From 5f594a08d72515257a35c6095d60936205275276 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 13 Aug 2018 15:59:56 -0700
Subject: [PATCH] wip, size theme
---
src/mol-app/ui/transform/backbone.tsx | 6 +-
src/mol-app/ui/transform/ball-and-stick.tsx | 6 +-
src/mol-app/ui/transform/carbohydrate.tsx | 6 +-
src/mol-app/ui/transform/cartoon.tsx | 6 +-
.../ui/transform/distance-restraint.tsx | 6 +-
src/mol-app/ui/transform/spacefill.tsx | 6 +-
src/mol-geo/representation/structure/index.ts | 4 +-
.../representation/ball-and-stick.ts | 4 +-
.../representation/distance-restraint.ts | 4 +-
.../visual/carbohydrate-link-cylinder.ts | 4 +-
.../visual/carbohydrate-symbol-mesh.ts | 4 +-
.../visual/cross-link-restraint-cylinder.ts | 4 +-
.../structure/visual/element-point.ts | 16 +--
.../visual/inter-unit-link-cylinder.ts | 4 +-
.../visual/intra-unit-link-cylinder.ts | 4 +-
.../structure/visual/util/common.ts | 23 ++--
.../structure/visual/util/element.ts | 24 +---
src/mol-geo/theme/index.ts | 20 ++--
src/mol-geo/theme/structure/size/index.ts | 19 ++-
src/mol-geo/theme/structure/size/physical.ts | 47 +++++---
src/mol-geo/theme/structure/size/uniform.ts | 22 ++++
src/mol-geo/util/color-data.ts | 38 +-----
src/mol-geo/util/marker-data.ts | 2 +-
src/mol-geo/util/size-data.ts | 109 +++++++++++++-----
src/mol-gl/_spec/renderer.spec.ts | 4 +-
src/mol-gl/renderable/point.ts | 4 +-
src/mol-gl/shader/point.vert | 6 +
27 files changed, 230 insertions(+), 172 deletions(-)
create mode 100644 src/mol-geo/theme/structure/size/uniform.ts
diff --git a/src/mol-app/ui/transform/backbone.tsx b/src/mol-app/ui/transform/backbone.tsx
index e93e15b56..37c8e8607 100644
--- a/src/mol-app/ui/transform/backbone.tsx
+++ b/src/mol-app/ui/transform/backbone.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { BackboneEntity } from 'mol-view/state/entity';
import { BackboneUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorThemeProps, SizeTheme, ColorThemeNames, ColorThemeName } from 'mol-geo/theme';
+import { ColorThemeProps, SizeThemeProps, ColorThemeNames, ColorThemeName } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -28,7 +28,7 @@ interface BackboneState {
detail: number
colorTheme: ColorThemeProps
colorValue: Color
- sizeTheme: SizeTheme
+ sizeTheme: SizeThemeProps
visible: boolean
alpha: number
depthMask: boolean
@@ -45,7 +45,7 @@ export class Backbone extends View<Controller<any>, BackboneState, { transform:
detail: 2,
colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
- sizeTheme: { name: 'uniform' } as SizeTheme,
+ sizeTheme: { name: 'uniform' } as SizeThemeProps,
visible: true,
alpha: 1,
depthMask: true,
diff --git a/src/mol-app/ui/transform/ball-and-stick.tsx b/src/mol-app/ui/transform/ball-and-stick.tsx
index f94afce44..d75ed5dab 100644
--- a/src/mol-app/ui/transform/ball-and-stick.tsx
+++ b/src/mol-app/ui/transform/ball-and-stick.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { DistanceRestraintEntity } from 'mol-view/state/entity';
import { DistanceRestraintUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeThemeProps, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -27,7 +27,7 @@ interface BallAndStickState {
flatShaded: boolean
colorTheme: ColorThemeProps
colorValue: Color
- sizeTheme: SizeTheme
+ sizeTheme: SizeThemeProps
visible: boolean
alpha: number
depthMask: boolean
@@ -48,7 +48,7 @@ export class BallAndStick extends View<Controller<any>, BallAndStickState, { tra
flatShaded: false,
colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
- sizeTheme: { name: 'uniform' } as SizeTheme,
+ sizeTheme: { name: 'uniform' } as SizeThemeProps,
visible: true,
alpha: 1,
depthMask: true,
diff --git a/src/mol-app/ui/transform/carbohydrate.tsx b/src/mol-app/ui/transform/carbohydrate.tsx
index c9a93065c..03906a204 100644
--- a/src/mol-app/ui/transform/carbohydrate.tsx
+++ b/src/mol-app/ui/transform/carbohydrate.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { CarbohydrateEntity } from 'mol-view/state/entity';
import { CarbohydrateUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeThemeProps, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -28,7 +28,7 @@ interface CarbohydrateState {
detail: number
colorTheme: ColorThemeProps
colorValue: Color
- sizeTheme: SizeTheme
+ sizeTheme: SizeThemeProps
visible: boolean
alpha: number
depthMask: boolean
@@ -49,7 +49,7 @@ export class Carbohydrate extends View<Controller<any>, CarbohydrateState, { tra
detail: 2,
colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
- sizeTheme: { name: 'uniform' } as SizeTheme,
+ sizeTheme: { name: 'uniform' } as SizeThemeProps,
visible: true,
alpha: 1,
depthMask: true,
diff --git a/src/mol-app/ui/transform/cartoon.tsx b/src/mol-app/ui/transform/cartoon.tsx
index f3bb8e664..4b6d7da14 100644
--- a/src/mol-app/ui/transform/cartoon.tsx
+++ b/src/mol-app/ui/transform/cartoon.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { CartoonEntity } from 'mol-view/state/entity';
import { CartoonUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeThemeProps, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -28,7 +28,7 @@ interface CartoonState {
detail: number
colorTheme: ColorThemeProps
colorValue: Color
- sizeTheme: SizeTheme
+ sizeTheme: SizeThemeProps
visible: boolean
alpha: number
depthMask: boolean
@@ -45,7 +45,7 @@ export class Cartoon extends View<Controller<any>, CartoonState, { transform: Ca
detail: 2,
colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
- sizeTheme: { name: 'uniform' } as SizeTheme,
+ sizeTheme: { name: 'uniform' } as SizeThemeProps,
visible: true,
alpha: 1,
depthMask: true,
diff --git a/src/mol-app/ui/transform/distance-restraint.tsx b/src/mol-app/ui/transform/distance-restraint.tsx
index 36a5f3361..d349db4dc 100644
--- a/src/mol-app/ui/transform/distance-restraint.tsx
+++ b/src/mol-app/ui/transform/distance-restraint.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { DistanceRestraintEntity } from 'mol-view/state/entity';
import { DistanceRestraintUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeThemeProps, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -27,7 +27,7 @@ interface DistanceRestraintState {
flatShaded: boolean
colorTheme: ColorThemeProps
colorValue: Color
- sizeTheme: SizeTheme
+ sizeTheme: SizeThemeProps
visible: boolean
alpha: number
depthMask: boolean
@@ -48,7 +48,7 @@ export class DistanceRestraint extends View<Controller<any>, DistanceRestraintSt
flatShaded: false,
colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
- sizeTheme: { name: 'uniform' } as SizeTheme,
+ sizeTheme: { name: 'uniform' } as SizeThemeProps,
visible: true,
alpha: 1,
depthMask: true,
diff --git a/src/mol-app/ui/transform/spacefill.tsx b/src/mol-app/ui/transform/spacefill.tsx
index 99e750e34..b1df35898 100644
--- a/src/mol-app/ui/transform/spacefill.tsx
+++ b/src/mol-app/ui/transform/spacefill.tsx
@@ -15,7 +15,7 @@ import { Toggle } from '../controls/common';
import { SpacefillEntity } from 'mol-view/state/entity';
import { SpacefillUpdate } from 'mol-view/state/transform'
import { StateContext } from 'mol-view/state/context';
-import { ColorThemeProps, SizeTheme, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
+import { ColorThemeProps, SizeThemeProps, ColorThemeName, ColorThemeNames } from 'mol-geo/theme';
import { Color, ColorNames } from 'mol-util/color';
import { Slider } from '../controls/slider';
import { VisualQuality } from 'mol-geo/representation/util';
@@ -28,7 +28,7 @@ interface SpacefillState {
detail: number
colorTheme: ColorThemeProps
colorValue: Color
- sizeTheme: SizeTheme
+ sizeTheme: SizeThemeProps
visible: boolean
alpha: number
depthMask: boolean
@@ -45,7 +45,7 @@ export class Spacefill extends View<Controller<any>, SpacefillState, { transform
detail: 2,
colorTheme: { name: 'element-symbol' } as ColorThemeProps,
colorValue: 0x000000,
- sizeTheme: { name: 'uniform' } as SizeTheme,
+ sizeTheme: { name: 'uniform' } as SizeThemeProps,
visible: true,
alpha: 1,
depthMask: true,
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 4a6505676..bf782aab9 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -7,7 +7,7 @@
import { Structure } from 'mol-model/structure';
import { Representation, RepresentationProps } from '..';
-import { ColorThemeProps, SizeTheme } from '../../theme';
+import { ColorThemeProps, SizeThemeProps } from '../../theme';
import { DefaultBaseProps, DefaultMeshProps } from '../util';
export interface StructureRepresentation<P extends RepresentationProps = {}> extends Representation<Structure, P> { }
@@ -15,7 +15,7 @@ export interface StructureRepresentation<P extends RepresentationProps = {}> ext
export const DefaultStructureProps = {
...DefaultBaseProps,
colorTheme: { name: 'unit-index' } as ColorThemeProps,
- sizeTheme: { name: 'physical' } as SizeTheme,
+ sizeTheme: { name: 'physical' } as SizeThemeProps,
}
export type StructureProps = typeof DefaultStructureProps
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 b32faf0ce..0b61537b1 100644
--- a/src/mol-geo/representation/structure/representation/ball-and-stick.ts
+++ b/src/mol-geo/representation/structure/representation/ball-and-stick.ts
@@ -12,14 +12,14 @@ import { Structure, Unit } from 'mol-model/structure';
import { Task } from 'mol-task';
import { Loci, isEmptyLoci } from 'mol-model/loci';
import { MarkerAction } from '../../../util/marker-data';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { InterUnitLinkVisual } from '../visual/inter-unit-link-cylinder';
export const DefaultBallAndStickProps = {
...DefaultElementSphereProps,
...DefaultIntraUnitLinkProps,
- sizeTheme: { name: 'uniform', value: 0.25 } as SizeTheme,
+ sizeTheme: { name: 'uniform', value: 0.25 } as SizeThemeProps,
unitKinds: [ Unit.Kind.Atomic ] as Unit.Kind[]
}
export type BallAndStickProps = typeof DefaultBallAndStickProps
diff --git a/src/mol-geo/representation/structure/representation/distance-restraint.ts b/src/mol-geo/representation/structure/representation/distance-restraint.ts
index 6618ce311..31c8d5d4e 100644
--- a/src/mol-geo/representation/structure/representation/distance-restraint.ts
+++ b/src/mol-geo/representation/structure/representation/distance-restraint.ts
@@ -10,12 +10,12 @@ import { Structure } from 'mol-model/structure';
import { Task } from 'mol-task';
import { Loci } from 'mol-model/loci';
import { MarkerAction } from '../../../util/marker-data';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { CrossLinkRestraintVisual, DefaultCrossLinkRestraintProps } from '../visual/cross-link-restraint-cylinder';
export const DefaultDistanceRestraintProps = {
...DefaultCrossLinkRestraintProps,
- sizeTheme: { name: 'uniform', value: 0.25 } as SizeTheme,
+ sizeTheme: { name: 'uniform', value: 0.25 } as SizeThemeProps,
}
export type DistanceRestraintProps = typeof DefaultDistanceRestraintProps
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 5ea1324b9..dab665622 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -10,7 +10,7 @@ import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { DefaultMeshProps } from '../../util';
import { Vec3 } from 'mol-math/linear-algebra';
import { LocationIterator } from './util/location-iterator';
@@ -52,7 +52,7 @@ export const DefaultCarbohydrateLinkProps = {
...DefaultMeshProps,
...DefaultStructureProps,
...DefaultLinkCylinderProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
+ sizeTheme: { name: 'physical', factor: 1 } as SizeThemeProps,
detail: 0,
unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
}
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 2b697f494..7eba34355 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -10,7 +10,7 @@ import { RuntimeContext } from 'mol-task'
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
@@ -115,7 +115,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
export const DefaultCarbohydrateSymbolProps = {
...DefaultMeshProps,
...DefaultStructureProps,
- sizeTheme: { name: 'physical', factor: 1 } as SizeTheme,
+ sizeTheme: { name: 'physical', factor: 1 } as SizeThemeProps,
detail: 0,
unitKinds: [ Unit.Kind.Atomic, Unit.Kind.Spheres ] as Unit.Kind[]
}
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 4467730ca..f93a8bbfe 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
@@ -12,7 +12,7 @@ import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { ComplexMeshVisual } from '../complex-visual';
import { LocationIterator } from './util/location-iterator';
import { Interval } from 'mol-data/int';
@@ -43,7 +43,7 @@ async function createCrossLinkRestraintCylinderMesh(ctx: RuntimeContext, structu
export const DefaultCrossLinkRestraintProps = {
...DefaultStructureProps,
...DefaultLinkCylinderProps,
- sizeTheme: { name: 'physical', factor: 0.3 } as SizeTheme,
+ sizeTheme: { name: 'physical', factor: 0.3 } as SizeThemeProps,
flipSided: false,
flatShaded: false,
}
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index db3483998..01764652e 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -11,8 +11,7 @@ import { Unit } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task'
import { UnitsVisual, DefaultStructureProps } from '..';
-import VertexMap from '../../../shape/vertex-map';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { getElementLoci } from './util/element';
import { createTransforms, createColors, createSizes } from './util/common';
import { deepEqual, defaults } from 'mol-util';
@@ -27,7 +26,7 @@ import { StructureElementIterator } from './util/location-iterator';
export const DefaultPointProps = {
...DefaultStructureProps,
- sizeTheme: { name: 'physical' } as SizeTheme
+ sizeTheme: { name: 'physical' } as SizeThemeProps
}
export type PointProps = Partial<typeof DefaultPointProps>
@@ -70,17 +69,12 @@ export default function PointVisual(): UnitsVisual<PointProps> {
const elementCount = _elements.length
const instanceCount = group.units.length
- const vertexMap = VertexMap.create(
- elementCount,
- elementCount + 1,
- fillSerial(new Uint32Array(elementCount)),
- fillSerial(new Uint32Array(elementCount + 1))
- )
+ const locationIt = StructureElementIterator.fromGroup(group)
const vertices = createPointVertices(_units[0])
const transforms = createTransforms(group)
- const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
- const size = createSizes(group, vertexMap, sizeTheme)
+ const color = createColors(locationIt, colorTheme)
+ const size = createSizes(locationIt, sizeTheme)
const marker = createMarkers(instanceCount * elementCount)
const values: PointValues = {
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 0bd2d0fbd..2ace15d06 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
@@ -12,7 +12,7 @@ import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { LinkIterator } from './util/location-iterator';
import { ComplexMeshVisual } from '../complex-visual';
import { Interval } from 'mol-data/int';
@@ -42,7 +42,7 @@ async function createInterUnitLinkCylinderMesh(ctx: RuntimeContext, structure: S
export const DefaultInterUnitLinkProps = {
...DefaultStructureProps,
...DefaultLinkCylinderProps,
- sizeTheme: { name: 'physical', factor: 0.3 } as SizeTheme,
+ sizeTheme: { name: 'physical', factor: 0.3 } as SizeThemeProps,
}
export type InterUnitLinkProps = typeof DefaultInterUnitLinkProps
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 2d2170585..ec5c170e5 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
@@ -13,7 +13,7 @@ import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { SizeTheme } from '../../../theme';
+import { SizeThemeProps } from '../../../theme';
import { LinkIterator } from './util/location-iterator';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { Interval } from 'mol-data/int';
@@ -58,7 +58,7 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
export const DefaultIntraUnitLinkProps = {
...DefaultUnitsMeshProps,
...DefaultLinkCylinderProps,
- sizeTheme: { name: 'physical', factor: 0.3 } as SizeTheme,
+ sizeTheme: { name: 'physical', factor: 0.3 } as SizeThemeProps,
}
export type IntraUnitLinkProps = typeof DefaultIntraUnitLinkProps
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index 3d5dbc7e2..3a578e16e 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -9,12 +9,10 @@ import { Unit, Structure } from 'mol-model/structure';
import { Mat4 } from 'mol-math/linear-algebra'
import { createUniformColor, ColorData, createElementColor, createElementInstanceColor, createInstanceColor } from '../../../../util/color-data';
-import { createUniformSize, SizeData } from '../../../../util/size-data';
-import { physicalSizeData } from '../../../../theme/structure/size/physical';
-import VertexMap from '../../../../shape/vertex-map';
-import { ColorThemeProps, SizeTheme } from '../../../../theme';
+import { createUniformSize, SizeData, createElementSize, createElementInstanceSize, createInstanceSize } from '../../../../util/size-data';
+import { ColorThemeProps, SizeThemeProps } from '../../../../theme';
import { ColorTheme } from '../../../../theme/structure/color';
-import { ValueCell, defaults } from 'mol-util';
+import { ValueCell } from 'mol-util';
import { LocationIterator } from './location-iterator';
import { Mesh } from '../../../../shape/mesh';
import { MeshValues } from 'mol-gl/renderable';
@@ -23,6 +21,7 @@ import { MeshProps, createMeshValues, createRenderableState } from '../../../uti
import { StructureProps } from '../..';
import { createMarkers } from '../../../../util/marker-data';
import { createMeshRenderObject } from 'mol-gl/render-object';
+import { SizeTheme } from '../../../../theme/structure/size';
export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: ValueCell<Float32Array>) {
const unitCount = units.length
@@ -47,16 +46,16 @@ export function createColors(locationIt: LocationIterator, props: ColorThemeProp
case 'element': return createElementColor(locationIt, colorTheme.color, colorData)
case 'elementInstance': return createElementInstanceColor(locationIt, colorTheme.color, colorData)
case 'instance': return createInstanceColor(locationIt, colorTheme.color, colorData)
- case 'attribute': throw new Error('not implemented') // TODO
}
}
-export function createSizes(group: Unit.SymmetryGroup, vertexMap: VertexMap, props: SizeTheme): SizeData {
- switch (props.name) {
- case 'uniform':
- return createUniformSize(props)
- case 'physical':
- return physicalSizeData(defaults(props.factor, 1), { group, vertexMap })
+export function createSizes(locationIt: LocationIterator, props: SizeThemeProps, sizeData?: SizeData): SizeData {
+ const sizeTheme = SizeTheme(props)
+ switch (sizeTheme.kind) {
+ case 'uniform': return createUniformSize(locationIt, sizeTheme.size, sizeData)
+ case 'element': return createElementSize(locationIt, sizeTheme.size, sizeData)
+ case 'elementInstance': return createElementInstanceSize(locationIt, sizeTheme.size, sizeData)
+ case 'instance': return createInstanceSize(locationIt, sizeTheme.size, sizeData)
}
}
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index 368f2b4de..4e03cc13a 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -6,38 +6,26 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { Unit, StructureElement } from 'mol-model/structure';
-import { SizeTheme } from '../../../../theme';
import { RuntimeContext } from 'mol-task';
import { sphereVertexCount } from '../../../../primitive/sphere';
import { Mesh } from '../../../../shape/mesh';
import { MeshBuilder } from '../../../../shape/mesh-builder';
-import { defaults } from 'mol-util';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { Interval, OrderedSet } from 'mol-data/int';
-import { getPhysicalRadius } from '../../../../theme/structure/size/physical';
import { PickingId } from '../../../../util/picking';
-
-export function getElementRadius(unit: Unit, props: SizeTheme): StructureElement.Property<number> {
- switch (props.name) {
- case 'uniform':
- return () => props.value
- case 'physical':
- const radius = getPhysicalRadius(unit)
- const factor = defaults(props.factor, 1)
- return (l) => radius(l) * factor
- }
-}
+import { SizeThemeProps } from '../../../../theme';
+import { SizeTheme } from '../../../../theme/structure/size';
export interface ElementSphereMeshProps {
- sizeTheme: SizeTheme,
+ sizeTheme: SizeThemeProps,
detail: number,
}
export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, props: ElementSphereMeshProps, mesh?: Mesh) {
- const { detail, sizeTheme } = props
+ const { detail } = props
const { elements } = unit;
- const radius = getElementRadius(unit, sizeTheme)
+ const sizeTheme = SizeTheme(props.sizeTheme)
const elementCount = elements.length;
const vertexCount = elementCount * sphereVertexCount(detail)
const meshBuilder = MeshBuilder.create(vertexCount, vertexCount / 2, mesh)
@@ -52,7 +40,7 @@ export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, p
pos(elements[i], v)
meshBuilder.setId(i)
- meshBuilder.addSphere(v, radius(l), detail)
+ meshBuilder.addSphere(v, sizeTheme.size(l), detail)
if (i % 10000 === 0 && ctx.shouldUpdate) {
await ctx.update({ message: 'Sphere mesh', current: i, max: elementCount });
diff --git a/src/mol-geo/theme/index.ts b/src/mol-geo/theme/index.ts
index 19791a5d6..0f08e600d 100644
--- a/src/mol-geo/theme/index.ts
+++ b/src/mol-geo/theme/index.ts
@@ -25,14 +25,18 @@ export const ColorThemeInfo = {
export type ColorThemeName = keyof typeof ColorThemeInfo
export const ColorThemeNames = Object.keys(ColorThemeInfo)
-export interface UniformSizeTheme {
- name: 'uniform',
- value: number
-}
+//
-export interface ScaleSizeTheme {
- name: 'physical' // van-der-Waals for atoms, given radius for coarse spheres
- factor?: number // scaling factor
+export interface SizeThemeProps {
+ name: 'physical' | 'uniform'
+ value?: number
+ factor?: number
+ structure?: Structure
}
-export type SizeTheme = UniformSizeTheme | ScaleSizeTheme
\ No newline at end of file
+export const SizeThemeInfo = {
+ 'physical': {},
+ 'uniform': {}
+}
+export type SizeThemeName = keyof typeof SizeThemeInfo
+export const SizeThemeNames = Object.keys(SizeThemeInfo)
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/index.ts b/src/mol-geo/theme/structure/size/index.ts
index 5878055d3..a67c32e8c 100644
--- a/src/mol-geo/theme/structure/size/index.ts
+++ b/src/mol-geo/theme/structure/size/index.ts
@@ -4,12 +4,19 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from 'mol-model/structure';
-import VertexMap from '../../../shape/vertex-map';
+import { SizeType, LocationSize } from '../../../util/size-data';
+import { SizeThemeProps } from '../..';
+import { PhysicalSizeTheme } from './physical';
+import { UniformSizeTheme } from './uniform';
-export interface StructureSizeDataProps {
- group: Unit.SymmetryGroup,
- vertexMap: VertexMap
+export interface SizeTheme {
+ kind: SizeType
+ size: LocationSize
}
-export { physicalSizeData } from './physical'
\ No newline at end of file
+export function SizeTheme(props: SizeThemeProps): SizeTheme {
+ switch (props.name) {
+ case 'physical': return PhysicalSizeTheme(props)
+ case 'uniform': return UniformSizeTheme(props)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/physical.ts b/src/mol-geo/theme/structure/size/physical.ts
index 712427e20..1e62e4847 100644
--- a/src/mol-geo/theme/structure/size/physical.ts
+++ b/src/mol-geo/theme/structure/size/physical.ts
@@ -4,9 +4,13 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { StructureElement, Unit, StructureProperties } from 'mol-model/structure';
-import { StructureSizeDataProps } from '.';
-import { createAttributeSize } from '../../../util/size-data';
+import { StructureElement, Unit, StructureProperties, Link } from 'mol-model/structure';
+import { Location } from 'mol-model/location';
+import { SizeTheme } from '.';
+import { SizeThemeProps } from '../..';
+
+const DefaultSize = 1
+const DefaultFactor = 1
export function getPhysicalRadius(unit: Unit): StructureElement.Property<number> {
if (Unit.isAtomic(unit)) {
@@ -22,18 +26,29 @@ export function getPhysicalRadius(unit: Unit): StructureElement.Property<number>
* Create attribute data with the physical size of an element,
* i.e. vdw for atoms and radius for coarse spheres
*/
-export function physicalSizeData(factor: number, props: StructureSizeDataProps) {
- const { group, vertexMap } = props
- const unit = group.units[0]
- const elements = group.elements;
- const radius = getPhysicalRadius(unit)
+export function PhysicalSizeTheme(props: SizeThemeProps): SizeTheme {
+ const factor = props.factor || DefaultFactor
const l = StructureElement.create()
- l.unit = unit
- return createAttributeSize({
- sizeFn: (elementIdx: number) => {
- l.element = elements[elementIdx]
- return radius(l) * factor
- },
- vertexMap
- })
+
+ function sizeFn(location: Location): number {
+ if (StructureElement.isLocation(location)) {
+ if (Unit.isAtomic(location.unit)) {
+ const radius = getPhysicalRadius(location.unit)
+ return factor * radius(location)
+ }
+ } else if (Link.isLocation(location)) {
+ if (Unit.isAtomic(location.aUnit)) {
+ const radius = getPhysicalRadius(location.aUnit)
+ l.unit = location.aUnit
+ l.element = location.aUnit.elements[location.aIndex]
+ return factor * radius(l)
+ }
+ }
+ return DefaultSize
+ }
+
+ return {
+ kind: 'element',
+ size: sizeFn
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/uniform.ts b/src/mol-geo/theme/structure/size/uniform.ts
new file mode 100644
index 000000000..e75b2a079
--- /dev/null
+++ b/src/mol-geo/theme/structure/size/uniform.ts
@@ -0,0 +1,22 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { SizeThemeProps } from '../..';
+import { SizeTheme } from '.';
+
+const DefaultSize = 1
+const DefaultFactor = 1
+
+export function UniformSizeTheme(props: SizeThemeProps): SizeTheme {
+ const value = props.value || DefaultSize
+ const factor = props.factor || DefaultFactor
+ const size = value * factor
+
+ return {
+ kind: 'uniform',
+ size: () => size
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/util/color-data.ts b/src/mol-geo/util/color-data.ts
index fc21510c4..5b89a4a07 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -11,7 +11,7 @@ import { Vec2, Vec3 } from 'mol-math/linear-algebra';
import { LocationIterator } from '../representation/structure/visual/util/location-iterator';
import { Location, NullLocation } from 'mol-model/location';
-export type ColorType = 'uniform' | 'attribute' | 'instance' | 'element' | 'elementInstance'
+export type ColorType = 'uniform' | 'instance' | 'element' | 'elementInstance'
export type ColorData = {
uColor: ValueCell<Vec3>,
@@ -53,40 +53,6 @@ export function createUniformColor(locationIt: LocationIterator, colorFn: Locati
return createValueColor(colorFn(NullLocation, false), colorData)
}
-// export interface AttributeColorProps {
-// colorFn: (elementIdx: number) => Color
-// vertexMap: VertexMap
-// }
-
-// /** Creates color attribute with color for each element (i.e. shared across instances/units) */
-// export function createAttributeColor(props: AttributeColorProps, colorData?: ColorData): ColorData {
-// const { colorFn, vertexMap } = props
-// const { idCount, offsetCount, offsets } = vertexMap
-// const colors = new Float32Array(idCount * 3);
-// for (let i = 0, il = offsetCount - 1; i < il; ++i) {
-// const start = offsets[i]
-// const end = offsets[i + 1]
-// const hexColor = colorFn(i)
-// for (let i = start, il = end; i < il; ++i) {
-// Color.toArrayNormalized(hexColor, colors, i * 3)
-// }
-// }
-// if (colorData) {
-// ValueCell.update(colorData.aColor, colors)
-// if (colorData.dColorType.ref.value !== 'attribute') {
-// ValueCell.update(colorData.dColorType, 'attribute')
-// }
-// return colorData
-// } else {
-// return {
-// uColor: ValueCell.create(Vec3.zero()),
-// aColor: ValueCell.create(colors),
-// ...createEmptyColorTexture(),
-// dColorType: ValueCell.create('attribute'),
-// }
-// }
-// }
-
export function createTextureColor(colors: TextureImage, type: ColorType, colorData?: ColorData): ColorData {
if (colorData) {
ValueCell.update(colorData.tColor, colors)
@@ -112,7 +78,7 @@ export function createInstanceColor(locationIt: LocationIterator, colorFn: Locat
const colors = colorData && colorData.tColor.ref.value.array.length >= instanceCount * 3 ? colorData.tColor.ref.value : createTextureImage(instanceCount, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
const v = locationIt.move()
- Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.index * 3)
+ Color.toArray(colorFn(v.location, v.isSecondary), colors.array, v.instanceIndex * 3)
locationIt.skipInstance()
}
return createTextureColor(colors, 'instance', colorData)
diff --git a/src/mol-geo/util/marker-data.ts b/src/mol-geo/util/marker-data.ts
index bda085fe9..93fa6b5c2 100644
--- a/src/mol-geo/util/marker-data.ts
+++ b/src/mol-geo/util/marker-data.ts
@@ -37,7 +37,7 @@ export function applyMarkerAction(array: Uint8Array, start: number, end: number,
if (v % 2 !== 0) {
v -= 1
changed = true
- }
+ }
break
case MarkerAction.Select:
v += 2
diff --git a/src/mol-geo/util/size-data.ts b/src/mol-geo/util/size-data.ts
index 296f1f921..25573107e 100644
--- a/src/mol-geo/util/size-data.ts
+++ b/src/mol-geo/util/size-data.ts
@@ -5,48 +5,103 @@
*/
import { ValueCell } from 'mol-util';
-import VertexMap from '../shape/vertex-map';
+import { Vec2 } from 'mol-math/linear-algebra';
+import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
+import { LocationIterator } from '../representation/structure/visual/util/location-iterator';
+import { Location, NullLocation } from 'mol-model/location';
+
+export type SizeType = 'uniform' | 'instance' | 'element' | 'elementInstance'
export type SizeData = {
uSize: ValueCell<number>,
aSize: ValueCell<Float32Array>,
+ tSize: ValueCell<TextureImage>,
+ uSizeTexSize: ValueCell<Vec2>,
dSizeType: ValueCell<string>,
}
-export interface UniformSizeProps {
- value: number
-}
+export type LocationSize = (location: Location) => number
-/** Creates size uniform */
-export function createUniformSize(props: UniformSizeProps): SizeData {
+const emptySizeTexture = { array: new Uint8Array(1), width: 1, height: 1 }
+function createEmptySizeTexture() {
return {
- uSize: ValueCell.create(props.value),
- aSize: ValueCell.create(new Float32Array(0)),
- dSizeType: ValueCell.create('uniform'),
+ tSize: ValueCell.create(emptySizeTexture),
+ uSizeTexSize: ValueCell.create(Vec2.create(1, 1))
+ }
+}
+
+export function createValueSize(value: number, sizeData?: SizeData): SizeData {
+ if (sizeData) {
+ ValueCell.update(sizeData.uSize, value)
+ if (sizeData.dSizeType.ref.value !== 'uniform') {
+ ValueCell.update(sizeData.dSizeType, 'uniform')
+ }
+ return sizeData
+ } else {
+ return {
+ uSize: ValueCell.create(value),
+ aSize: ValueCell.create(new Float32Array(0)),
+ ...createEmptySizeTexture(),
+ dSizeType: ValueCell.create('uniform'),
+ }
}
}
-export interface AttributeSizeProps {
- sizeFn: (elementIdx: number) => number
- vertexMap: VertexMap
+/** Creates size uniform */
+export function createUniformSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
+ return createValueSize(sizeFn(NullLocation), sizeData)
}
-/** Creates size attribute with size for each element (i.e. shared across indtances/units) */
-export function createAttributeSize(props: AttributeSizeProps): SizeData {
- const { sizeFn, vertexMap } = props
- const { idCount, offsetCount, offsets } = vertexMap
- const sizes = new Float32Array(idCount);
- for (let i = 0, il = offsetCount - 1; i < il; ++i) {
- const start = offsets[i]
- const end = offsets[i + 1]
- const size = sizeFn(i)
- for (let i = start, il = end; i < il; ++i) {
- sizes[i] = size
+export function createTextureSize(sizes: TextureImage, type: SizeType, sizeData?: SizeData): SizeData {
+ if (sizeData) {
+ ValueCell.update(sizeData.tSize, sizes)
+ ValueCell.update(sizeData.uSizeTexSize, Vec2.create(sizes.width, sizes.height))
+ if (sizeData.dSizeType.ref.value !== type) {
+ ValueCell.update(sizeData.dSizeType, type)
+ }
+ return sizeData
+ } else {
+ return {
+ uSize: ValueCell.create(0),
+ aSize: ValueCell.create(new Float32Array(0)),
+ tSize: ValueCell.create(sizes),
+ uSizeTexSize: ValueCell.create(Vec2.create(sizes.width, sizes.height)),
+ dSizeType: ValueCell.create(type),
}
}
- return {
- uSize: ValueCell.create(0),
- aSize: ValueCell.create(sizes),
- dSizeType: ValueCell.create('attribute'),
+}
+
+/** Creates size texture with size for each instance/unit */
+export function createInstanceSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
+ const { instanceCount} = locationIt
+ const sizes = sizeData && sizeData.tSize.ref.value.array.length >= instanceCount ? sizeData.tSize.ref.value : createTextureImage(instanceCount, 1)
+ while (locationIt.hasNext && !locationIt.isNextNewInstance) {
+ const v = locationIt.move()
+ sizes.array[v.instanceIndex] = sizeFn(v.location)
+ locationIt.skipInstance()
+ }
+ return createTextureSize(sizes, 'instance', sizeData)
+}
+
+/** Creates size texture with size for each element (i.e. shared across instances/units) */
+export function createElementSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
+ const { elementCount } = locationIt
+ const sizes = sizeData && sizeData.tSize.ref.value.array.length >= elementCount ? sizeData.tSize.ref.value : createTextureImage(elementCount, 1)
+ while (locationIt.hasNext && !locationIt.isNextNewInstance) {
+ const v = locationIt.move()
+ sizes.array[v.elementIndex] = sizeFn(v.location)
+ }
+ return createTextureSize(sizes, 'element', sizeData)
+}
+
+/** Creates size texture with size for each element instance (i.e. for each unit) */
+export function createElementInstanceSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
+ const { elementCount, instanceCount } = locationIt
+ const count = instanceCount * elementCount
+ const sizes = sizeData && sizeData.tSize.ref.value.array.length >= count ? sizeData.tSize.ref.value : createTextureImage(count, 1)
+ while (locationIt.hasNext && !locationIt.isNextNewInstance) {
+ const v = locationIt.move()
+ sizes.array[v.index] = sizeFn(v.location)
}
+ return createTextureSize(sizes, 'elementInstance', sizeData)
}
\ No newline at end of file
diff --git a/src/mol-gl/_spec/renderer.spec.ts b/src/mol-gl/_spec/renderer.spec.ts
index c314659a2..ce124dc0d 100644
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -12,7 +12,7 @@ import { ValueCell } from 'mol-util';
import Renderer from '../renderer';
import { createValueColor } from 'mol-geo/util/color-data';
-import { createUniformSize } from 'mol-geo/util/size-data';
+import { createValueSize } from 'mol-geo/util/size-data';
import { createContext } from '../webgl/context';
import { RenderableState } from '../renderable';
import { createPointRenderObject } from '../render-object';
@@ -48,7 +48,7 @@ function createPoints() {
const aElementId = ValueCell.create(fillSerial(new Float32Array(3)))
const aInstanceId = ValueCell.create(fillSerial(new Float32Array(1)))
const color = createValueColor(0xFF0000)
- const size = createUniformSize({ value: 1 })
+ const size = createValueSize(1)
const marker = createEmptyMarkers()
const aTransform = ValueCell.create(new Float32Array(16))
diff --git a/src/mol-gl/renderable/point.ts b/src/mol-gl/renderable/point.ts
index e036a809f..155c3f206 100644
--- a/src/mol-gl/renderable/point.ts
+++ b/src/mol-gl/renderable/point.ts
@@ -7,7 +7,7 @@
import { Renderable, RenderableState, createRenderable } from '../renderable'
import { Context } from '../webgl/context';
import { createRenderItem } from '../webgl/render-item';
-import { GlobalUniformSchema, BaseSchema, AttributeSpec, UniformSpec, DefineSpec, Values, InternalSchema } from './schema';
+import { GlobalUniformSchema, BaseSchema, AttributeSpec, UniformSpec, DefineSpec, Values, InternalSchema, TextureSpec } from './schema';
import { PointShaderCode } from '../shader-code';
import { ValueCell } from 'mol-util';
@@ -15,6 +15,8 @@ export const PointSchema = {
...BaseSchema,
aSize: AttributeSpec('float32', 1, 0),
uSize: UniformSpec('f'),
+ uSizeTexSize: UniformSpec('v2'),
+ tSize: TextureSpec('alpha', 'ubyte'),
dSizeType: DefineSpec('string', ['uniform', 'attribute']),
dPointSizeAttenuation: DefineSpec('boolean'),
}
diff --git a/src/mol-gl/shader/point.vert b/src/mol-gl/shader/point.vert
index 8e2c29ef1..f8061d958 100644
--- a/src/mol-gl/shader/point.vert
+++ b/src/mol-gl/shader/point.vert
@@ -32,6 +32,12 @@ void main(){
float size = uSize;
#elif defined(dSizeType_attribute)
float size = aSize;
+ #elif defined(dSizeType_instance)
+ float size = readFromTexture(tSize, aInstanceId, uSizeTexSize).r;
+ #elif defined(dSizeType_element)
+ float size = readFromTexture(tSize, aElementId, uSizeTexSize).r;
+ #elif defined(dSizeType_elementInstance)
+ float size = readFromTexture(tSize, aInstanceId * float(uElementCount) + aElementId, uSizeTexSize).r;
#endif
#ifdef dPointSizeAttenuation
--
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