diff --git a/src/apps/canvas/index.ts b/src/apps/canvas/index.ts
index 8eccc6e3ca305930da0819164b54bdef15723717..a886ec738436f30173ec17924acd86d639617608 100644
--- a/src/apps/canvas/index.ts
+++ b/src/apps/canvas/index.ts
@@ -8,7 +8,7 @@ import './index.html'
import Viewer from 'mol-view/viewer';
import CIF, { CifBlock } from 'mol-io/reader/cif'
-import { parse as parseObj } from 'mol-io/reader/obj/parser'
+// import { parse as parseObj } from 'mol-io/reader/obj/parser'
import { readUrlAs } from 'mol-util/read'
import { Model, Format, Structure, StructureSymmetry } from 'mol-model/structure';
import { CartoonRepresentation } from 'mol-geo/representation/structure/representation/cartoon';
@@ -17,9 +17,11 @@ import { EveryLoci } from 'mol-model/loci';
import { MarkerAction } from 'mol-geo/util/marker-data';
import { labelFirst } from 'mol-view/label';
import { Queries as Q, StructureProperties as SP, StructureSelection, StructureQuery } from 'mol-model/structure';
-import { MeshBuilder } from 'mol-geo/shape/mesh-builder';
-import { CustomRepresentation } from 'mol-geo/representation/custom';
-import { Vec3 } from 'mol-math/linear-algebra';
+import { MeshBuilder } from 'mol-geo/mesh/mesh-builder';
+import { ShapeRepresentation } from 'mol-geo/representation/shape';
+import { Vec3, Mat4 } from 'mol-math/linear-algebra';
+import { Shape } from 'mol-model/shape';
+import { Color } from 'mol-util/color';
const container = document.getElementById('container')
if (!container) throw new Error('Can not find element with id "container".')
@@ -50,13 +52,13 @@ viewer.input.move.subscribe(({x, y, inside, buttons}) => {
})
-async function getObjFromUrl(url: string) {
- const data = await readUrlAs(url, false) as string
- const comp = parseObj(data)
- const parsed = await comp.run()
- if (parsed.isError) throw parsed
- return parsed.result
-}
+// async function getObjFromUrl(url: string) {
+// const data = await readUrlAs(url, false) as string
+// const comp = parseObj(data)
+// const parsed = await comp.run()
+// if (parsed.isError) throw parsed
+// return parsed.result
+// }
async function getCifFromUrl(url: string) {
const data = await readUrlAs(url, false)
@@ -111,18 +113,34 @@ async function init() {
}).run()
viewer.add(ballStickRepr)
- // create a custom mesh
+ // create a mesh
const meshBuilder = MeshBuilder.create(256, 128)
- meshBuilder.setId(0)
+ const groupColors: Color[] = []
+ const groupLabels: string[] = []
+ // red sphere
+ meshBuilder.setGroup(0)
+ groupColors[0] = Color(0xFF2233)
+ groupLabels[0] = 'red sphere'
meshBuilder.addSphere(Vec3.create(0, 0, 0), 4, 2)
+ // green cube
+ meshBuilder.setGroup(1)
+ groupColors[1] = Color(0x2233FF)
+ groupLabels[1] = 'blue cube'
+ const t = Mat4.identity()
+ Mat4.setTranslation(t, Vec3.create(10, 0, 0))
+ Mat4.scale(t, t, Vec3.create(3, 3, 3))
+ meshBuilder.addBox(t)
const mesh = meshBuilder.getMesh()
- // Mesh.computeNormalsImmediate(mesh)
+ // const mesh = getObjFromUrl('mesh.obj')
- // mesh = getObjFromUrl('mesh.obj')
+ // create shape from mesh
+ const shape = Shape.create(mesh, 'myShape', group => groupColors[group], group => groupLabels[group])
- // add representation from custom mesh
- const customRepr = CustomRepresentation()
- await customRepr.create(mesh, {
+ // add representation from shape
+ const customRepr = ShapeRepresentation()
+ await customRepr.create(shape, {
+ colorTheme: { name: 'shape-group' },
+ // colorTheme: { name: 'uniform', value: Color(0xFFCC22) },
useFog: false // TODO fog not working properly
}).run()
viewer.add(customRepr)
diff --git a/src/mol-app/ui/visualization/viewport.tsx b/src/mol-app/ui/visualization/viewport.tsx
index ba402a6d7d1f6e81e1968b11a02d635bc78c209c..d23f182e1b5bbfa3731d1f98edc7fa2cb9243692 100644
--- a/src/mol-app/ui/visualization/viewport.tsx
+++ b/src/mol-app/ui/visualization/viewport.tsx
@@ -151,7 +151,7 @@ export class Viewport extends View<ViewportController, ViewportState, { noWebGl?
images: {
'object': viewer.getImageData('pickObject'),
'instance': viewer.getImageData('pickInstance'),
- 'element': viewer.getImageData('pickElement')
+ 'group': viewer.getImageData('pickGroup')
}
})
})
@@ -168,7 +168,7 @@ export class Viewport extends View<ViewportController, ViewportState, { noWebGl?
// TODO use LabelLoci event and make configurable
const label = labelFirst(loci)
- const info = `Object: ${p.objectId}, Instance: ${p.instanceId}, Element: ${p.elementId}, Label: ${label}`
+ const info = `Object: ${p.objectId}, Instance: ${p.instanceId}, Group: ${p.groupId}, Label: ${label}`
this.setState({ info })
})
diff --git a/src/mol-geo/shape/mesh-builder.ts b/src/mol-geo/mesh/mesh-builder.ts
similarity index 90%
rename from src/mol-geo/shape/mesh-builder.ts
rename to src/mol-geo/mesh/mesh-builder.ts
index f3dafe8a41d33153039a6af87bb1dee4bfd44e81..c34b2ea477f5ce98f0fe5c49108f46fbe865827c 100644
--- a/src/mol-geo/shape/mesh-builder.ts
+++ b/src/mol-geo/mesh/mesh-builder.ts
@@ -19,7 +19,7 @@ import { StarProps, Star } from '../primitive/star';
import { Octahedron, PerforatedOctahedron } from '../primitive/octahedron';
import { Primitive } from '../primitive/primitive';
import { DiamondPrism, PentagonalPrism, HexagonalPrism } from '../primitive/prism';
-import { OctagonalPyramide, PerforatedOctagonalPyramide } from '../primitive/pyramid';
+import { OctagonalPyramide, PerforatedOctagonalPyramid } from '../primitive/pyramid';
import { PerforatedBox, Box } from '../primitive/box';
import { Wedge } from '../primitive/wedge';
@@ -49,7 +49,7 @@ export interface MeshBuilder {
addSphere(center: Vec3, radius: number, detail: number): void
addTube(centers: ArrayLike<number>, normals: ArrayLike<number>, binormals: ArrayLike<number>, linearSegments: number, radialSegments: number, width: number, height: number, waveFactor: number, startCap: boolean, endCap: boolean): void
addSheet(centers: ArrayLike<number>, normals: ArrayLike<number>, binormals: ArrayLike<number>, linearSegments: number, width: number, height: number, arrowHeight: number, startCap: boolean, endCap: boolean): void
- setId(id: number): void
+ setGroup(id: number): void
getMesh(): Mesh
}
@@ -114,10 +114,9 @@ export namespace MeshBuilder {
const indices = ChunkedArray.create(Uint32Array, 3, chunkSize * 3, mesh ? mesh.indexBuffer.ref.value : initialCount * 3);
const state: MeshBuilderState = { vertices, normals, indices };
- const ids = ChunkedArray.create(Float32Array, 1, chunkSize, mesh ? mesh.idBuffer.ref.value : initialCount);
- const offsets = ChunkedArray.create(Uint32Array, 1, chunkSize, mesh ? mesh.offsetBuffer.ref.value : initialCount);
+ const groups = ChunkedArray.create(Float32Array, 1, chunkSize, mesh ? mesh.groupBuffer.ref.value : initialCount);
- let currentId = -1
+ let currentGroup = -1
function add(t: Mat4, _vertices: ArrayLike<number>, _normals: ArrayLike<number>, _indices: ArrayLike<number>) {
const { elementCount } = vertices
@@ -131,8 +130,8 @@ export namespace MeshBuilder {
Vec3.fromArray(tmpV, _normals, i)
Vec3.transformMat3(tmpV, tmpV, n)
ChunkedArray.add3(normals, tmpV[0], tmpV[1], tmpV[2]);
- // id
- ChunkedArray.add(ids, currentId);
+ // group
+ ChunkedArray.add(groups, currentGroup);
}
for (let i = 0, il = _indices.length; i < il; i += 3) {
ChunkedArray.add3(indices, _indices[i] + elementCount, _indices[i + 1] + elementCount, _indices[i + 2] + elementCount);
@@ -174,7 +173,7 @@ export namespace MeshBuilder {
add(t, vertices, normals, indices)
},
addPerforatedOctagonalPyramid: (t: Mat4) => {
- const { vertices, normals, indices } = PerforatedOctagonalPyramide()
+ const { vertices, normals, indices } = PerforatedOctagonalPyramid()
add(t, vertices, normals, indices)
},
addStar: (t: Mat4, props?: StarProps) => {
@@ -242,36 +241,28 @@ export namespace MeshBuilder {
},
addTube: (centers: ArrayLike<number>, normals: ArrayLike<number>, binormals: ArrayLike<number>, linearSegments: number, radialSegments: number, width: number, height: number, waveFactor: number, startCap: boolean, endCap: boolean) => {
const addedVertexCount = addTube(centers, normals, binormals, linearSegments, radialSegments, width, height, waveFactor, startCap, endCap, state)
- for (let i = 0, il = addedVertexCount; i < il; ++i) ChunkedArray.add(ids, currentId);
+ for (let i = 0, il = addedVertexCount; i < il; ++i) ChunkedArray.add(groups, currentGroup);
},
addSheet: (controls: ArrayLike<number>, normals: ArrayLike<number>, binormals: ArrayLike<number>, linearSegments: number, width: number, height: number, arrowHeight: number, startCap: boolean, endCap: boolean) => {
const addedVertexCount = addSheet(controls, normals, binormals, linearSegments, width, height, arrowHeight, startCap, endCap, state)
- for (let i = 0, il = addedVertexCount; i < il; ++i) ChunkedArray.add(ids, currentId);
+ for (let i = 0, il = addedVertexCount; i < il; ++i) ChunkedArray.add(groups, currentGroup);
},
- setId: (id: number) => {
- if (currentId !== id) {
- currentId = id
- ChunkedArray.add(offsets, vertices.elementCount)
- }
+ setGroup: (group: number) => {
+ currentGroup = group
},
getMesh: () => {
- ChunkedArray.add(offsets, vertices.elementCount)
const vb = ChunkedArray.compact(vertices, true) as Float32Array
const ib = ChunkedArray.compact(indices, true) as Uint32Array
const nb = ChunkedArray.compact(normals, true) as Float32Array
- const idb = ChunkedArray.compact(ids, true) as Float32Array
- const ob = ChunkedArray.compact(offsets, true) as Uint32Array
+ const idb = ChunkedArray.compact(groups, true) as Float32Array
return {
vertexCount: vertices.elementCount,
triangleCount: indices.elementCount,
- offsetCount: offsets.elementCount,
vertexBuffer: mesh ? ValueCell.update(mesh.vertexBuffer, vb) : ValueCell.create(vb),
indexBuffer: mesh ? ValueCell.update(mesh.indexBuffer, ib) : ValueCell.create(ib),
normalBuffer: mesh ? ValueCell.update(mesh.normalBuffer, nb) : ValueCell.create(nb),
- idBuffer: mesh ? ValueCell.update(mesh.idBuffer, idb) : ValueCell.create(idb),
- offsetBuffer: mesh ? ValueCell.update(mesh.offsetBuffer, ob) : ValueCell.create(ob),
+ groupBuffer: mesh ? ValueCell.update(mesh.groupBuffer, idb) : ValueCell.create(idb),
normalsComputed: true,
- offsetsComputed: true,
}
}
}
diff --git a/src/mol-geo/shape/mesh.ts b/src/mol-geo/mesh/mesh.ts
similarity index 91%
rename from src/mol-geo/shape/mesh.ts
rename to src/mol-geo/mesh/mesh.ts
index 9447404a353e906a8ee0d27708bd6b7743509160..7b525f6e753f875e4c96869124d7f859ecbed196 100644
--- a/src/mol-geo/shape/mesh.ts
+++ b/src/mol-geo/mesh/mesh.ts
@@ -15,8 +15,6 @@ export interface Mesh {
vertexCount: number,
/** Number of triangles in the mesh */
triangleCount: number,
- /** Number of offsets in the mesh */
- offsetCount: number,
/** Vertex buffer as array of xyz values wrapped in a value cell */
vertexBuffer: ValueCell<Float32Array>,
@@ -24,15 +22,11 @@ export interface Mesh {
indexBuffer: ValueCell<Uint32Array>,
/** Normal buffer as array of xyz values for each vertex wrapped in a value cell */
normalBuffer: ValueCell<Float32Array>,
- /** Id buffer as array of ids for each vertex wrapped in a value cell */
- idBuffer: ValueCell<Float32Array>,
- /** Offset buffer as array of offsets for id ranges wrapped in a value cell */
- offsetBuffer: ValueCell<Uint32Array>,
+ /** Group buffer as array of group ids for each vertex wrapped in a value cell */
+ groupBuffer: ValueCell<Float32Array>,
/** Flag indicating if normals are computed for the current set of vertices */
normalsComputed: boolean,
- /** Flag indicating if offsets are computed for the current set of ids */
- offsetsComputed: boolean,
/** Bounding sphere of the mesh */
boundingSphere?: Sphere3D
@@ -43,19 +37,15 @@ export namespace Mesh {
const vb = mesh ? mesh.vertexBuffer.ref.value : new Float32Array(0)
const ib = mesh ? mesh.indexBuffer.ref.value : new Uint32Array(0)
const nb = mesh ? mesh.normalBuffer.ref.value : new Float32Array(0)
- const idb = mesh ? mesh.idBuffer.ref.value : new Float32Array(0)
- const ob = mesh ? mesh.offsetBuffer.ref.value : new Uint32Array(0)
+ const idb = mesh ? mesh.groupBuffer.ref.value : new Float32Array(0)
return {
vertexCount: 0,
triangleCount: 0,
- offsetCount: 0,
vertexBuffer: mesh ? ValueCell.update(mesh.vertexBuffer, vb) : ValueCell.create(vb),
indexBuffer: mesh ? ValueCell.update(mesh.indexBuffer, ib) : ValueCell.create(ib),
normalBuffer: mesh ? ValueCell.update(mesh.normalBuffer, nb) : ValueCell.create(nb),
- idBuffer: mesh ? ValueCell.update(mesh.idBuffer, idb) : ValueCell.create(idb),
- offsetBuffer: mesh ? ValueCell.update(mesh.offsetBuffer, ob) : ValueCell.create(ob),
+ groupBuffer: mesh ? ValueCell.update(mesh.groupBuffer, idb) : ValueCell.create(idb),
normalsComputed: true,
- offsetsComputed: true,
}
}
diff --git a/src/mol-geo/primitive/pyramid.ts b/src/mol-geo/primitive/pyramid.ts
index 1a0fb1ae9bf801d9eb575f1c0e67950be5288d70..f865a923658eec18d9bd29d2729ec31edca8cc24 100644
--- a/src/mol-geo/primitive/pyramid.ts
+++ b/src/mol-geo/primitive/pyramid.ts
@@ -62,7 +62,7 @@ export function OctagonalPyramide() {
//
let perforatedOctagonalPyramide: Primitive
-export function PerforatedOctagonalPyramide() {
+export function PerforatedOctagonalPyramid() {
if (!perforatedOctagonalPyramide) {
const points = polygon(8, true)
const vertices = new Float32Array(8 * 3 + 6)
diff --git a/src/mol-geo/primitive/sheet.ts b/src/mol-geo/primitive/sheet.ts
index e4130a5be57e25d9204754ed0dcf265b5f26ab66..e2da5dfc08d1bcbe30f635edcb0081d2421ab847 100644
--- a/src/mol-geo/primitive/sheet.ts
+++ b/src/mol-geo/primitive/sheet.ts
@@ -7,7 +7,7 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
-import { MeshBuilderState } from '../shape/mesh-builder';
+import { MeshBuilderState } from '../mesh/mesh-builder';
const tA = Vec3.zero()
const tB = Vec3.zero()
diff --git a/src/mol-geo/primitive/tube.ts b/src/mol-geo/primitive/tube.ts
index 92d8a182cd787892cc7b0a7b55f193edcd942eda..333b7cc8718b435ffb60a6982aefa478dbc790d1 100644
--- a/src/mol-geo/primitive/tube.ts
+++ b/src/mol-geo/primitive/tube.ts
@@ -7,7 +7,7 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { ChunkedArray } from 'mol-data/util';
-import { MeshBuilderState } from '../shape/mesh-builder';
+import { MeshBuilderState } from '../mesh/mesh-builder';
const normalVector = Vec3.zero()
const binormalVector = Vec3.zero()
diff --git a/src/mol-geo/representation/custom/index.ts b/src/mol-geo/representation/custom/index.ts
deleted file mode 100644
index 4189a143f0e87a1a4bc3f93e3bab9373828397ed..0000000000000000000000000000000000000000
--- a/src/mol-geo/representation/custom/index.ts
+++ /dev/null
@@ -1,108 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Task } from 'mol-task'
-import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object';
-import { RepresentationProps, Representation } from '..';
-import { PickingId } from '../../util/picking';
-import { Loci, EmptyLoci, CustomLoci, isCustomLoci, isEveryLoci } from 'mol-model/loci';
-import { MarkerAction, applyMarkerAction, createMarkers } from '../../util/marker-data';
-import { createRenderableState, createMeshValues, createIdentityTransform, DefaultMeshProps } from '../util';
-import { Mesh } from '../../shape/mesh';
-import { getMeshData } from '../../util/mesh-data';
-import { MeshValues } from 'mol-gl/renderable';
-import { createValueColor } from '../../util/color-data';
-import { Color } from 'mol-util/color';
-import { CustomLocation } from 'mol-model/location';
-import { ValueCell } from 'mol-util';
-
-export interface CustomRepresentation<P extends RepresentationProps = {}> extends Representation<Mesh, P> { }
-
-export const DefaultCustomProps = {
- ...DefaultMeshProps,
-}
-export type CustomProps = typeof DefaultCustomProps
-
-export function CustomRepresentation<P extends CustomProps>(): CustomRepresentation<P> {
- const renderObjects: RenderObject[] = []
- let _renderObject: MeshRenderObject
- let _mesh: Mesh
- let _props: P
-
- function create(mesh: Mesh, props: Partial<P> = {}) {
- _props = Object.assign({}, DefaultCustomProps, _props, props)
- return Task.create('CustomRepresentation.create', async ctx => {
- renderObjects.length = 0
- _mesh = mesh
-
- const elementCount = mesh.triangleCount
- const instanceCount = 1
-
- const color = createValueColor(Color(0x7ec0ee))
- const marker = createMarkers(instanceCount * elementCount)
- const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
-
- const values: MeshValues = {
- ...getMeshData(mesh),
- ...createMeshValues(_props, counts),
- aTransform: createIdentityTransform(),
- ...color,
- ...marker,
-
- elements: mesh.indexBuffer,
- }
- const state = createRenderableState(_props)
-
- _renderObject = createMeshRenderObject(values, state)
- renderObjects.push(_renderObject)
- });
- }
-
- function update(props: Partial<P>) {
- return Task.create('CustomRepresentation.update', async ctx => {
- // TODO
- })
- }
-
- return {
- get renderObjects () { return renderObjects },
- get props () { return _props },
- create,
- update,
- getLoci(pickingId: PickingId) {
- const { objectId, elementId } = pickingId
- if (_renderObject.id === objectId) {
- return CustomLoci([ CustomLocation(_mesh, elementId) ])
- }
- return EmptyLoci
- },
- mark(loci: Loci, action: MarkerAction) {
- const { tMarker } = _renderObject.values
- let changed = false
- if (isEveryLoci(loci)) {
- if (applyMarkerAction(tMarker.ref.value.array, 0, _mesh.triangleCount, action)) changed = true
- changed = true
- } else if (isCustomLoci(loci)) {
- for (const l of loci.locations) {
- if (l.data === _mesh) {
- if (applyMarkerAction(tMarker.ref.value.array, 0, _mesh.triangleCount, action)) changed = true
- // TODO
- // const idx = l.key
- // if (idx !== undefined) {
- // if (applyMarkerAction(tMarker.ref.value.array, idx, idx + 1, action)) changed = true
- // }
- }
- }
- }
- if (changed) {
- ValueCell.update(tMarker, tMarker.ref.value)
- }
- },
- destroy() {
- // TODO
- }
- }
-}
\ No newline at end of file
diff --git a/src/mol-geo/representation/shape/index.ts b/src/mol-geo/representation/shape/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ea5faf1d688a942bc983594217d69dff2f14ceaa
--- /dev/null
+++ b/src/mol-geo/representation/shape/index.ts
@@ -0,0 +1,128 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from 'mol-task'
+import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object';
+import { RepresentationProps, Representation } from '..';
+import { PickingId } from '../../util/picking';
+import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
+import { MarkerAction, applyMarkerAction, createMarkers } from '../../util/marker-data';
+import { createRenderableState, createMeshValues, createIdentityTransform, DefaultMeshProps } from '../util';
+import { getMeshData } from '../../util/mesh-data';
+import { MeshValues } from 'mol-gl/renderable';
+import { ValueCell } from 'mol-util';
+import { ColorThemeProps } from 'mol-view/theme/color';
+import { Shape } from 'mol-model/shape';
+import { LocationIterator } from '../../util/location-iterator';
+import { arrayMax } from 'mol-util/array';
+import { createColors } from '../structure/visual/util/common';
+import { OrderedSet, Interval } from 'mol-data/int';
+
+export interface ShapeRepresentation<P extends RepresentationProps = {}> extends Representation<Shape, P> { }
+
+export const DefaultShapeProps = {
+ ...DefaultMeshProps,
+ colorTheme: { name: 'shape-group' } as ColorThemeProps
+}
+export type ShapeProps = typeof DefaultShapeProps
+
+export function ShapeRepresentation<P extends ShapeProps>(): ShapeRepresentation<P> {
+ const renderObjects: RenderObject[] = []
+ let _renderObject: MeshRenderObject
+ let _shape: Shape
+ let _props: P
+
+ function create(shape: Shape, props: Partial<P> = {}) {
+ _props = Object.assign({}, DefaultShapeProps, _props, props)
+ _shape = shape
+
+ return Task.create('ShapeRepresentation.create', async ctx => {
+ renderObjects.length = 0
+
+ const mesh = shape.mesh
+ const locationIt = ShapeGroupIterator.fromShape(shape)
+ const { groupCount, instanceCount } = locationIt
+
+ const color = createColors(locationIt, _props.colorTheme)
+ const marker = createMarkers(instanceCount * groupCount)
+ const counts = { drawCount: mesh.triangleCount * 3, groupCount, instanceCount }
+
+ const values: MeshValues = {
+ ...getMeshData(mesh),
+ ...createMeshValues(_props, counts),
+ aTransform: createIdentityTransform(),
+ ...color,
+ ...marker,
+
+ elements: mesh.indexBuffer,
+ }
+ const state = createRenderableState(_props)
+
+ _renderObject = createMeshRenderObject(values, state)
+ console.log(_renderObject)
+ renderObjects.push(_renderObject)
+ });
+ }
+
+ function update(props: Partial<P>) {
+ return Task.create('ShapeRepresentation.update', async ctx => {
+ // TODO
+ })
+ }
+
+ return {
+ get renderObjects () { return renderObjects },
+ get props () { return _props },
+ create,
+ update,
+ getLoci(pickingId: PickingId) {
+ const { objectId, groupId } = pickingId
+ if (_renderObject.id === objectId) {
+ return Shape.Loci([ { shape: _shape, ids: OrderedSet.ofSingleton(groupId) } ])
+ }
+ return EmptyLoci
+ },
+ mark(loci: Loci, action: MarkerAction) {
+ const { tMarker } = _renderObject.values
+ let changed = false
+ if (isEveryLoci(loci)) {
+ if (applyMarkerAction(tMarker.ref.value.array, 0, _shape.mesh.triangleCount, action)) changed = true
+ } else if (Shape.isLoci(loci)) {
+ for (const g of loci.groups) {
+ if (Interval.is(g.ids)) {
+ const start = Interval.start(g.ids)
+ const end = Interval.end(g.ids)
+ if (applyMarkerAction(tMarker.ref.value.array, start, end, action)) changed = true
+ } else {
+ for (let i = 0, _i = g.ids.length; i < _i; i++) {
+ const idx = g.ids[i];
+ if (applyMarkerAction(tMarker.ref.value.array, idx, idx + 1, action)) changed = true
+ }
+ }
+ }
+ }
+ if (changed) {
+ ValueCell.update(tMarker, tMarker.ref.value)
+ }
+ },
+ destroy() {
+ // TODO
+ }
+ }
+}
+
+export namespace ShapeGroupIterator {
+ export function fromShape(shape: Shape): LocationIterator {
+ const groupCount = arrayMax(shape.mesh.groupBuffer.ref.value) + 1
+ const instanceCount = 1
+ const location = Shape.Location(shape)
+ const getLocation = (groupIndex: number) => {
+ location.group = groupIndex
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/complex-representation.ts b/src/mol-geo/representation/structure/complex-representation.ts
index d19f96b263525cd4fe6ac280e3cd890ccd675391..6a258b24ca99cf9ccc9edc5d1297b306ac483051 100644
--- a/src/mol-geo/representation/structure/complex-representation.ts
+++ b/src/mol-geo/representation/structure/complex-representation.ts
@@ -22,7 +22,7 @@ export function ComplexRepresentation<P extends StructureProps>(visualCtor: () =
function create(structure: Structure, props: Partial<P> = {}) {
_props = Object.assign({}, DefaultStructureProps, _props, props, getQualityProps(props, structure))
- _props.colorTheme!.structure = structure
+ _props.colorTheme.structure = structure
return Task.create('Creating StructureRepresentation', async ctx => {
if (!_structure) {
@@ -44,7 +44,7 @@ export function ComplexRepresentation<P extends StructureProps>(visualCtor: () =
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
+ _props.colorTheme.structure = _structure
if (!await visual.update(ctx, _props)) {
await visual.create(ctx, _structure, _props)
diff --git a/src/mol-geo/representation/structure/complex-visual.ts b/src/mol-geo/representation/structure/complex-visual.ts
index 083a610e728721a6c293aa595f0ce1b44ac84a78..063ecf36dc20499485644fb736b9f853f2b1b4bf 100644
--- a/src/mol-geo/representation/structure/complex-visual.ts
+++ b/src/mol-geo/representation/structure/complex-visual.ts
@@ -7,9 +7,9 @@
import { Structure } from 'mol-model/structure';
import { Visual } from '..';
import { MeshRenderObject } from 'mol-gl/render-object';
-import { Mesh } from '../../shape/mesh';
+import { Mesh } from '../../mesh/mesh';
import { RuntimeContext } from 'mol-task';
-import { LocationIterator } from './visual/util/location-iterator';
+import { LocationIterator } from '../../util/location-iterator';
import { createComplexMeshRenderObject, createColors } from './visual/util/common';
import { StructureProps, DefaultStructureMeshProps, MeshUpdateState } from '.';
import { deepEqual, ValueCell } from 'mol-util';
@@ -96,7 +96,7 @@ export function ComplexMeshVisual<P extends ComplexMeshProps>(builder: ComplexMe
},
mark(loci: Loci, action: MarkerAction) {
const { tMarker } = renderObject.values
- const { elementCount, instanceCount } = locationIt
+ const { groupCount, instanceCount } = locationIt
function apply(interval: Interval) {
const start = Interval.start(interval)
@@ -106,7 +106,7 @@ export function ComplexMeshVisual<P extends ComplexMeshProps>(builder: ComplexMe
let changed = false
if (isEveryLoci(loci)) {
- apply(Interval.ofBounds(0, elementCount * instanceCount))
+ apply(Interval.ofBounds(0, groupCount * instanceCount))
changed = true
} else {
changed = mark(loci, currentStructure, apply)
diff --git a/src/mol-geo/representation/structure/units-visual.ts b/src/mol-geo/representation/structure/units-visual.ts
index 9118f2b48afdc14ae21957ac2f56f8e8a3c563d6..d7ebb4b9bc5ccc140c3091671ba836e8fbc87f6a 100644
--- a/src/mol-geo/representation/structure/units-visual.ts
+++ b/src/mol-geo/representation/structure/units-visual.ts
@@ -9,8 +9,8 @@ import { RepresentationProps, Visual } from '..';
import { DefaultStructureMeshProps, MeshUpdateState } from '.';
import { RuntimeContext } from 'mol-task';
import { PickingId } from '../../util/picking';
-import { LocationIterator } from './visual/util/location-iterator';
-import { Mesh } from '../../shape/mesh';
+import { LocationIterator } from '../../util/location-iterator';
+import { Mesh } from '../../mesh/mesh';
import { MarkerAction, applyMarkerAction } from '../../util/marker-data';
import { Loci, isEveryLoci } from 'mol-model/loci';
import { MeshRenderObject } from 'mol-gl/render-object';
@@ -101,7 +101,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
},
mark(loci: Loci, action: MarkerAction) {
const { tMarker } = renderObject.values
- const { elementCount, instanceCount } = locationIt
+ const { groupCount, instanceCount } = locationIt
function apply(interval: Interval) {
const start = Interval.start(interval)
@@ -111,7 +111,7 @@ export function UnitsMeshVisual<P extends UnitsMeshProps>(builder: UnitsMeshVisu
let changed = false
if (isEveryLoci(loci)) {
- apply(Interval.ofBounds(0, elementCount * instanceCount))
+ apply(Interval.ofBounds(0, groupCount * instanceCount))
changed = true
} else {
changed = mark(loci, currentGroup, apply)
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 a315ba72dbc38bc18bc8ea4116f4ca100e02155e..6526391f04326d93df99dd68f5c35c69de5d16c0 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts
@@ -7,12 +7,12 @@
import { Unit, Structure, Link, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, ComplexVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../shape/mesh';
+import { Mesh } from '../../../mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { DefaultMeshProps } from '../../util';
import { Vec3 } from 'mol-math/linear-algebra';
-import { LocationIterator } from './util/location-iterator';
+import { LocationIterator } from '../../../util/location-iterator';
import { createLinkCylinderMesh, DefaultLinkCylinderProps, LinkCylinderProps } from './util/link';
import { OrderedSet, Interval } from 'mol-data/int';
import { ComplexMeshVisual } from '../complex-visual';
@@ -85,11 +85,11 @@ export function CarbohydrateLinkVisual(): ComplexVisual<CarbohydrateLinkProps> {
function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
const { elements, links } = structure.carbohydrates
- const elementCount = links.length
+ const groupCount = links.length
const instanceCount = 1
const location = Link.Location()
- const getLocation = (elementIndex: number, instanceIndex: number) => {
- const link = links[elementIndex]
+ const getLocation = (groupIndex: number) => {
+ const link = links[groupIndex]
const carbA = elements[link.carbohydrateIndexA]
const carbB = elements[link.carbohydrateIndexB]
const indexA = OrderedSet.findPredecessorIndex(carbA.unit.elements, carbA.anomericCarbon)
@@ -100,14 +100,14 @@ function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
location.bIndex = indexB as StructureElement.UnitIndex
return location
}
- return LocationIterator(elementCount, instanceCount, getLocation)
+ return LocationIterator(groupCount, instanceCount, getLocation)
}
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
- const { objectId, elementId } = pickingId
+ const { objectId, groupId } = pickingId
if (id === objectId) {
const { links, elements } = structure.carbohydrates
- const l = links[elementId]
+ const l = links[groupId]
const carbA = elements[l.carbohydrateIndexA]
const carbB = elements[l.carbohydrateIndexB]
const indexA = OrderedSet.findPredecessorIndex(carbA.unit.elements, carbA.anomericCarbon)
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 142791e62b0ad390e04ce01df6aee8b0a25f4a7b..7832c86b0dce966cec6b87d13d634e4f3e273074 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -7,13 +7,13 @@
import { Unit, Structure, StructureElement } from 'mol-model/structure';
import { ComplexVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../shape/mesh';
+import { Mesh } from '../../../mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { MeshBuilder } from '../../../shape/mesh-builder';
+import { MeshBuilder } from '../../../mesh/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants';
-import { LocationIterator } from './util/location-iterator';
+import { LocationIterator } from '../../../util/location-iterator';
import { OrderedSet, Interval } from 'mol-data/int';
import { ComplexMeshVisual, DefaultComplexMeshProps } from '../complex-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
@@ -49,7 +49,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
Mat4.targetTo(t, center, pd, normal)
Mat4.setTranslation(t, center)
- builder.setId(i * 2)
+ builder.setGroup(i * 2)
switch (shapeType) {
case SaccharideShapes.FilledSphere:
@@ -63,7 +63,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
Mat4.scaleUniformly(t, t, side)
builder.addPerforatedBox(t)
Mat4.mul(t, t, Mat4.rotZ90X180)
- builder.setId(i * 2 + 1)
+ builder.setGroup(i * 2 + 1)
builder.addPerforatedBox(t)
break;
case SaccharideShapes.FilledCone:
@@ -74,7 +74,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
Mat4.scaleUniformly(t, t, side * 1.2)
builder.addPerforatedOctagonalPyramid(t)
Mat4.mul(t, t, Mat4.rotZ90)
- builder.setId(i * 2 + 1)
+ builder.setGroup(i * 2 + 1)
builder.addPerforatedOctagonalPyramid(t)
break
case SaccharideShapes.FlatBox:
@@ -96,7 +96,7 @@ async function createCarbohydrateSymbolMesh(ctx: RuntimeContext, structure: Stru
Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4))
builder.addPerforatedOctahedron(t)
Mat4.mul(t, t, Mat4.rotY90)
- builder.setId(i * 2 + 1)
+ builder.setGroup(i * 2 + 1)
builder.addPerforatedOctahedron(t)
break
case SaccharideShapes.FlatDiamond:
@@ -142,11 +142,11 @@ export function CarbohydrateSymbolVisual(): ComplexVisual<CarbohydrateSymbolProp
function CarbohydrateElementIterator(structure: Structure): LocationIterator {
const carbElements = structure.carbohydrates.elements
- const elementCount = carbElements.length * 2
+ const groupCount = carbElements.length * 2
const instanceCount = 1
const location = StructureElement.create()
- function getLocation (elementIndex: number, instanceIndex: number) {
- const carb = carbElements[Math.floor(elementIndex / 2)]
+ function getLocation (groupIndex: number, instanceIndex: number) {
+ const carb = carbElements[Math.floor(groupIndex / 2)]
location.unit = carb.unit
location.element = carb.anomericCarbon
return location
@@ -154,13 +154,13 @@ function CarbohydrateElementIterator(structure: Structure): LocationIterator {
function isSecondary (elementIndex: number, instanceIndex: number) {
return (elementIndex % 2) === 1
}
- return LocationIterator(elementCount, instanceCount, getLocation, isSecondary)
+ return LocationIterator(groupCount, instanceCount, getLocation, isSecondary)
}
function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: number) {
- const { objectId, elementId } = pickingId
+ const { objectId, groupId } = pickingId
if (id === objectId) {
- const carb = structure.carbohydrates.elements[Math.floor(elementId / 2)]
+ const carb = structure.carbohydrates.elements[Math.floor(groupId / 2)]
const { unit } = carb
const index = OrderedSet.findPredecessorIndex(unit.elements, carb.anomericCarbon)
const indices = OrderedSet.ofSingleton(index as StructureElement.UnitIndex)
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 de81e58df39a4d2da5573d99895442b6b651fbca..6bd885217c6132fbbdce6ed6ed481aeb68afda33 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
@@ -8,12 +8,12 @@ import { Link, Structure, StructureElement } from 'mol-model/structure';
import { ComplexVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh } from './util/link';
-import { Mesh } from '../../../shape/mesh';
+import { Mesh } from '../../../mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { ComplexMeshVisual, DefaultComplexMeshProps } from '../complex-visual';
-import { LocationIterator } from './util/location-iterator';
+import { LocationIterator } from '../../../util/location-iterator';
import { Interval } from 'mol-data/int';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { BitFlags } from 'mol-util';
@@ -73,24 +73,24 @@ export function CrossLinkRestraintVisual(): ComplexVisual<CrossLinkRestraintProp
function CrossLinkRestraintIterator(structure: Structure): LocationIterator {
const { pairs } = structure.crossLinkRestraints
- const elementCount = pairs.length
+ const groupCount = pairs.length
const instanceCount = 1
const location = Link.Location()
- const getLocation = (elementIndex: number) => {
- const pair = pairs[elementIndex]
+ const getLocation = (groupIndex: number) => {
+ const pair = pairs[groupIndex]
location.aUnit = pair.unitA
location.aIndex = pair.indexA
location.bUnit = pair.unitB
location.bIndex = pair.indexB
return location
}
- return LocationIterator(elementCount, instanceCount, getLocation)
+ return LocationIterator(groupCount, instanceCount, getLocation)
}
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
- const { objectId, elementId } = pickingId
+ const { objectId, groupId } = pickingId
if (id === objectId) {
- const pair = structure.crossLinkRestraints.pairs[elementId]
+ const pair = structure.crossLinkRestraints.pairs[groupId]
if (pair) {
return Link.Loci([ Link.Location(pair.unitA, pair.indexA, pair.unitB, pair.indexB) ])
}
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index 57306c4b9765092b471cead32cb6342c20023c26..e58f1bee17d71ac6a7605317fb6000a6ce448ca4 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -11,7 +11,7 @@ import { Unit } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task'
import { UnitsVisual, DefaultStructureProps } from '..';
-import { getElementLoci } from './util/element';
+import { getElementLoci, StructureElementIterator } from './util/element';
import { createTransforms, createColors, createSizes } from './util/common';
import { deepEqual, defaults } from 'mol-util';
import { SortedArray } from 'mol-data/int';
@@ -21,7 +21,6 @@ import { Loci } from 'mol-model/loci';
import { MarkerAction, createMarkers } from '../../../util/marker-data';
import { Vec3 } from 'mol-math/linear-algebra';
import { fillSerial } from 'mol-util/array';
-import { StructureElementIterator } from './util/location-iterator';
import { SizeThemeProps } from 'mol-view/theme/size';
export const DefaultPointProps = {
@@ -79,16 +78,16 @@ export default function PointVisual(): UnitsVisual<PointProps> {
const values: PointValues = {
aPosition: ValueCell.create(vertices),
- aElementId: ValueCell.create(fillSerial(new Float32Array(elementCount))),
+ aGroup: ValueCell.create(fillSerial(new Float32Array(elementCount))),
aTransform: transforms,
- aInstanceId: ValueCell.create(fillSerial(new Float32Array(instanceCount))),
+ aInstance: ValueCell.create(fillSerial(new Float32Array(instanceCount))),
...color,
...marker,
...size,
uAlpha: ValueCell.create(defaults(props.alpha, 1.0)),
uInstanceCount: ValueCell.create(instanceCount),
- uElementCount: ValueCell.create(group.elements.length),
+ uGroupCount: ValueCell.create(group.elements.length),
drawCount: ValueCell.create(vertices.length / 3),
instanceCount: ValueCell.create(instanceCount),
diff --git a/src/mol-geo/representation/structure/visual/element-sphere.ts b/src/mol-geo/representation/structure/visual/element-sphere.ts
index 8f151ccf110b1511946edc83bb8c8f255dd701cc..523e19e1e3d62d8cc1a0c0ce6c3d1fdc4b699c14 100644
--- a/src/mol-geo/representation/structure/visual/element-sphere.ts
+++ b/src/mol-geo/representation/structure/visual/element-sphere.ts
@@ -6,8 +6,7 @@
*/
import { UnitsVisual, MeshUpdateState } from '..';
-import { createElementSphereMesh, markElement, getElementLoci } from './util/element';
-import { StructureElementIterator } from './util/location-iterator';
+import { createElementSphereMesh, markElement, getElementLoci, StructureElementIterator } from './util/element';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
export const DefaultElementSphereProps = {
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 40d6c5709e25357a57971fc5195683f53437671b..813da2a3b9ce6864298fe0e8424972e05ab97b7a 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
@@ -7,12 +7,11 @@
import { Link, Structure, StructureElement } from 'mol-model/structure';
import { ComplexVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh } from './util/link';
-import { Mesh } from '../../../shape/mesh';
+import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh, LinkIterator } from './util/link';
+import { Mesh } from '../../../mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { LinkIterator } from './util/location-iterator';
import { ComplexMeshVisual, DefaultComplexMeshProps } from '../complex-visual';
import { Interval } from 'mol-data/int';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
@@ -70,9 +69,9 @@ export function InterUnitLinkVisual(): ComplexVisual<InterUnitLinkProps> {
}
function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
- const { objectId, elementId } = pickingId
+ const { objectId, groupId } = pickingId
if (id === objectId) {
- const bond = structure.links.bonds[elementId]
+ const bond = structure.links.bonds[groupId]
return Link.Loci([
Link.Location(
bond.unitA, bond.indexA as StructureElement.UnitIndex,
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 12c1a7c0cc0734e417fc6cfabf1b9d5194e30a74..bf3e964bc6788f9b2f36e47324de31e147e6eb40 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
@@ -8,12 +8,11 @@
import { Unit, Link, StructureElement } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh } from './util/link';
-import { Mesh } from '../../../shape/mesh';
+import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh, LinkIterator } from './util/link';
+import { Mesh } from '../../../mesh/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, EmptyLoci } from 'mol-model/loci';
-import { LinkIterator } from './util/location-iterator';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { Interval } from 'mol-data/int';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
@@ -82,13 +81,13 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
}
function getLinkLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number) {
- const { objectId, instanceId, elementId } = pickingId
+ const { objectId, instanceId, groupId } = pickingId
const unit = group.units[instanceId]
if (id === objectId && Unit.isAtomic(unit)) {
return Link.Loci([
Link.Location(
- unit, unit.links.a[elementId] as StructureElement.UnitIndex,
- unit, unit.links.b[elementId] as StructureElement.UnitIndex
+ unit, unit.links.a[groupId] as StructureElement.UnitIndex,
+ unit, unit.links.b[groupId] as StructureElement.UnitIndex
)
])
}
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 eb4ffed1f450e0c598a74142f4fe8a5168c3f07b..29659c6d6a5a9070015e74f2a0cfb89be99c1346 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -7,14 +7,13 @@
import { Unit } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../shape/mesh';
-import { MeshBuilder } from '../../../shape/mesh-builder';
-import { getElementLoci, markElement } from './util/element';
+import { Mesh } from '../../../mesh/mesh';
+import { MeshBuilder } from '../../../mesh/mesh-builder';
+import { getElementLoci, markElement, StructureElementIterator } from './util/element';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
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()
@@ -30,6 +29,7 @@ const center = Vec3.zero()
const t = Mat4.identity()
const sVec = Vec3.zero()
+// TODO define props, should be scalable
async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -88,7 +88,7 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props:
Vec3.scaleAndAdd(center, p1, v12, height / 2 - 0.2)
Mat4.scale(t, t, Vec3.set(sVec, width, depth, height))
Mat4.setTranslation(t, center)
- builder.setId(SortedArray.findPredecessorIndex(elements, idx6))
+ builder.setGroup(SortedArray.findPredecessorIndex(elements, idx6))
builder.addBox(t)
builder.addCylinder(p5, p6, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
}
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 a80dae5b8a1882a6e93e797c749797873a1f8367..ed141df814c330834c3ef894ee5388e4ed1e579a 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -7,12 +7,11 @@
import { Unit } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../shape/mesh';
-import { MeshBuilder } from '../../../shape/mesh-builder';
+import { Mesh } from '../../../mesh/mesh';
+import { MeshBuilder } from '../../../mesh/mesh-builder';
import { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
-import { getElementLoci, markElement } from './util/element';
+import { getElementLoci, markElement, StructureElementIterator } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
-import { StructureElementIterator } from './util/location-iterator';
import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { CylinderProps } from '../../../primitive/cylinder';
@@ -47,11 +46,11 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
pos(centerB.element, pB)
cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerA)
- builder.setId(OrderedSet.findPredecessorIndex(elements, centerA.element))
+ builder.setGroup(OrderedSet.findPredecessorIndex(elements, centerA.element))
builder.addCylinder(pA, pB, 0.5, cylinderProps)
cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerB)
- builder.setId(OrderedSet.findPredecessorIndex(elements, centerB.element))
+ builder.setGroup(OrderedSet.findPredecessorIndex(elements, centerB.element))
builder.addCylinder(pB, pA, 0.5, cylinderProps)
if (i % 10000 === 0 && ctx.shouldUpdate) {
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 b6eaf79647a2004288a76212be17ce0f6090618a..07b965453e6ed83a4a291a37ec9130ab941d3e3a 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -7,13 +7,12 @@
import { Unit } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { markElement, getElementLoci } from './util/element';
-import { Mesh } from '../../../shape/mesh';
-import { MeshBuilder } from '../../../shape/mesh-builder';
+import { markElement, getElementLoci, StructureElementIterator } from './util/element';
+import { Mesh } from '../../../mesh/mesh';
+import { MeshBuilder } from '../../../mesh/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';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { OrderedSet } from 'mol-data/int';
@@ -49,7 +48,7 @@ async function createPolymerDirectionWedgeMesh(ctx: RuntimeContext, unit: Unit,
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setId(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
+ builder.setGroup(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
const isNucleic = v.moleculeType === MoleculeType.DNA || v.moleculeType === MoleculeType.RNA
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
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 f5a12fdc6673a805a0e2a2c252ac2dc3b54476a1..e01feada50bdbb3e72ed9ea9bbd45bdfec4c36c6 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -7,12 +7,11 @@
import { Unit, StructureElement } from 'mol-model/structure';
import { UnitsVisual } from '..';
import { RuntimeContext } from 'mol-task'
-import { Mesh } from '../../../shape/mesh';
-import { MeshBuilder } from '../../../shape/mesh-builder';
+import { Mesh } from '../../../mesh/mesh';
+import { MeshBuilder } from '../../../mesh/mesh-builder';
import { getPolymerGapCount, PolymerGapIterator } from './util/polymer';
-import { getElementLoci, markElement } from './util/element';
+import { getElementLoci, markElement, StructureElementIterator } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
-import { StructureElementIterator } from './util/location-iterator';
import { UnitsMeshVisual, DefaultUnitsMeshProps } from '../units-visual';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { CylinderProps } from '../../../primitive/cylinder';
@@ -48,7 +47,7 @@ async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, pro
while (polymerGapIt.hasNext) {
const { centerA, centerB } = polymerGapIt.move()
if (centerA.element === centerB.element) {
- builder.setId(centerA.element)
+ builder.setGroup(centerA.element)
pos(elements[centerA.element], pA)
builder.addSphere(pA, 0.6, 0)
} else {
@@ -59,12 +58,12 @@ async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, pro
l.element = elmA
cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(l)
- builder.setId(centerA.element)
+ builder.setGroup(centerA.element)
builder.addFixedCountDashedCylinder(pA, pB, 0.5, segmentCount, cylinderProps)
l.element = elmB
cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(l)
- builder.setId(centerB.element)
+ builder.setGroup(centerB.element)
builder.addFixedCountDashedCylinder(pB, pA, 0.5, segmentCount, cylinderProps)
}
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 da04a008c769a1214ee024875f64ee4dbe317e84..eb8efab672a2858fa1248f4fbe1afc10ce01e618 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -7,12 +7,11 @@
import { Unit } from 'mol-model/structure';
import { UnitsVisual, MeshUpdateState } from '..';
import { RuntimeContext } from 'mol-task'
-import { markElement, getElementLoci } from './util/element';
-import { Mesh } from '../../../shape/mesh';
-import { MeshBuilder } from '../../../shape/mesh-builder';
+import { markElement, getElementLoci, StructureElementIterator } from './util/element';
+import { Mesh } from '../../../mesh/mesh';
+import { MeshBuilder } from '../../../mesh/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';
import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
import { OrderedSet } from 'mol-data/int';
@@ -44,7 +43,7 @@ async function createPolymerTraceMesh(ctx: RuntimeContext, unit: Unit, props: Po
const polymerTraceIt = PolymerTraceIterator(unit)
while (polymerTraceIt.hasNext) {
const v = polymerTraceIt.move()
- builder.setId(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
+ builder.setGroup(OrderedSet.findPredecessorIndex(unit.elements, v.center.element))
const isNucleic = v.moleculeType === MoleculeType.DNA || v.moleculeType === MoleculeType.RNA
const isSheet = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Beta)
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index 406abfd2e93c228f20e54db68ee8e7b29f4a7154..e069563c8771d3a7d6281a4f91720be24a3b6c27 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -8,11 +8,11 @@
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, createElementSize, createElementInstanceSize, createInstanceSize } from '../../../../util/size-data';
+import { createUniformColor, ColorData, createGroupColor, createGroupInstanceColor, createInstanceColor } from '../../../../util/color-data';
+import { createUniformSize, SizeData, createGroupSize, createGroupInstanceSize, createInstanceSize } from '../../../../util/size-data';
import { ValueCell } from 'mol-util';
-import { LocationIterator } from './location-iterator';
-import { Mesh } from '../../../../shape/mesh';
+import { LocationIterator } from '../../../../util/location-iterator';
+import { Mesh } from '../../../../mesh/mesh';
import { MeshValues } from 'mol-gl/renderable';
import { getMeshData } from '../../../../util/mesh-data';
import { MeshProps, createMeshValues, createRenderableState, createIdentityTransform } from '../../../util';
@@ -36,8 +36,8 @@ export function createColors(locationIt: LocationIterator, props: ColorThemeProp
const colorTheme = ColorTheme(props)
switch (colorTheme.kind) {
case 'uniform': return createUniformColor(locationIt, colorTheme.color, colorData)
- case 'element': return createElementColor(locationIt, colorTheme.color, colorData)
- case 'elementInstance': return createElementInstanceColor(locationIt, colorTheme.color, colorData)
+ case 'group': return createGroupColor(locationIt, colorTheme.color, colorData)
+ case 'groupInstance': return createGroupInstanceColor(locationIt, colorTheme.color, colorData)
case 'instance': return createInstanceColor(locationIt, colorTheme.color, colorData)
}
}
@@ -46,8 +46,8 @@ export function createSizes(locationIt: LocationIterator, props: SizeThemeProps,
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 'group': return createGroupSize(locationIt, sizeTheme.size, sizeData)
+ case 'groupInstance': return createGroupInstanceSize(locationIt, sizeTheme.size, sizeData)
case 'instance': return createInstanceSize(locationIt, sizeTheme.size, sizeData)
}
}
@@ -55,11 +55,11 @@ export function createSizes(locationIt: LocationIterator, props: SizeThemeProps,
type StructureMeshProps = Required<MeshProps & StructureProps>
function _createMeshValues(transforms: ValueCell<Float32Array>, mesh: Mesh, locationIt: LocationIterator, props: StructureMeshProps): MeshValues {
- const { instanceCount, elementCount } = locationIt
+ const { instanceCount, groupCount } = locationIt
const color = createColors(locationIt, props.colorTheme)
- const marker = createMarkers(instanceCount * elementCount)
+ const marker = createMarkers(instanceCount * groupCount)
- const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
+ const counts = { drawCount: mesh.triangleCount * 3, groupCount, instanceCount }
return {
...getMeshData(mesh),
diff --git a/src/mol-geo/representation/structure/visual/util/element.ts b/src/mol-geo/representation/structure/visual/util/element.ts
index 89934754869f743e1321cadd11697e14e4296517..dd1ea7d1314e10815b4eefdd0829973c3dbff467 100644
--- a/src/mol-geo/representation/structure/visual/util/element.ts
+++ b/src/mol-geo/representation/structure/visual/util/element.ts
@@ -8,12 +8,13 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { Unit, StructureElement } from 'mol-model/structure';
import { RuntimeContext } from 'mol-task';
import { sphereVertexCount } from '../../../../primitive/sphere';
-import { Mesh } from '../../../../shape/mesh';
-import { MeshBuilder } from '../../../../shape/mesh-builder';
+import { Mesh } from '../../../../mesh/mesh';
+import { MeshBuilder } from '../../../../mesh/mesh-builder';
import { Loci, EmptyLoci } from 'mol-model/loci';
import { Interval, OrderedSet } from 'mol-data/int';
import { PickingId } from '../../../../util/picking';
import { SizeTheme, SizeThemeProps } from 'mol-view/theme/size';
+import { LocationIterator } from '../../../../util/location-iterator';
export interface ElementSphereMeshProps {
sizeTheme: SizeThemeProps,
@@ -38,7 +39,7 @@ export async function createElementSphereMesh(ctx: RuntimeContext, unit: Unit, p
l.element = elements[i]
pos(elements[i], v)
- meshBuilder.setId(i)
+ meshBuilder.setGroup(i)
meshBuilder.addSphere(v, sizeTheme.size(l), detail)
if (i % 10000 === 0 && ctx.shouldUpdate) {
@@ -74,11 +75,25 @@ export function markElement(loci: Loci, group: Unit.SymmetryGroup, apply: (inter
}
export function getElementLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number) {
- const { objectId, instanceId, elementId } = pickingId
+ const { objectId, instanceId, groupId } = pickingId
if (id === objectId) {
const unit = group.units[instanceId]
- const indices = OrderedSet.ofSingleton(elementId as StructureElement.UnitIndex);
+ const indices = OrderedSet.ofSingleton(groupId as StructureElement.UnitIndex);
return StructureElement.Loci([{ unit, indices }])
}
return EmptyLoci
+}
+
+export namespace StructureElementIterator {
+ export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
+ const unit = group.units[0]
+ const groupCount = group.elements.length
+ const instanceCount = group.units.length
+ const location = StructureElement.create(unit)
+ const getLocation = (groupIndex: number) => {
+ location.element = unit.elements[groupIndex]
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/link.ts b/src/mol-geo/representation/structure/visual/util/link.ts
index fa687917bbe58f663a6f17704de70c78d5a1341e..f41776cfc29091f0beb02c9bdb9cc5e86bcf4ddd 100644
--- a/src/mol-geo/representation/structure/visual/util/link.ts
+++ b/src/mol-geo/representation/structure/visual/util/link.ts
@@ -6,12 +6,14 @@
import { Vec3 } from 'mol-math/linear-algebra';
import { RuntimeContext } from 'mol-task';
-import { Mesh } from '../../../../shape/mesh';
-import { MeshBuilder } from '../../../../shape/mesh-builder';
+import { Mesh } from '../../../../mesh/mesh';
+import { MeshBuilder } from '../../../../mesh/mesh-builder';
import { LinkType } from 'mol-model/structure/model/types';
import { DefaultMeshProps } from '../../../util';
import { SizeThemeProps } from 'mol-view/theme/size';
import { CylinderProps } from '../../../../primitive/cylinder';
+import { LocationIterator } from '../../../../util/location-iterator';
+import { Unit, StructureElement, Structure, Link } from 'mol-model/structure';
export const DefaultLinkCylinderProps = {
...DefaultMeshProps,
@@ -87,7 +89,7 @@ export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: L
const linkRadius = radius(edgeIndex)
const o = order(edgeIndex)
const f = flags(edgeIndex)
- meshBuilder.setId(edgeIndex)
+ meshBuilder.setGroup(edgeIndex)
if (LinkType.is(f, LinkType.Flag.MetallicCoordination)) {
// show metall coordinations with dashed cylinders
@@ -116,4 +118,33 @@ export async function createLinkCylinderMesh(ctx: RuntimeContext, linkBuilder: L
}
return meshBuilder.getMesh()
+}
+
+export namespace LinkIterator {
+ export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
+ const unit = group.units[0]
+ const groupCount = Unit.isAtomic(unit) ? unit.links.edgeCount * 2 : 0
+ const instanceCount = group.units.length
+ const location = StructureElement.create(unit)
+ const getLocation = (groupIndex: number) => {
+ location.element = unit.elements[(unit as Unit.Atomic).links.a[groupIndex]]
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
+
+ export function fromStructure(structure: Structure): LocationIterator {
+ const groupCount = structure.links.bondCount
+ const instanceCount = 1
+ const location = Link.Location()
+ const getLocation = (groupIndex: number) => {
+ const bond = structure.links.bonds[groupIndex]
+ location.aUnit = bond.unitA
+ location.aIndex = bond.indexA as StructureElement.UnitIndex
+ location.bUnit = bond.unitB
+ location.bIndex = bond.indexB as StructureElement.UnitIndex
+ return location
+ }
+ return LocationIterator(groupCount, instanceCount, getLocation)
+ }
}
\ No newline at end of file
diff --git a/src/mol-geo/representation/structure/visual/util/location-iterator.ts b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
deleted file mode 100644
index aad0da64abdedce9ec3d4221379b91f56e256255..0000000000000000000000000000000000000000
--- a/src/mol-geo/representation/structure/visual/util/location-iterator.ts
+++ /dev/null
@@ -1,141 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Iterator } from 'mol-data';
-import { Unit, StructureElement, Structure, Link } from 'mol-model/structure';
-import { NullLocation, Location } from 'mol-model/location';
-
-export interface LocationValue {
- location: Location
- index: number
- elementIndex: number
- instanceIndex: number
- isSecondary: boolean
-}
-
-export const NullLocationValue: LocationValue = {
- location: NullLocation,
- index: 0,
- elementIndex: 0,
- instanceIndex: 0,
- isSecondary: false
-}
-
-export interface LocationIterator extends Iterator<LocationValue> {
- readonly hasNext: boolean
- readonly isNextNewInstance: boolean
- readonly elementCount: number
- readonly instanceCount: number
- move(): LocationValue
- reset(): void
- skipInstance(): void
-}
-
-type LocationGetter = (elementIndex: number, instanceIndex: number) => Location
-type IsSecondaryGetter = (elementIndex: number, instanceIndex: number) => boolean
-
-export function LocationIterator(elementCount: number, instanceCount: number, getLocation: LocationGetter, isSecondary: IsSecondaryGetter = () => false): LocationIterator {
- const value: LocationValue = {
- location: NullLocation as Location,
- index: 0,
- elementIndex: 0,
- instanceIndex: 0,
- isSecondary: false
- }
-
- let hasNext = value.elementIndex < elementCount
- let isNextNewInstance = false
- let elementIndex = 0
- let instanceIndex = 0
-
- return {
- get hasNext () { return hasNext },
- get isNextNewInstance () { return isNextNewInstance },
- get elementCount () { return elementCount },
- get instanceCount () { return instanceCount },
- move() {
- if (hasNext) {
- value.elementIndex = elementIndex
- value.instanceIndex = instanceIndex
- value.index = instanceIndex * elementCount + elementIndex
- value.location = getLocation(elementIndex, instanceIndex)
- value.isSecondary = isSecondary(elementIndex, instanceIndex)
- ++elementIndex
- if (elementIndex === elementCount) {
- ++instanceIndex
- isNextNewInstance = true
- if (instanceIndex < instanceCount) elementIndex = 0
- } else {
- isNextNewInstance = false
- }
- hasNext = elementIndex < elementCount
- }
- return value
- },
- reset() {
- value.location = NullLocation
- value.index = 0
- value.elementIndex = 0
- value.instanceIndex = 0
- value.isSecondary = false
-
- hasNext = value.elementIndex < elementCount
- isNextNewInstance = false
- elementIndex = 0
- instanceIndex = 0
- },
- skipInstance() {
- if (hasNext && value.instanceIndex === instanceIndex) {
- ++instanceIndex
- elementIndex = 0
- hasNext = instanceIndex < instanceCount
- }
- }
- }
-}
-
-export namespace StructureElementIterator {
- export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
- const unit = group.units[0]
- const elementCount = group.elements.length
- const instanceCount = group.units.length
- const location = StructureElement.create(unit)
- const getLocation = (elementIndex: number) => {
- location.element = unit.elements[elementIndex]
- return location
- }
- return LocationIterator(elementCount, instanceCount, getLocation)
- }
-}
-
-export namespace LinkIterator {
- export function fromGroup(group: Unit.SymmetryGroup): LocationIterator {
- const unit = group.units[0]
- const elementCount = Unit.isAtomic(unit) ? unit.links.edgeCount * 2 : 0
- const instanceCount = group.units.length
- const location = StructureElement.create(unit)
- const getLocation = (elementIndex: number) => {
- location.element = unit.elements[(unit as Unit.Atomic).links.a[elementIndex]]
- return location
- }
- return LocationIterator(elementCount, instanceCount, getLocation)
- }
-
- export function fromStructure(structure: Structure): LocationIterator {
- const elementCount = structure.links.bondCount
- const instanceCount = 1
- const location = Link.Location()
- const getLocation = (elementIndex: number) => {
- const bond = structure.links.bonds[elementIndex]
- location.aUnit = bond.unitA
- location.aIndex = bond.indexA as StructureElement.UnitIndex
- location.bUnit = bond.unitB
- location.bIndex = bond.indexB as StructureElement.UnitIndex
- return location
- }
- return LocationIterator(elementCount, instanceCount, getLocation)
- }
-}
\ No newline at end of file
diff --git a/src/mol-geo/representation/util.ts b/src/mol-geo/representation/util.ts
index 410623a925372b241e4c3e4f28e5f6c578b99b10..4edca150e52f42e76d67a5b28fd3f76754d4ed19 100644
--- a/src/mol-geo/representation/util.ts
+++ b/src/mol-geo/representation/util.ts
@@ -35,14 +35,14 @@ export function createIdentityTransform(transforms?: ValueCell<Float32Array>) {
return transforms ? ValueCell.update(transforms, identityTransform) : ValueCell.create(identityTransform)
}
-type Counts = { drawCount: number, elementCount: number, instanceCount: number }
+type Counts = { drawCount: number, groupCount: number, instanceCount: number }
export function createBaseValues(props: Required<BaseProps>, counts: Counts) {
return {
uAlpha: ValueCell.create(props.alpha),
uInstanceCount: ValueCell.create(counts.instanceCount),
- uElementCount: ValueCell.create(counts.elementCount),
- aInstanceId: ValueCell.create(fillSerial(new Float32Array(counts.instanceCount))),
+ uGroupCount: ValueCell.create(counts.groupCount),
+ aInstance: ValueCell.create(fillSerial(new Float32Array(counts.instanceCount))),
drawCount: ValueCell.create(counts.drawCount),
instanceCount: ValueCell.create(counts.instanceCount),
}
diff --git a/src/mol-geo/representation/volume/surface.ts b/src/mol-geo/representation/volume/surface.ts
index 82e1a5e25afe79e404090c57ccc08157740ebed8..1d289273d6e5783431b9185c98c8d09c3d1778ae 100644
--- a/src/mol-geo/representation/volume/surface.ts
+++ b/src/mol-geo/representation/volume/surface.ts
@@ -8,7 +8,7 @@
import { VolumeData, VolumeIsoValue } from 'mol-model/volume'
import { Task, RuntimeContext } from 'mol-task'
import { computeMarchingCubes } from '../../util/marching-cubes/algorithm';
-import { Mesh } from '../../shape/mesh';
+import { Mesh } from '../../mesh/mesh';
import { VolumeVisual } from '.';
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object';
import { ValueCell, defaults } from 'mol-util';
@@ -72,13 +72,13 @@ export default function SurfaceVisual(): VolumeVisual<SurfaceProps> {
const values: MeshValues = {
...getMeshData(mesh),
aTransform: ValueCell.create(new Float32Array(Mat4.identity())),
- aInstanceId: ValueCell.create(fillSerial(new Float32Array(instanceCount))),
+ aInstance: ValueCell.create(fillSerial(new Float32Array(instanceCount))),
...color,
...marker,
uAlpha: ValueCell.create(defaults(props.alpha, 1.0)),
uInstanceCount: ValueCell.create(instanceCount),
- uElementCount: ValueCell.create(mesh.triangleCount),
+ uGroupCount: ValueCell.create(mesh.triangleCount),
elements: mesh.indexBuffer,
diff --git a/src/mol-geo/shape/vertex-map.ts b/src/mol-geo/shape/vertex-map.ts
deleted file mode 100644
index 0211ed33334dc08b5a065d9dc7250d88fc156450..0000000000000000000000000000000000000000
--- a/src/mol-geo/shape/vertex-map.ts
+++ /dev/null
@@ -1,53 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ChunkedArray } from 'mol-data/util';
-import { Mesh } from './mesh';
-
-/** Mapping between vertices and ids */
-interface VertexMap {
- idCount: number,
- offsetCount: number,
- ids: Helpers.NumberArray
- offsets: Uint32Array,
-}
-
-function createOffsets(idCount: number, ids: Helpers.NumberArray) {
- const offsets = ChunkedArray.create(Uint32Array, 1, 1024, 2048);
- let prevId = ids[0]
- ChunkedArray.add(offsets, 0)
- for (let i = 1; i < idCount; ++i) {
- if (prevId !== ids[i]) {
- prevId = ids[i]
- ChunkedArray.add(offsets, i)
- }
- }
- ChunkedArray.add(offsets, idCount)
- return ChunkedArray.compact(offsets, false) as Uint32Array
-}
-
-namespace VertexMap {
- export function create(idCount: number, offsetCount: number, ids: Helpers.NumberArray, offsets: Uint32Array): VertexMap {
- return {
- idCount,
- offsetCount,
- ids,
- offsets
- }
- }
-
- export function fromMesh(mesh: Mesh) {
- const ids = mesh.idBuffer.ref.value
- const offsets = createOffsets(mesh.vertexCount, ids)
- return create(mesh.vertexCount, offsets.length, ids, offsets)
- }
-
- export function rangeFromId (id: number, vertexMap: VertexMap) {
- return [0, 0]
- }
-}
-
-export default VertexMap
\ 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 47e7eaf1d2383bdcc81eebf46a45d6864b1fb913..d8f0c3d2e72397637ce8d6064e6d834e31dfeb8b 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -8,16 +8,16 @@ import { ValueCell } from 'mol-util';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { Color } from 'mol-util/color';
import { Vec2, Vec3 } from 'mol-math/linear-algebra';
-import { LocationIterator } from '../representation/structure/visual/util/location-iterator';
+import { LocationIterator } from './location-iterator';
import { Location, NullLocation } from 'mol-model/location';
-export type ColorType = 'uniform' | 'instance' | 'element' | 'elementInstance'
+export type ColorType = 'uniform' | 'instance' | 'group' | 'groupInstance'
export type ColorData = {
uColor: ValueCell<Vec3>,
aColor: ValueCell<Float32Array>,
tColor: ValueCell<TextureImage>,
- uColorTexSize: ValueCell<Vec2>,
+ uColorTexDim: ValueCell<Vec2>,
dColorType: ValueCell<string>,
}
@@ -27,7 +27,7 @@ const emptyColorTexture = { array: new Uint8Array(3), width: 1, height: 1 }
function createEmptyColorTexture() {
return {
tColor: ValueCell.create(emptyColorTexture),
- uColorTexSize: ValueCell.create(Vec2.create(1, 1))
+ uColorTexDim: ValueCell.create(Vec2.create(1, 1))
}
}
@@ -56,7 +56,7 @@ export function createUniformColor(locationIt: LocationIterator, colorFn: Locati
export function createTextureColor(colors: TextureImage, type: ColorType, colorData?: ColorData): ColorData {
if (colorData) {
ValueCell.update(colorData.tColor, colors)
- ValueCell.update(colorData.uColorTexSize, Vec2.create(colors.width, colors.height))
+ ValueCell.update(colorData.uColorTexDim, Vec2.create(colors.width, colors.height))
if (colorData.dColorType.ref.value !== type) {
ValueCell.update(colorData.dColorType, type)
}
@@ -66,7 +66,7 @@ export function createTextureColor(colors: TextureImage, type: ColorType, colorD
uColor: ValueCell.create(Vec3.zero()),
aColor: ValueCell.create(new Float32Array(0)),
tColor: ValueCell.create(colors),
- uColorTexSize: ValueCell.create(Vec2.create(colors.width, colors.height)),
+ uColorTexDim: ValueCell.create(Vec2.create(colors.width, colors.height)),
dColorType: ValueCell.create(type),
}
}
@@ -84,25 +84,25 @@ export function createInstanceColor(locationIt: LocationIterator, colorFn: Locat
return createTextureColor(colors, 'instance', colorData)
}
-/** Creates color texture with color for each element (i.e. shared across instances/units) */
-export function createElementColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
- const { elementCount } = locationIt
- const colors = colorData && colorData.tColor.ref.value.array.length >= elementCount * 3 ? colorData.tColor.ref.value : createTextureImage(elementCount, 3)
+/** Creates color texture with color for each group (i.e. shared across instances/units) */
+export function createGroupColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
+ const { groupCount } = locationIt
+ const colors = colorData && colorData.tColor.ref.value.array.length >= groupCount * 3 ? colorData.tColor.ref.value : createTextureImage(groupCount, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
- const { location, isSecondary, elementIndex } = locationIt.move()
- Color.toArray(colorFn(location, isSecondary), colors.array, elementIndex * 3)
+ const { location, isSecondary, groupIndex } = locationIt.move()
+ Color.toArray(colorFn(location, isSecondary), colors.array, groupIndex * 3)
}
- return createTextureColor(colors, 'element', colorData)
+ return createTextureColor(colors, 'group', colorData)
}
-/** Creates color texture with color for each element instance (i.e. for each unit) */
-export function createElementInstanceColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
- const { elementCount, instanceCount } = locationIt
- const count = instanceCount * elementCount
+/** Creates color texture with color for each group in each instance (i.e. for each unit) */
+export function createGroupInstanceColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
+ const { groupCount, instanceCount } = locationIt
+ const count = instanceCount * groupCount
const colors = colorData && colorData.tColor.ref.value.array.length >= count * 3 ? colorData.tColor.ref.value : createTextureImage(count, 3)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
const { location, isSecondary, index } = locationIt.move()
Color.toArray(colorFn(location, isSecondary), colors.array, index * 3)
}
- return createTextureColor(colors, 'elementInstance', colorData)
+ return createTextureColor(colors, 'groupInstance', colorData)
}
\ No newline at end of file
diff --git a/src/mol-geo/util/location-iterator.ts b/src/mol-geo/util/location-iterator.ts
new file mode 100644
index 0000000000000000000000000000000000000000..435d0c45c3be8181456098ec99331c4cf7f579d5
--- /dev/null
+++ b/src/mol-geo/util/location-iterator.ts
@@ -0,0 +1,97 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Iterator } from 'mol-data';
+import { NullLocation, Location } from 'mol-model/location';
+
+export interface LocationValue {
+ location: Location
+ index: number
+ groupIndex: number
+ instanceIndex: number
+ isSecondary: boolean
+}
+
+export const NullLocationValue: LocationValue = {
+ location: NullLocation,
+ index: 0,
+ groupIndex: 0,
+ instanceIndex: 0,
+ isSecondary: false
+}
+
+export interface LocationIterator extends Iterator<LocationValue> {
+ readonly hasNext: boolean
+ readonly isNextNewInstance: boolean
+ readonly groupCount: number
+ readonly instanceCount: number
+ move(): LocationValue
+ reset(): void
+ skipInstance(): void
+}
+
+type LocationGetter = (groupIndex: number, instanceIndex: number) => Location
+type IsSecondaryGetter = (groupIndex: number, instanceIndex: number) => boolean
+
+export function LocationIterator(groupCount: number, instanceCount: number, getLocation: LocationGetter, isSecondary: IsSecondaryGetter = () => false): LocationIterator {
+ const value: LocationValue = {
+ location: NullLocation as Location,
+ index: 0,
+ groupIndex: 0,
+ instanceIndex: 0,
+ isSecondary: false
+ }
+
+ let hasNext = value.groupIndex < groupCount
+ let isNextNewInstance = false
+ let groupIndex = 0
+ let instanceIndex = 0
+
+ return {
+ get hasNext () { return hasNext },
+ get isNextNewInstance () { return isNextNewInstance },
+ get groupCount () { return groupCount },
+ get instanceCount () { return instanceCount },
+ move() {
+ if (hasNext) {
+ value.groupIndex = groupIndex
+ value.instanceIndex = instanceIndex
+ value.index = instanceIndex * groupCount + groupIndex
+ value.location = getLocation(groupIndex, instanceIndex)
+ value.isSecondary = isSecondary(groupIndex, instanceIndex)
+ ++groupIndex
+ if (groupIndex === groupCount) {
+ ++instanceIndex
+ isNextNewInstance = true
+ if (instanceIndex < instanceCount) groupIndex = 0
+ } else {
+ isNextNewInstance = false
+ }
+ hasNext = groupIndex < groupCount
+ }
+ return value
+ },
+ reset() {
+ value.location = NullLocation
+ value.index = 0
+ value.groupIndex = 0
+ value.instanceIndex = 0
+ value.isSecondary = false
+
+ hasNext = value.groupIndex < groupCount
+ isNextNewInstance = false
+ groupIndex = 0
+ instanceIndex = 0
+ },
+ skipInstance() {
+ if (hasNext && value.instanceIndex === instanceIndex) {
+ ++instanceIndex
+ groupIndex = 0
+ hasNext = instanceIndex < instanceCount
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 4b2eaf964996164cd06ccdebd141e8a57b8a20ce..f636ff582c8160ce384eea92873779f726301a0f 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -7,7 +7,7 @@
import { Task, RuntimeContext } from 'mol-task'
import { ChunkedArray } from 'mol-data/util'
import { Tensor } from 'mol-math/linear-algebra'
-import { Mesh } from '../../shape/mesh'
+import { Mesh } from '../../mesh/mesh'
import { Index, EdgeIdInfo, CubeEdges, EdgeTable, TriTable } from './tables'
import { ValueCell } from 'mol-util'
@@ -76,18 +76,15 @@ class MarchingCubesComputation {
const ret: Mesh = {
vertexCount: this.state.vertexCount,
triangleCount: this.state.triangleCount,
- offsetCount: 0,
vertexBuffer: os ? ValueCell.update(os.vertexBuffer, vb) : ValueCell.create(vb),
indexBuffer: os ? ValueCell.update(os.indexBuffer, ib) : ValueCell.create(ib),
normalBuffer: os ? os.normalBuffer : ValueCell.create(new Float32Array(0)),
- idBuffer: this.state.assignIds
- ? os && os.idBuffer
- ? ValueCell.update(os.idBuffer, ChunkedArray.compact(this.state.idBuffer) as Float32Array)
+ groupBuffer: this.state.assignIds
+ ? os && os.groupBuffer
+ ? ValueCell.update(os.groupBuffer, ChunkedArray.compact(this.state.idBuffer) as Float32Array)
: ValueCell.create(ChunkedArray.compact(this.state.idBuffer) as Float32Array)
: ValueCell.create(new Float32Array(0)),
- offsetBuffer: os ? os.offsetBuffer : ValueCell.create(new Uint32Array(0)),
- normalsComputed: false,
- offsetsComputed: false
+ normalsComputed: false
}
return ret;
diff --git a/src/mol-geo/util/marker-data.ts b/src/mol-geo/util/marker-data.ts
index 93fa6b5c21fd5684735d1784d6602d9239e30756..55dc2494560d9bc734dba5a1a11f73f835f797b7 100644
--- a/src/mol-geo/util/marker-data.ts
+++ b/src/mol-geo/util/marker-data.ts
@@ -10,7 +10,7 @@ import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
export type MarkerData = {
tMarker: ValueCell<TextureImage>
- uMarkerTexSize: ValueCell<Vec2>
+ uMarkerTexDim: ValueCell<Vec2>
}
export enum MarkerAction {
@@ -77,26 +77,26 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
: createTextureImage(count, 1)
if (markerData) {
ValueCell.update(markerData.tMarker, markers)
- ValueCell.update(markerData.uMarkerTexSize, Vec2.create(markers.width, markers.height))
+ ValueCell.update(markerData.uMarkerTexDim, Vec2.create(markers.width, markers.height))
return markerData
} else {
return {
tMarker: ValueCell.create(markers),
- uMarkerTexSize: ValueCell.create(Vec2.create(markers.width, markers.height)),
+ uMarkerTexDim: ValueCell.create(Vec2.create(markers.width, markers.height)),
}
}
}
const emptyMarkerTexture = { array: new Uint8Array(1), width: 1, height: 1 }
-export function createEmptyMarkers(markerData?: MarkerData) {
+export function createEmptyMarkers(markerData?: MarkerData): MarkerData {
if (markerData) {
ValueCell.update(markerData.tMarker, emptyMarkerTexture)
- ValueCell.update(markerData.uMarkerTexSize, Vec2.create(1, 1))
+ ValueCell.update(markerData.uMarkerTexDim, Vec2.create(1, 1))
return markerData
} else {
return {
tMarker: ValueCell.create(emptyMarkerTexture),
- uMarkerTexSize: ValueCell.create(Vec2.create(1, 1)),
+ uMarkerTexDim: ValueCell.create(Vec2.create(1, 1)),
}
}
}
\ No newline at end of file
diff --git a/src/mol-geo/util/mesh-data.ts b/src/mol-geo/util/mesh-data.ts
index 9fd9add8ec596c4dc8bd917b777adcaf4a9d2784..0451ee98a8bfee2d7e2790c69a40a3144ca6ba69 100644
--- a/src/mol-geo/util/mesh-data.ts
+++ b/src/mol-geo/util/mesh-data.ts
@@ -5,18 +5,18 @@
*/
import { ValueCell } from 'mol-util/value-cell'
-import { Mesh } from '../shape/mesh';
+import { Mesh } from '../mesh/mesh';
type MeshData = {
aPosition: ValueCell<Float32Array>,
aNormal: ValueCell<Float32Array>,
- aElementId: ValueCell<Float32Array>,
+ aGroup: ValueCell<Float32Array>,
}
export function getMeshData(mesh: Mesh): MeshData {
return {
aPosition: mesh.vertexBuffer,
aNormal: mesh.normalBuffer,
- aElementId: mesh.idBuffer,
+ aGroup: mesh.groupBuffer,
}
}
\ No newline at end of file
diff --git a/src/mol-geo/util/picking.ts b/src/mol-geo/util/picking.ts
index 00d12d6fd6d297ad232fb81720eb0dc8dd63f252..07f2bf743ea1d5b18717a002910ce1a246684cb0 100644
--- a/src/mol-geo/util/picking.ts
+++ b/src/mol-geo/util/picking.ts
@@ -18,7 +18,7 @@ export function decodeIdRGBA(r: number, g: number, b: number) {
export interface PickingId {
objectId: number
instanceId: number
- elementId: number
+ groupId: number
}
export interface PickingInfo {
diff --git a/src/mol-geo/util/size-data.ts b/src/mol-geo/util/size-data.ts
index 25573107e59c5a52ba3541af8b41e649207c6a3a..f1a59a8fa6448b1931576d5d8c3b3b2f4e0af48c 100644
--- a/src/mol-geo/util/size-data.ts
+++ b/src/mol-geo/util/size-data.ts
@@ -7,16 +7,16 @@
import { ValueCell } from 'mol-util';
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 { LocationIterator } from './location-iterator';
import { Location, NullLocation } from 'mol-model/location';
-export type SizeType = 'uniform' | 'instance' | 'element' | 'elementInstance'
+export type SizeType = 'uniform' | 'instance' | 'group' | 'groupInstance'
export type SizeData = {
uSize: ValueCell<number>,
aSize: ValueCell<Float32Array>,
tSize: ValueCell<TextureImage>,
- uSizeTexSize: ValueCell<Vec2>,
+ uSizeTexDim: ValueCell<Vec2>,
dSizeType: ValueCell<string>,
}
@@ -26,7 +26,7 @@ const emptySizeTexture = { array: new Uint8Array(1), width: 1, height: 1 }
function createEmptySizeTexture() {
return {
tSize: ValueCell.create(emptySizeTexture),
- uSizeTexSize: ValueCell.create(Vec2.create(1, 1))
+ uSizeTexDim: ValueCell.create(Vec2.create(1, 1))
}
}
@@ -55,7 +55,7 @@ export function createUniformSize(locationIt: LocationIterator, sizeFn: Location
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))
+ ValueCell.update(sizeData.uSizeTexDim, Vec2.create(sizes.width, sizes.height))
if (sizeData.dSizeType.ref.value !== type) {
ValueCell.update(sizeData.dSizeType, type)
}
@@ -65,7 +65,7 @@ export function createTextureSize(sizes: TextureImage, type: SizeType, sizeData?
uSize: ValueCell.create(0),
aSize: ValueCell.create(new Float32Array(0)),
tSize: ValueCell.create(sizes),
- uSizeTexSize: ValueCell.create(Vec2.create(sizes.width, sizes.height)),
+ uSizeTexDim: ValueCell.create(Vec2.create(sizes.width, sizes.height)),
dSizeType: ValueCell.create(type),
}
}
@@ -83,25 +83,25 @@ export function createInstanceSize(locationIt: LocationIterator, sizeFn: Locatio
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)
+/** Creates size texture with size for each group (i.e. shared across instances/units) */
+export function createGroupSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
+ const { groupCount } = locationIt
+ const sizes = sizeData && sizeData.tSize.ref.value.array.length >= groupCount ? sizeData.tSize.ref.value : createTextureImage(groupCount, 1)
while (locationIt.hasNext && !locationIt.isNextNewInstance) {
const v = locationIt.move()
- sizes.array[v.elementIndex] = sizeFn(v.location)
+ sizes.array[v.groupIndex] = sizeFn(v.location)
}
- return createTextureSize(sizes, 'element', sizeData)
+ return createTextureSize(sizes, 'group', 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
+/** Creates size texture with size for each group in each instance (i.e. for each unit) */
+export function createGroupInstanceSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
+ const { groupCount, instanceCount } = locationIt
+ const count = instanceCount * groupCount
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)
+ return createTextureSize(sizes, 'groupInstance', 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 f6474217fbdd9a30d4a59a4e184843b37192a348..e4d5b6c6cbf4230d2d8618c3a47fbd4dd9a5fe3f 100644
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -46,8 +46,8 @@ function createRenderer(gl: WebGLRenderingContext) {
function createPoints() {
const aPosition = ValueCell.create(new Float32Array([0, -1, 0, -1, 0, 0, 1, 1, 0]))
- const aElementId = ValueCell.create(fillSerial(new Float32Array(3)))
- const aInstanceId = ValueCell.create(fillSerial(new Float32Array(1)))
+ const aGroup = ValueCell.create(fillSerial(new Float32Array(3)))
+ const aInstance = ValueCell.create(fillSerial(new Float32Array(1)))
const color = createValueColor(Color(0xFF0000))
const size = createValueSize(1)
const marker = createEmptyMarkers()
@@ -58,16 +58,16 @@ function createPoints() {
const values: PointValues = {
aPosition,
- aElementId,
+ aGroup,
aTransform,
- aInstanceId,
+ aInstance,
...color,
...marker,
...size,
uAlpha: ValueCell.create(1.0),
uInstanceCount: ValueCell.create(1),
- uElementCount: ValueCell.create(3),
+ uGroupCount: ValueCell.create(3),
drawCount: ValueCell.create(3),
instanceCount: ValueCell.create(1),
diff --git a/src/mol-gl/renderable/point.ts b/src/mol-gl/renderable/point.ts
index 155c3f2069d12c341cd12f3db63412e33daf3fa4..f229413889610ccd4ff9a160476debd2fcc33b9b 100644
--- a/src/mol-gl/renderable/point.ts
+++ b/src/mol-gl/renderable/point.ts
@@ -15,7 +15,7 @@ export const PointSchema = {
...BaseSchema,
aSize: AttributeSpec('float32', 1, 0),
uSize: UniformSpec('f'),
- uSizeTexSize: UniformSpec('v2'),
+ uSizeTexDim: UniformSpec('v2'),
tSize: TextureSpec('alpha', 'ubyte'),
dSizeType: DefineSpec('string', ['uniform', 'attribute']),
dPointSizeAttenuation: DefineSpec('boolean'),
diff --git a/src/mol-gl/renderable/schema.ts b/src/mol-gl/renderable/schema.ts
index adfa5985b56104dc556ab8938b7d672fdc9a8ab7..7364e731b384e90cfe0224981c202a60e232f4ee 100644
--- a/src/mol-gl/renderable/schema.ts
+++ b/src/mol-gl/renderable/schema.ts
@@ -142,18 +142,18 @@ export const InternalSchema = {
}
export const BaseSchema = {
- aInstanceId: AttributeSpec('float32', 1, 1),
+ aInstance: AttributeSpec('float32', 1, 1),
aPosition: AttributeSpec('float32', 3, 0),
- aElementId: AttributeSpec('float32', 1, 0),
+ aGroup: AttributeSpec('float32', 1, 0),
aTransform: AttributeSpec('float32', 16, 1),
aColor: AttributeSpec('float32', 3, 0),
uAlpha: UniformSpec('f'),
uInstanceCount: UniformSpec('i'),
- uElementCount: UniformSpec('i'),
+ uGroupCount: UniformSpec('i'),
uColor: UniformSpec('v3'),
- uColorTexSize: UniformSpec('v2'),
- uMarkerTexSize: UniformSpec('v2'),
+ uColorTexDim: UniformSpec('v2'),
+ uMarkerTexDim: UniformSpec('v2'),
tColor: TextureSpec('rgb', 'ubyte'),
tMarker: TextureSpec('alpha', 'ubyte'),
@@ -161,7 +161,7 @@ export const BaseSchema = {
drawCount: ValueSpec('number'),
instanceCount: ValueSpec('number'),
- dColorType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'element', 'element_instance']),
+ dColorType: DefineSpec('string', ['uniform', 'attribute', 'instance', 'group', 'group_instance']),
dUseFog: DefineSpec('boolean'),
}
export type BaseSchema = typeof BaseSchema
diff --git a/src/mol-gl/shader/chunks/assign-color-varying.glsl b/src/mol-gl/shader/chunks/assign-color-varying.glsl
index b5848197a89b908cb5664869d1206f90eb222042..f4f5dad7358e2e52f052023500745156e891bd75 100644
--- a/src/mol-gl/shader/chunks/assign-color-varying.glsl
+++ b/src/mol-gl/shader/chunks/assign-color-varying.glsl
@@ -1,15 +1,15 @@
#if defined(dColorType_attribute)
vColor.rgb = aColor;
#elif defined(dColorType_instance)
- vColor.rgb = readFromTexture(tColor, aInstanceId, uColorTexSize).rgb;
-#elif defined(dColorType_element)
- vColor.rgb = readFromTexture(tColor, aElementId, uColorTexSize).rgb;
-#elif defined(dColorType_elementInstance)
- vColor.rgb = readFromTexture(tColor, aInstanceId * float(uElementCount) + aElementId, uColorTexSize).rgb;
+ vColor.rgb = readFromTexture(tColor, aInstance, uColorTexDim).rgb;
+#elif defined(dColorType_group)
+ vColor.rgb = readFromTexture(tColor, aGroup, uColorTexDim).rgb;
+#elif defined(dColorType_groupInstance)
+ vColor.rgb = readFromTexture(tColor, aGroup * float(uGroupCount) + aGroup, uColorTexDim).rgb;
#elif defined(dColorType_objectPicking)
vColor = encodeIdRGBA(float(uObjectId));
#elif defined(dColorType_instancePicking)
- vColor = encodeIdRGBA(aInstanceId);
-#elif defined(dColorType_elementPicking)
- vColor = encodeIdRGBA(aElementId);
+ vColor = encodeIdRGBA(aInstance);
+#elif defined(dColorType_groupPicking)
+ vColor = encodeIdRGBA(aGroup);
#endif
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/assign-marker-varying.glsl b/src/mol-gl/shader/chunks/assign-marker-varying.glsl
index 1afbdd7cfbeca72ebeb83a4bcaef4c91063874cd..38c3e0a474debc92226378e42368c7b42362f693 100644
--- a/src/mol-gl/shader/chunks/assign-marker-varying.glsl
+++ b/src/mol-gl/shader/chunks/assign-marker-varying.glsl
@@ -1 +1 @@
-vMarker = readFromTexture(tMarker, aInstanceId * float(uElementCount) + aElementId, uMarkerTexSize).a;
\ No newline at end of file
+vMarker = readFromTexture(tMarker, aInstance * float(uGroupCount) + aGroup, uMarkerTexDim).a;
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/assign-material-color.glsl b/src/mol-gl/shader/chunks/assign-material-color.glsl
index fa0ecfad09dbbcc4ce57d156b4e488381407b690..5969c88c34b534a0556d2da9f30e6b22f41a557e 100644
--- a/src/mol-gl/shader/chunks/assign-material-color.glsl
+++ b/src/mol-gl/shader/chunks/assign-material-color.glsl
@@ -1,5 +1,5 @@
#if defined(dColorType_uniform)
vec4 material = vec4(uColor, 1.0);
-#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_element) || defined(dColorType_elementInstance) || defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_elementPicking)
+#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance) || defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
vec4 material = vColor;
#endif
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/color-frag-params.glsl b/src/mol-gl/shader/chunks/color-frag-params.glsl
index 55731de96863282a6d664f51276b3e19d335dc87..caa12c98d9c2eea2a48767fcea185a419b761fe0 100644
--- a/src/mol-gl/shader/chunks/color-frag-params.glsl
+++ b/src/mol-gl/shader/chunks/color-frag-params.glsl
@@ -1,5 +1,5 @@
#if defined(dColorType_uniform)
uniform vec3 uColor;
-#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_element) || defined(dColorType_elementInstance) || defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_elementPicking)
+#elif defined(dColorType_attribute) || defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance) || defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
varying vec4 vColor;
#endif
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/color-vert-params.glsl b/src/mol-gl/shader/chunks/color-vert-params.glsl
index 8f49becee4630b39320a3660dcae7adc8a6aafcd..63318ea3c6c4caac90718bae39ae37267a77b860 100644
--- a/src/mol-gl/shader/chunks/color-vert-params.glsl
+++ b/src/mol-gl/shader/chunks/color-vert-params.glsl
@@ -3,11 +3,11 @@
#elif defined(dColorType_attribute)
varying vec4 vColor;
attribute vec3 aColor;
-#elif defined(dColorType_instance) || defined(dColorType_element) || defined(dColorType_elementInstance)
+#elif defined(dColorType_instance) || defined(dColorType_group) || defined(dColorType_groupInstance)
varying vec4 vColor;
- uniform vec2 uColorTexSize;
+ uniform vec2 uColorTexDim;
uniform sampler2D tColor;
-#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_elementPicking)
+#elif defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
varying vec4 vColor;
#pragma glslify: encodeIdRGBA = require(../utils/encode-id-rgba.glsl)
#endif
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/common-frag-params.glsl b/src/mol-gl/shader/chunks/common-frag-params.glsl
index 7470f1041311568d7010e15b2f73c67d09651585..a1b1b64d8eb9b2a560e4de1b101bb5cc331748ab 100644
--- a/src/mol-gl/shader/chunks/common-frag-params.glsl
+++ b/src/mol-gl/shader/chunks/common-frag-params.glsl
@@ -1,6 +1,6 @@
uniform int uObjectId;
uniform int uInstanceCount;
-uniform int uElementCount;
+uniform int uGroupCount;
uniform vec3 uHighlightColor;
uniform vec3 uSelectColor;
diff --git a/src/mol-gl/shader/chunks/common-vert-params.glsl b/src/mol-gl/shader/chunks/common-vert-params.glsl
index 27d1dd0b338b166efc5479233cd2670fc489f62c..30bc2caea18865056975654eeccac9b43348ba66 100644
--- a/src/mol-gl/shader/chunks/common-vert-params.glsl
+++ b/src/mol-gl/shader/chunks/common-vert-params.glsl
@@ -2,9 +2,9 @@ uniform mat4 uProjection, uModel, uView;
uniform int uObjectId;
uniform int uInstanceCount;
-uniform int uElementCount;
+uniform int uGroupCount;
-uniform vec2 uMarkerTexSize;
+uniform vec2 uMarkerTexDim;
uniform sampler2D tMarker;
varying float vMarker;
#pragma glslify: readFromTexture = require(../utils/read-from-texture.glsl)
\ No newline at end of file
diff --git a/src/mol-gl/shader/mesh.frag b/src/mol-gl/shader/mesh.frag
index cc387cb22b293464889921d6f48c91bdd9b1a7f2..ce282933ea1281f35e1699e3d0acc373ec3a814f 100644
--- a/src/mol-gl/shader/mesh.frag
+++ b/src/mol-gl/shader/mesh.frag
@@ -38,7 +38,7 @@ void main() {
// material color
#pragma glslify: import('./chunks/assign-material-color.glsl')
- #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_elementPicking)
+ #if defined(dColorType_objectPicking) || defined(dColorType_instancePicking) || defined(dColorType_groupPicking)
// gl_FragColor = vec4(material.r, material.g, material.a, 1.0);
gl_FragColor = material;
#else
diff --git a/src/mol-gl/shader/mesh.vert b/src/mol-gl/shader/mesh.vert
index 0f7b837d2cd7569c1997ff057ca32cc4fc2f4e5a..af38be41e65a3be4d05412a1cadd618ce5d38438 100644
--- a/src/mol-gl/shader/mesh.vert
+++ b/src/mol-gl/shader/mesh.vert
@@ -12,8 +12,8 @@ precision highp int;
attribute vec3 aPosition;
attribute mat4 aTransform;
-attribute float aInstanceId;
-attribute float aElementId;
+attribute float aInstance;
+attribute float aGroup;
#ifndef dFlatShaded
attribute vec3 aNormal;
diff --git a/src/mol-gl/shader/point.vert b/src/mol-gl/shader/point.vert
index f8061d9587c4139f22e8cc723c604152e3387658..950ba3db17bef0d249d56e2ebac4e63a0222d3fb 100644
--- a/src/mol-gl/shader/point.vert
+++ b/src/mol-gl/shader/point.vert
@@ -21,8 +21,8 @@ uniform float uViewportHeight;
attribute vec3 aPosition;
attribute mat4 aTransform;
-attribute float aInstanceId;
-attribute float aElementId;
+attribute float aInstance;
+attribute float aGroup;
void main(){
#pragma glslify: import('./chunks/assign-color-varying.glsl')
@@ -33,11 +33,11 @@ void main(){
#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;
+ float size = readFromTexture(tSize, aInstance, uSizeTexDim).r;
+ #elif defined(dSizeType_group)
+ float size = readFromTexture(tSize, aGroup, uSizeTexDim).r;
+ #elif defined(dSizeType_groupInstance)
+ float size = readFromTexture(tSize, aInstance * float(uGroupCount) + aGroup, uSizeTexDim).r;
#endif
#ifdef dPointSizeAttenuation
diff --git a/src/mol-gl/shader/utils/read-from-texture.glsl b/src/mol-gl/shader/utils/read-from-texture.glsl
index 10b4e9d60c09519c17cd0b5a3fe60e27a8bb7fe6..a43c9d528af35cd1a2be41dfb2d18d3b2c240bf1 100644
--- a/src/mol-gl/shader/utils/read-from-texture.glsl
+++ b/src/mol-gl/shader/utils/read-from-texture.glsl
@@ -4,10 +4,10 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-vec4 readFromTexture (const in sampler2D tex, const in float i, const in vec2 size) {
- float x = mod(i, size.x);
- float y = floor(i / size.x);
- vec2 uv = (vec2(x, y) + 0.5) / size;
+vec4 readFromTexture (const in sampler2D tex, const in float i, const in vec2 dim) {
+ float x = mod(i, dim.x);
+ float y = floor(i / dim.x);
+ vec2 uv = (vec2(x, y) + 0.5) / dim;
return texture2D(tex, uv);
}
#pragma glslify: export(readFromTexture)
\ No newline at end of file
diff --git a/src/mol-gl/webgl/render-item.ts b/src/mol-gl/webgl/render-item.ts
index a9a8244b0571a8877afbb116b711e18902fcbe36..284591374c09de8e144518f3bff698b72036fc20 100644
--- a/src/mol-gl/webgl/render-item.ts
+++ b/src/mol-gl/webgl/render-item.ts
@@ -45,7 +45,7 @@ const RenderVariantDefines = {
'draw': {},
'pickObject': { dColorType: ValueCell.create('objectPicking') },
'pickInstance': { dColorType: ValueCell.create('instancePicking') },
- 'pickElement': { dColorType: ValueCell.create('elementPicking') }
+ 'pickGroup': { dColorType: ValueCell.create('groupPicking') }
}
export type RenderVariant = keyof typeof RenderVariantDefines
diff --git a/src/mol-io/reader/obj/parser.ts b/src/mol-io/reader/obj/parser.ts
index 10dafa091ab984da0e002885ce905d38b3320921..46cd16ccb151b1fb0ab69afa873c83f33a09e0b8 100644
--- a/src/mol-io/reader/obj/parser.ts
+++ b/src/mol-io/reader/obj/parser.ts
@@ -6,12 +6,13 @@
import Result from '../result'
import { Task, RuntimeContext } from 'mol-task'
-import { Mesh } from 'mol-geo/shape/mesh';
+import { Mesh } from 'mol-geo/mesh/mesh';
async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<Mesh>> {
// TODO
- const result: Mesh = Mesh.createEmpty();
- return Result.success(result);
+ const mesh: Mesh = Mesh.createEmpty();
+ // Mesh.computeNormalsImmediate(mesh)
+ return Result.success(mesh);
}
export function parse(data: string) {
diff --git a/src/mol-model/location.ts b/src/mol-model/location.ts
index 2ce2fdb16040b042398f90421ab997213b2576d8..39546ddac69d0642e20e7f5d232b824d798e2c90 100644
--- a/src/mol-model/location.ts
+++ b/src/mol-model/location.ts
@@ -6,6 +6,7 @@
import { StructureElement } from './structure'
import { Link } from './structure/structure/unit/links'
+import { Shape } from './shape/shape';
/** A null value Location */
export const NullLocation = { kind: 'null-location' as 'null-location' }
@@ -14,17 +15,4 @@ export function isNullLocation(x: any): x is NullLocation {
return !!x && x.kind === 'null-location';
}
-/** A custom Location */
-export interface CustomLocation<D = any, K = any> {
- readonly kind: 'custom-location'
- data: D
- key: K
-}
-export function CustomLocation<D, K>(data: D, key: K): CustomLocation<D, K> {
- return { kind: 'custom-location', data, key }
-}
-export function isCustomLocation(x: any): x is CustomLocation<any, any> {
- return !!x && x.kind === 'custom-location';
-}
-
-export type Location = StructureElement | Link.Location | NullLocation | CustomLocation
\ No newline at end of file
+export type Location = StructureElement | Link.Location | Shape.Location | NullLocation
\ No newline at end of file
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index 47c737cee1fa03301264ac6a94840e8be3d7a6e4..d84498e133ae0e709429c81c6b57a5a715f981b2 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -6,7 +6,7 @@
import { StructureElement } from './structure'
import { Link } from './structure/structure/unit/links'
-import { CustomLocation } from './location';
+import { Shape } from './shape';
/** A Loci that includes every loci */
export const EveryLoci = { kind: 'every-loci' as 'every-loci' }
@@ -22,16 +22,4 @@ export function isEmptyLoci(x: any): x is EmptyLoci {
return !!x && x.kind === 'empty-loci';
}
-/** A Loci of custom locations */
-export interface CustomLoci<D = any, K = any> {
- readonly kind: 'custom-loci'
- readonly locations: ReadonlyArray<CustomLocation>
-}
-export function CustomLoci<D, K>(locations: CustomLocation<D, K>[]): CustomLoci<D, K> {
- return { kind: 'custom-loci', locations }
-}
-export function isCustomLoci(x: any): x is CustomLoci {
- return !!x && x.kind === 'custom-loci';
-}
-
-export type Loci = StructureElement.Loci | Link.Loci | EveryLoci | EmptyLoci | CustomLoci
\ No newline at end of file
+export type Loci = StructureElement.Loci | Link.Loci | EveryLoci | EmptyLoci | Shape.Loci
\ No newline at end of file
diff --git a/src/mol-model/shape.ts b/src/mol-model/shape.ts
new file mode 100644
index 0000000000000000000000000000000000000000..fc1125ad411cce5f45eef76efc8f423fbeb09512
--- /dev/null
+++ b/src/mol-model/shape.ts
@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export * from './shape/shape'
\ No newline at end of file
diff --git a/src/mol-model/shape/shape.ts b/src/mol-model/shape/shape.ts
new file mode 100644
index 0000000000000000000000000000000000000000..16aa5b0fcb2a714d8809d3118ff30b04d8d2ecc9
--- /dev/null
+++ b/src/mol-model/shape/shape.ts
@@ -0,0 +1,54 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mesh } from 'mol-geo/mesh/mesh';
+import { Color } from 'mol-util/color';
+import { UUID } from 'mol-util';
+import { OrderedSet } from 'mol-data/int';
+
+export interface Shape {
+ readonly id: UUID
+ readonly name: string
+ readonly mesh: Mesh
+ getColor(group: number): Color
+ getLabel(group: number): string
+}
+
+export namespace Shape {
+ export function create(mesh: Mesh, name: string, getColor: (group: number) => Color, getLabel: (group: number) => string): Shape {
+ return { id: UUID.create(), name, mesh, getColor, getLabel }
+ }
+
+ export interface Location {
+ readonly kind: 'group-location'
+ shape: Shape
+ group: number
+ }
+
+ export function Location(shape?: Shape, group?: number): Location {
+ return { kind: 'group-location', shape: shape!, group: group || 0 };
+ }
+
+ export function isLocation(x: any): x is Location {
+ return !!x && x.kind === 'group-location';
+ }
+
+ export interface Loci {
+ readonly kind: 'group-loci',
+ readonly groups: ReadonlyArray<{
+ shape: Shape,
+ ids: OrderedSet<number>
+ }>
+ }
+
+ export function Loci(groups: ArrayLike<{ shape: Shape, ids: OrderedSet<number> }>): Loci {
+ return { kind: 'group-loci', groups: groups as Loci['groups'] };
+ }
+
+ export function isLoci(x: any): x is Loci {
+ return !!x && x.kind === 'group-loci';
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index 6c31ccd7483b52d341fea903aedbccf6df848d34..0c83fbcd981cba97b08393086738f339d080aa4b 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -18,7 +18,7 @@ interface StructureElement<U = Unit> {
namespace StructureElement {
export function create(unit?: Unit, element?: ElementIndex): StructureElement {
- return { kind: 'element-location', unit: unit as any, element: element || (0 as ElementIndex) };
+ return { kind: 'element-location', unit: unit!, element: element || (0 as ElementIndex) };
}
// TODO: when nominal types are available, make this indexed by UnitIndex
diff --git a/src/mol-util/array.ts b/src/mol-util/array.ts
index d3dfa14a95f7bc2e030ef609e5effaf8a8f1ff08..11998ff2d6d9391ca612620e34f2e5d5706bb641 100644
--- a/src/mol-util/array.ts
+++ b/src/mol-util/array.ts
@@ -4,6 +4,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
+// TODO move to mol-math as Vector???
+
+/** Get the maximum value in an array */
export function arrayMax(array: Helpers.NumberArray) {
let max = -Infinity
for (let i = 0, il = array.length; i < il; ++i) {
@@ -12,6 +15,7 @@ export function arrayMax(array: Helpers.NumberArray) {
return max
}
+/** Get the minimum value in an array */
export function arrayMin(array: Helpers.NumberArray) {
let min = Infinity
for (let i = 0, il = array.length; i < il; ++i) {
@@ -20,6 +24,7 @@ export function arrayMin(array: Helpers.NumberArray) {
return min
}
+/** Get the sum of values in an array */
export function arraySum(array: Helpers.NumberArray, stride = 1, offset = 0) {
const n = array.length
let sum = 0
@@ -29,10 +34,12 @@ export function arraySum(array: Helpers.NumberArray, stride = 1, offset = 0) {
return sum
}
+/** Get the mean of values in an array */
export function arrayMean(array: Helpers.NumberArray, stride = 1, offset = 0) {
return arraySum(array, stride, offset) / (array.length / stride)
}
+/** Get the root mean square of values in an array */
export function arrayRms(array: Helpers.NumberArray) {
const n = array.length
let sumSq = 0
@@ -43,6 +50,7 @@ export function arrayRms(array: Helpers.NumberArray) {
return Math.sqrt(sumSq / n)
}
+/** Fill an array with serial numbers starting from 0 */
export function fillSerial<T extends Helpers.NumberArray> (array: T) {
const n = array.length
for (let i = 0; i < n; ++i) array[ i ] = i
diff --git a/src/mol-view/label.ts b/src/mol-view/label.ts
index 2211c5da2bd184ac13702bb1d0829dfb15fbceda..baeb1eccfff71247e3889d7cefe4910433882b68 100644
--- a/src/mol-view/label.ts
+++ b/src/mol-view/label.ts
@@ -12,7 +12,7 @@ import { OrderedSet } from 'mol-data/int';
const elementLocA = StructureElement.create()
const elementLocB = StructureElement.create()
-function setElementLocation(loc: StructureElement, unit: Unit, index: number) {
+function setElementLocation(loc: StructureElement, unit: Unit, index: StructureElement.UnitIndex) {
loc.unit = unit
loc.element = unit.elements[index]
}
@@ -36,8 +36,13 @@ export function labelFirst(loci: Loci): string {
} else {
return 'Unknown'
}
- case 'custom-loci':
- return 'Custom'
+ case 'group-loci':
+ const g = loci.groups[0]
+ if (g) {
+ return g.shape.getLabel(OrderedSet.getAt(g.ids, 0))
+ } else {
+ return 'Unknown'
+ }
case 'every-loci':
return 'Everything'
case 'empty-loci':
diff --git a/src/mol-view/theme/color.ts b/src/mol-view/theme/color.ts
index ba8fec56a0fa4883ffe7e4121f73fdb974b20154..f02f54b3a11d757f1d636d71a99a12f8d414ee1f 100644
--- a/src/mol-view/theme/color.ts
+++ b/src/mol-view/theme/color.ts
@@ -15,6 +15,7 @@ import { ElementSymbolColorTheme } from './color/element-symbol';
import { UnitIndexColorTheme } from './color/unit-index';
import { UniformColorTheme } from './color/uniform';
import { CrossLinkColorTheme } from './color/cross-link';
+import { ShapeGroupColorTheme } from './color/shape-group';
export interface ColorTheme {
kind: ColorType
@@ -30,6 +31,7 @@ export function ColorTheme(props: ColorThemeProps): ColorTheme {
case 'element-symbol': return ElementSymbolColorTheme(props)
case 'unit-index': return UnitIndexColorTheme(props)
case 'uniform': return UniformColorTheme(props)
+ case 'shape-group': return ShapeGroupColorTheme(props)
}
}
@@ -47,7 +49,8 @@ export const ColorThemeInfo = {
'chain-id': {},
'element-symbol': {},
'unit-index': {},
- 'uniform': {}
+ 'uniform': {},
+ 'shape-group': {}
}
export type ColorThemeName = keyof typeof ColorThemeInfo
export const ColorThemeNames = Object.keys(ColorThemeInfo)
\ No newline at end of file
diff --git a/src/mol-view/theme/color/carbohydrate-symbol.ts b/src/mol-view/theme/color/carbohydrate-symbol.ts
index 8ccdf51d91b9dde4fb39bc7fead5f459f687a65e..7c3093a0b2ffce1e3e8ac4e865516bf8976f1ce7 100644
--- a/src/mol-view/theme/color/carbohydrate-symbol.ts
+++ b/src/mol-view/theme/color/carbohydrate-symbol.ts
@@ -47,7 +47,7 @@ export function CarbohydrateSymbolColorTheme(props: ColorThemeProps): ColorTheme
}
return {
- kind: 'element',
+ kind: 'group',
color: colorFn
}
}
\ No newline at end of file
diff --git a/src/mol-view/theme/color/chain-id.ts b/src/mol-view/theme/color/chain-id.ts
index 8a40badbf5188c939212c49153421b2ec58ecfc9..9e15eec0f430d12805b680c155c03033cc7223e8 100644
--- a/src/mol-view/theme/color/chain-id.ts
+++ b/src/mol-view/theme/color/chain-id.ts
@@ -43,7 +43,7 @@ export function ChainIdColorTheme(props: ColorThemeProps): ColorTheme {
}
return {
- kind: 'element',
+ kind: 'group',
color: colorFn
}
}
\ No newline at end of file
diff --git a/src/mol-view/theme/color/cross-link.ts b/src/mol-view/theme/color/cross-link.ts
index aa80d8b26557a24d0f5951dc6160f45dfe7ac95f..5a4709dc550531cafeb512eef140987399612dfd 100644
--- a/src/mol-view/theme/color/cross-link.ts
+++ b/src/mol-view/theme/color/cross-link.ts
@@ -42,7 +42,7 @@ export function CrossLinkColorTheme(props: ColorThemeProps): ColorTheme {
}
return {
- kind: 'element',
+ kind: 'group',
color: colorFn
}
}
\ No newline at end of file
diff --git a/src/mol-view/theme/color/element-index.ts b/src/mol-view/theme/color/element-index.ts
index 78daf537ace4e0efd16eec0641c374c7c4d4b367..f6abd54f3cdee2a02e2531e660a9b93449d831ba 100644
--- a/src/mol-view/theme/color/element-index.ts
+++ b/src/mol-view/theme/color/element-index.ts
@@ -44,7 +44,7 @@ export function ElementIndexColorTheme(props: ColorThemeProps): ColorTheme {
}
return {
- kind: 'elementInstance',
+ kind: 'groupInstance',
color: colorFn
}
}
\ No newline at end of file
diff --git a/src/mol-view/theme/color/element-symbol.ts b/src/mol-view/theme/color/element-symbol.ts
index 0a8be64caea01c68611df96b29ce9c10d5fdd743..eaa64ebb687eff4b8b8d2d9888ff5215a298eba6 100644
--- a/src/mol-view/theme/color/element-symbol.ts
+++ b/src/mol-view/theme/color/element-symbol.ts
@@ -39,7 +39,7 @@ export function ElementSymbolColorTheme(props: ColorThemeProps): ColorTheme {
}
return {
- kind: 'element',
+ kind: 'group',
color: colorFn
}
}
\ No newline at end of file
diff --git a/src/mol-view/theme/color/shape-group.ts b/src/mol-view/theme/color/shape-group.ts
new file mode 100644
index 0000000000000000000000000000000000000000..815ab6dbbd515f180c5c416706c91ef1837920df
--- /dev/null
+++ b/src/mol-view/theme/color/shape-group.ts
@@ -0,0 +1,24 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ColorTheme, ColorThemeProps } from '../color';
+import { Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { Shape } from 'mol-model/shape';
+
+const DefaultColor = 0xCCCCCC as Color
+
+export function ShapeGroupColorTheme(props: ColorThemeProps): ColorTheme {
+ return {
+ kind: 'group',
+ color: (location: Location): Color => {
+ if (Shape.isLocation(location)) {
+ return location.shape.getColor(location.group)
+ }
+ return DefaultColor
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/mol-view/theme/size/physical.ts b/src/mol-view/theme/size/physical.ts
index e034b5c2c0670bc7641e2d26102e7d500d91066a..87c7ccefe0c8ebe717d9269bf032fa077d7b7668 100644
--- a/src/mol-view/theme/size/physical.ts
+++ b/src/mol-view/theme/size/physical.ts
@@ -42,7 +42,7 @@ export function PhysicalSizeTheme(props: SizeThemeProps): SizeTheme {
}
return {
- kind: 'element',
+ kind: 'group',
size: sizeFn
}
}
\ No newline at end of file
diff --git a/src/mol-view/viewer.ts b/src/mol-view/viewer.ts
index addf444decb7f26f324fa726c3cfa1f306e8a0f4..d3eb6d3d22ebb55237a9c35a776fe7b698307bde 100644
--- a/src/mol-view/viewer.ts
+++ b/src/mol-view/viewer.ts
@@ -109,7 +109,7 @@ namespace Viewer {
const pickHeight = Math.round(canvas.height * pickScale)
const objectPickTarget = createRenderTarget(ctx, pickWidth, pickHeight)
const instancePickTarget = createRenderTarget(ctx, pickWidth, pickHeight)
- const elementPickTarget = createRenderTarget(ctx, pickWidth, pickHeight)
+ const groupPickTarget = createRenderTarget(ctx, pickWidth, pickHeight)
let pickDirty = true
let drawPending = false
@@ -165,7 +165,7 @@ namespace Viewer {
switch (variant) {
case 'pickObject': objectPickTarget.bind(); break;
case 'pickInstance': instancePickTarget.bind(); break;
- case 'pickElement': elementPickTarget.bind(); break;
+ case 'pickGroup': groupPickTarget.bind(); break;
case 'draw':
ctx.unbindFramebuffer();
renderer.setViewport(0, 0, canvas.width, canvas.height);
@@ -210,7 +210,7 @@ namespace Viewer {
function pick() {
render('pickObject', pickDirty)
render('pickInstance', pickDirty)
- render('pickElement', pickDirty)
+ render('pickGroup', pickDirty)
pickDirty = false
}
@@ -232,11 +232,11 @@ namespace Viewer {
ctx.readPixels(xp, yp, 1, 1, buffer)
const instanceId = decodeIdRGBA(buffer[0], buffer[1], buffer[2])
- elementPickTarget.bind()
+ groupPickTarget.bind()
ctx.readPixels(xp, yp, 1, 1, buffer)
- const elementId = decodeIdRGBA(buffer[0], buffer[1], buffer[2])
+ const groupId = decodeIdRGBA(buffer[0], buffer[1], buffer[2])
- return { objectId, instanceId, elementId }
+ return { objectId, instanceId, groupId }
}
handleResize()
@@ -303,7 +303,7 @@ namespace Viewer {
case 'draw': return renderer.getImageData()
case 'pickObject': return objectPickTarget.getImageData()
case 'pickInstance': return instancePickTarget.getImageData()
- case 'pickElement': return elementPickTarget.getImageData()
+ case 'pickGroup': return groupPickTarget.getImageData()
}
},
reprCount,
@@ -334,7 +334,7 @@ namespace Viewer {
const pickHeight = Math.round(canvas.height * pickScale)
objectPickTarget.setSize(pickWidth, pickHeight)
instancePickTarget.setSize(pickWidth, pickHeight)
- elementPickTarget.setSize(pickWidth, pickHeight)
+ groupPickTarget.setSize(pickWidth, pickHeight)
}
}
}