mmcifEntity)
})
-export type ModelToSpacefill = StateTransform<ModelEntity, SpacefillEntity, SpacefillProps>
+export type ModelToSpacefill = StateTransform<ModelEntity, SpacefillEntity, Partial<SpacefillProps>>
export const ModelToSpacefill: ModelToSpacefill = StateTransform.create('model', 'spacefill', 'model-to-spacefill',
- async function (ctx: StateContext, modelEntity: ModelEntity, props: SpacefillProps = {}) {
+ async function (ctx: StateContext, modelEntity: ModelEntity, props: Partial<SpacefillProps> = {}) {
const structureEntity = await ModelToStructure.apply(ctx, modelEntity)
// StructureToBond.apply(ctx, structureEntity, props)
return StructureToSpacefill.apply(ctx, structureEntity, props)
})
-export type MmcifUrlToSpacefill = StateTransform<UrlEntity, SpacefillEntity, SpacefillProps>
+export type MmcifUrlToSpacefill = StateTransform<UrlEntity, SpacefillEntity, Partial<SpacefillProps>>
export const MmcifUrlToSpacefill: MmcifUrlToSpacefill = StateTransform.create('url', 'spacefill', 'url-to-spacefill',
- async function (ctx: StateContext, urlEntity: UrlEntity, props: SpacefillProps = {}) {
+ async function (ctx: StateContext, urlEntity: UrlEntity, props: Partial<SpacefillProps> = {}) {
const modelEntity = await MmcifUrlToModel.apply(ctx, urlEntity)
return ModelToSpacefill.apply(ctx, modelEntity, props)
})
-export type MmcifFileToSpacefill = StateTransform<FileEntity, SpacefillEntity, SpacefillProps>
+export type MmcifFileToSpacefill = StateTransform<FileEntity, SpacefillEntity, Partial<SpacefillProps>>
export const MmcifFileToSpacefill: MmcifFileToSpacefill = StateTransform.create('file', 'spacefill', 'file-to-spacefill',
- async function (ctx: StateContext, fileEntity: FileEntity, props: SpacefillProps = {}) {
+ async function (ctx: StateContext, fileEntity: FileEntity, props: Partial<SpacefillProps> = {}) {
const modelEntity = await MmcifFileToModel.apply(ctx, fileEntity)
return ModelToSpacefill.apply(ctx, modelEntity, props)
})
\ No newline at end of file
--
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