From 2357eea1f749f79ec8e8f6d52f412baf504b03f0 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 7 Aug 2018 17:33:41 -0700
Subject: [PATCH] wip, themeing, coloring, location iterator
---
.../visual/carbohydrate-symbol-mesh.ts | 4 +-
.../visual/cross-link-restraint-cylinder.ts | 18 +--
.../structure/visual/element-point.ts | 3 +-
.../structure/visual/element-sphere.ts | 7 +-
.../visual/inter-unit-link-cylinder.ts | 34 +++--
.../visual/intra-unit-link-cylinder.ts | 36 +++--
.../structure/visual/nucleotide-block-mesh.ts | 6 +-
.../visual/polymer-backbone-cylinder.ts | 6 +-
.../visual/polymer-direction-wedge.ts | 6 +-
.../structure/visual/polymer-gap-cylinder.ts | 6 +-
.../structure/visual/polymer-trace-mesh.ts | 6 +-
.../structure/visual/util/common.ts | 15 +-
.../visual/util/location-iterator.ts | 123 ++++++++++++++++
src/mol-geo/representation/volume/surface.ts | 4 +-
src/mol-geo/theme/structure/color/chain-id.ts | 68 +++------
.../theme/structure/color/element-index.ts | 17 ++-
.../theme/structure/color/element-symbol.ts | 31 +++--
src/mol-geo/theme/structure/color/index.ts | 2 +-
.../theme/structure/color/instance-index.ts | 18 +--
src/mol-geo/util/color-data.ts | 131 ++++++++----------
src/mol-gl/_spec/renderer.spec.ts | 4 +-
src/mol-model/location.ts | 17 +++
src/mol-model/loci.ts | 2 +-
src/mol-model/structure/structure/element.ts | 9 +-
.../structure/structure/unit/links.ts | 22 ++-
src/mol-view/stage.ts | 4 +-
26 files changed, 376 insertions(+), 223 deletions(-)
create mode 100644 src/mol-geo/representation/structure/visual/util/location-iterator.ts
create mode 100644 src/mol-model/location.ts
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 7d65aec3a..eb65b9e8d 100644
--- a/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts
@@ -21,7 +21,7 @@ import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
-import { createUniformColor } from '../../../util/color-data';
+import { createValueColor } from '../../../util/color-data';
import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/structure/carbohydrates/constants';
const t = Mat4.identity()
@@ -173,7 +173,7 @@ export function CarbohydrateSymbolVisual(): StructureVisual<CarbohydrateSymbolPr
// console.log(mesh)
const transforms = createIdentityTransform()
- const color = createUniformColor({ value: 0x999911 }) // TODO
+ const color = createValueColor(0x999911) // TODO
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
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 2500032d1..ea48347d2 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
@@ -7,7 +7,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Link, Structure } from 'mol-model/structure';
+import { Link, Structure, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, StructureVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh } from './util/link';
@@ -16,7 +16,7 @@ import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
-import { createUniformColor } from '../../../util/color-data';
+import { createValueColor } from '../../../util/color-data';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, createMarkers, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
@@ -74,7 +74,7 @@ export function CrossLinkRestraintVisual(): StructureVisual<CrossLinkRestraintPr
mesh = await createCrossLinkRestraintCylinderMesh(ctx, structure, currentProps)
const transforms = createIdentityTransform()
- const color = createUniformColor({ value: 0x119911 }) // TODO
+ const color = createValueColor(0x119911) // TODO
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -121,12 +121,12 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
if (id === objectId) {
const pair = structure.crossLinkRestraints.pairs[elementId]
if (pair) {
- return Link.Loci([{
- aUnit: pair.unitA,
- aIndex: pair.indexA,
- bUnit: pair.unitB,
- bIndex: pair.indexB
- }])
+ return Link.Loci([
+ Link.Location(
+ pair.unitA, pair.indexA as StructureElement.UnitIndex,
+ pair.unitB, pair.indexB as StructureElement.UnitIndex
+ )
+ ])
}
}
return EmptyLoci
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index 22218af48..55a4b30eb 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -23,6 +23,7 @@ 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';
export const DefaultPointProps = {
...DefaultStructureProps,
@@ -78,7 +79,7 @@ export default function PointVisual(): UnitsVisual<PointProps> {
const vertices = createPointVertices(_units[0])
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const size = createSizes(group, vertexMap, sizeTheme)
const marker = createMarkers(instanceCount * elementCount)
diff --git a/src/mol-geo/representation/structure/visual/element-sphere.ts b/src/mol-geo/representation/structure/visual/element-sphere.ts
index 53a2a3c0e..f1680f02c 100644
--- a/src/mol-geo/representation/structure/visual/element-sphere.ts
+++ b/src/mol-geo/representation/structure/visual/element-sphere.ts
@@ -22,6 +22,7 @@ import { createMarkers, MarkerAction } from '../../../util/marker-data';
import { Loci } from 'mol-model/loci';
import { SizeTheme } from '../../../theme';
import { createMeshValues, updateMeshValues, updateRenderableState, createRenderableState, DefaultMeshProps } from '../../util';
+import { StructureElementIterator } from './util/location-iterator';
export const DefaultElementSphereProps = {
...DefaultMeshProps,
@@ -55,7 +56,7 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
: Mesh.createEmpty(mesh)
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -92,9 +93,7 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
}
if (updateColor) {
- const elementCount = currentGroup.elements.length
- if (ctx.shouldUpdate) await ctx.update('Computing sphere colors');
- createColors(currentGroup, elementCount, newProps.colorTheme, renderObject.values)
+ createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
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 69c898238..585fd7c99 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
@@ -7,7 +7,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Link, Structure } from 'mol-model/structure';
+import { Link, Structure, StructureElement } from 'mol-model/structure';
import { DefaultStructureProps, StructureVisual } from '..';
import { RuntimeContext } from 'mol-task'
import { LinkCylinderProps, DefaultLinkCylinderProps, createLinkCylinderMesh } from './util/link';
@@ -16,13 +16,13 @@ import { getMeshData } from '../../../util/mesh-data';
import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { Vec3 } from 'mol-math/linear-algebra';
-import { createUniformColor } from '../../../util/color-data';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, createMarkers, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
-import { createIdentityTransform } from './util/common';
+import { createIdentityTransform, createColors } from './util/common';
import { updateMeshValues, updateRenderableState, createMeshValues, createRenderableState } from '../../util';
-// import { chainIdLinkColorData } from '../../../theme/structure/color/chain-id';
+import { LinkIterator } from './util/location-iterator';
+import { deepEqual } from 'mol-util';
async function createInterUnitLinkCylinderMesh(ctx: RuntimeContext, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
const links = structure.links
@@ -65,13 +65,14 @@ export function InterUnitLinkVisual(): StructureVisual<InterUnitLinkProps> {
currentProps = Object.assign({}, DefaultInterUnitLinkProps, props)
currentStructure = structure
+ const { colorTheme } = { ...DefaultInterUnitLinkProps, ...props }
const elementCount = structure.links.bondCount
const instanceCount = 1
mesh = await createInterUnitLinkCylinderMesh(ctx, structure, currentProps)
const transforms = createIdentityTransform()
- const color = createUniformColor({ value: 0x999911 }) // TODO
+ const color = createColors(LinkIterator.fromStructure(structure), colorTheme) // TODO
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -93,12 +94,23 @@ export function InterUnitLinkVisual(): StructureVisual<InterUnitLinkProps> {
if (!renderObject) return false
+ let updateColor = false
+
// TODO create in-place
if (currentProps.radialSegments !== newProps.radialSegments) return false
+ if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
+ updateColor = true
+ }
+
+ if (updateColor) {
+ createColors(LinkIterator.fromStructure(currentStructure), newProps.colorTheme, renderObject.values)
+ }
+
updateMeshValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps)
+ currentProps = newProps
return false
},
getLoci(pickingId: PickingId) {
@@ -117,12 +129,12 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
const { objectId, elementId } = pickingId
if (id === objectId) {
const bond = structure.links.bonds[elementId]
- return Link.Loci([{
- aUnit: bond.unitA,
- aIndex: bond.indexA,
- bUnit: bond.unitB,
- bIndex: bond.indexB
- }])
+ return Link.Loci([
+ Link.Location(
+ bond.unitA, bond.indexA as StructureElement.UnitIndex,
+ bond.unitB, bond.indexB as StructureElement.UnitIndex
+ )
+ ])
}
return EmptyLoci
}
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 2a519bbf3..fc4dcaf3e 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
@@ -8,7 +8,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object'
-import { Unit, Link } from 'mol-model/structure';
+import { Unit, Link, StructureElement } from 'mol-model/structure';
import { UnitsVisual, DefaultStructureProps } from '..';
import { RuntimeContext } from 'mol-task'
import { DefaultLinkCylinderProps, LinkCylinderProps, createLinkCylinderMesh } from './util/link';
@@ -21,9 +21,10 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, createMarkers, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
-import { chainIdLinkColorData } from '../../../theme/structure/color/chain-id';
-import { createTransforms } from './util/common';
-import { createMeshValues, createRenderableState, updateMeshValues, updateRenderableState } from '../../util';
+import { createTransforms, createColors } from './util/common';
+import { createMeshValues, createRenderableState, updateMeshValues, updateRenderableState, DefaultMeshProps } from '../../util';
+import { LinkIterator } from './util/location-iterator';
+import { deepEqual } from 'mol-util';
async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, props: LinkCylinderProps, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -63,6 +64,7 @@ async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit,
}
export const DefaultIntraUnitLinkProps = {
+ ...DefaultMeshProps,
...DefaultStructureProps,
...DefaultLinkCylinderProps,
sizeTheme: { name: 'physical', factor: 0.3 } as SizeTheme,
@@ -81,6 +83,7 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
currentProps = Object.assign({}, DefaultIntraUnitLinkProps, props)
currentGroup = group
+ const { colorTheme } = { ...DefaultIntraUnitLinkProps, ...props }
const unit = group.units[0]
const elementCount = Unit.isAtomic(unit) ? unit.links.edgeCount * 2 : 0
const instanceCount = group.units.length
@@ -88,7 +91,7 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
mesh = await createIntraUnitLinkCylinderMesh(ctx, unit, currentProps)
const transforms = createTransforms(group)
- const color = chainIdLinkColorData({ group, elementCount }) // TODO
+ const color = createColors(LinkIterator.fromGroup(currentGroup), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -110,12 +113,23 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
if (!renderObject) return false
+ let updateColor = false
+
// TODO create in-place
if (currentProps.radialSegments !== newProps.radialSegments) return false
+ if (!deepEqual(newProps.colorTheme, currentProps.colorTheme)) {
+ updateColor = true
+ }
+
+ if (updateColor) {
+ createColors(LinkIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
+ }
+
updateMeshValues(renderObject.values, newProps)
updateRenderableState(renderObject.state, newProps)
+ currentProps = newProps
return true
},
getLoci(pickingId: PickingId) {
@@ -134,12 +148,12 @@ function getLinkLoci(pickingId: PickingId, group: Unit.SymmetryGroup, id: number
const { objectId, instanceId, elementId } = pickingId
const unit = group.units[instanceId]
if (id === objectId && Unit.isAtomic(unit)) {
- return Link.Loci([{
- aUnit: unit,
- aIndex: unit.links.a[elementId],
- bUnit: unit,
- bIndex: unit.links.b[elementId]
- }])
+ return Link.Loci([
+ Link.Location(
+ unit, unit.links.a[elementId] as StructureElement.UnitIndex,
+ unit, unit.links.b[elementId] as StructureElement.UnitIndex
+ )
+ ])
}
return EmptyLoci
}
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 dc081e27d..bf55d079d 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -26,6 +26,7 @@ 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';
const p1 = Vec3.zero()
const p2 = Vec3.zero()
@@ -145,7 +146,7 @@ export function NucleotideBlockVisual(): UnitsVisual<NucleotideBlockProps> {
// console.log(mesh)
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -182,9 +183,8 @@ export function NucleotideBlockVisual(): UnitsVisual<NucleotideBlockProps> {
}
if (updateColor) {
- const elementCount = currentGroup.elements.length
if (ctx.shouldUpdate) await ctx.update('Computing nucleotide block colors');
- createColors(currentGroup, elementCount, newProps.colorTheme, renderObject.values)
+ createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
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 956fe0fdb..518e0ce12 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -24,6 +24,7 @@ import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerBackboneIterator } from './util/polymer';
import { getElementLoci, markElement } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
+import { StructureElementIterator } from './util/location-iterator';
async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerElementCount = getPolymerElementCount(unit)
@@ -91,7 +92,7 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
// console.log(mesh)
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -128,9 +129,8 @@ export function PolymerBackboneVisual(): UnitsVisual<PolymerBackboneProps> {
}
if (updateColor) {
- const elementCount = currentGroup.elements.length
if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
- createColors(currentGroup, elementCount, newProps.colorTheme, renderObject.values)
+ createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
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 76390e3ef..fcd583315 100644
--- a/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts
@@ -26,6 +26,7 @@ import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment } from './util/polymer';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
+import { StructureElementIterator } from './util/location-iterator';
const t = Mat4.identity()
const sVec = Vec3.zero()
@@ -118,7 +119,7 @@ export function PolymerDirectionVisual(): UnitsVisual<PolymerDirectionProps> {
: Mesh.createEmpty(mesh)
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -154,9 +155,8 @@ export function PolymerDirectionVisual(): UnitsVisual<PolymerDirectionProps> {
}
if (updateColor) {
- const elementCount = currentGroup.elements.length
if (ctx.shouldUpdate) await ctx.update('Computing direction colors');
- createColors(currentGroup, elementCount, newProps.colorTheme, renderObject.values)
+ createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
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 d1f289ec9..4940c5f53 100644
--- a/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts
@@ -24,6 +24,7 @@ import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerGapCount, PolymerGapIterator } from './util/polymer';
import { getElementLoci, markElement } from './util/element';
import { Vec3 } from 'mol-math/linear-algebra';
+import { StructureElementIterator } from './util/location-iterator';
async function createPolymerGapCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
const polymerGapCount = getPolymerGapCount(unit)
@@ -97,7 +98,7 @@ export function PolymerGapVisual(): UnitsVisual<PolymerGapProps> {
// console.log(mesh)
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -134,9 +135,8 @@ export function PolymerGapVisual(): UnitsVisual<PolymerGapProps> {
}
if (updateColor) {
- const elementCount = currentGroup.elements.length
if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
- createColors(currentGroup, elementCount, newProps.colorTheme, renderObject.values)
+ createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
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 8d97c06f0..3b37589e8 100644
--- a/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts
@@ -25,6 +25,7 @@ import { createMeshValues, updateMeshValues, updateRenderableState, createRender
import { MeshBuilder } from '../../../shape/mesh-builder';
import { getPolymerElementCount, PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment } from './util/polymer';
import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
+import { StructureElementIterator } from './util/location-iterator';
// TODO handle polymer ends properly
@@ -111,7 +112,7 @@ export function PolymerTraceVisual(): UnitsVisual<PolymerTraceProps> {
: Mesh.createEmpty(mesh)
const transforms = createTransforms(group)
- const color = createColors(group, elementCount, colorTheme)
+ const color = createColors(StructureElementIterator.fromGroup(group), colorTheme)
const marker = createMarkers(instanceCount * elementCount)
const counts = { drawCount: mesh.triangleCount * 3, elementCount, instanceCount }
@@ -147,9 +148,8 @@ export function PolymerTraceVisual(): UnitsVisual<PolymerTraceProps> {
}
if (updateColor) {
- const elementCount = currentGroup.elements.length
if (ctx.shouldUpdate) await ctx.update('Computing trace colors');
- createColors(currentGroup, elementCount, newProps.colorTheme, renderObject.values)
+ createColors(StructureElementIterator.fromGroup(currentGroup), newProps.colorTheme, renderObject.values)
}
updateMeshValues(renderObject.values, newProps)
diff --git a/src/mol-geo/representation/structure/visual/util/common.ts b/src/mol-geo/representation/structure/visual/util/common.ts
index 4b8c39719..e2e43030f 100644
--- a/src/mol-geo/representation/structure/visual/util/common.ts
+++ b/src/mol-geo/representation/structure/visual/util/common.ts
@@ -13,8 +13,9 @@ import { createUniformSize, SizeData } from '../../../../util/size-data';
import { physicalSizeData } from '../../../../theme/structure/size/physical';
import VertexMap from '../../../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../../../theme';
-import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdElementColorData } from '../../../../theme/structure/color';
+import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../../../theme/structure/color';
import { ValueCell, defaults } from 'mol-util';
+import { LocationIterator } from './location-iterator';
export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: ValueCell<Float32Array>) {
const unitCount = units.length
@@ -32,18 +33,18 @@ export function createIdentityTransform(transforms?: ValueCell<Float32Array>) {
return transforms ? ValueCell.update(transforms, identityTransform) : ValueCell.create(identityTransform)
}
-export function createColors(group: Unit.SymmetryGroup, elementCount: number, props: ColorTheme, colorData?: ColorData) {
+export function createColors(locationIt: LocationIterator, props: ColorTheme, colorData?: ColorData) {
switch (props.name) {
case 'atom-index':
- return elementIndexColorData({ group, elementCount }, colorData)
+ return elementIndexColorData(locationIt, colorData)
case 'chain-id':
- return chainIdElementColorData({ group, elementCount }, colorData)
+ return chainIdColorData(locationIt, colorData)
case 'element-symbol':
- return elementSymbolColorData({ group, elementCount }, colorData)
+ return elementSymbolColorData(locationIt, colorData)
case 'instance-index':
- return instanceIndexColorData({ group, elementCount }, colorData)
+ return instanceIndexColorData(locationIt, colorData)
case 'uniform':
- return createUniformColor(props, colorData)
+ return createUniformColor(locationIt, () => props.value, colorData)
}
}
diff --git a/src/mol-geo/representation/structure/visual/util/location-iterator.ts b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
new file mode 100644
index 000000000..5dc3d76ce
--- /dev/null
+++ b/src/mol-geo/representation/structure/visual/util/location-iterator.ts
@@ -0,0 +1,123 @@
+/**
+ * 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
+}
+
+export const NullLocationValue = {
+ location: NullLocation,
+ index: 0,
+ elementIndex: 0,
+ instanceIndex: 0
+}
+
+export interface LocationIterator extends Iterator<LocationValue> {
+ readonly hasNext: boolean
+ readonly isNextNewInstance: boolean
+ readonly elementCount: number
+ readonly instanceCount: number
+ move(): LocationValue
+ skipInstance(): void
+}
+
+type LocationGetter = (elementIndex: number, instanceIndex: number) => Location
+
+export function LocationIterator(elementCount: number, instanceCount: number, getLocation: LocationGetter): LocationIterator {
+ const value = {
+ location: NullLocation as Location,
+ index: 0,
+ elementIndex: 0,
+ instanceIndex: 0
+ }
+
+ 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)
+ ++elementIndex
+ if (elementIndex === elementCount) {
+ ++instanceIndex
+ isNextNewInstance = true
+ if (instanceIndex < instanceCount) elementIndex = 0
+ } else {
+ isNextNewInstance = false
+ }
+ hasNext = elementIndex < elementCount
+ }
+ return value
+ },
+ 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, instanceIndex: 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, instanceIndex: 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, instanceIndex: 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/volume/surface.ts b/src/mol-geo/representation/volume/surface.ts
index dca3c980d..3fcd4b89c 100644
--- a/src/mol-geo/representation/volume/surface.ts
+++ b/src/mol-geo/representation/volume/surface.ts
@@ -13,7 +13,7 @@ import { VolumeVisual } from '.';
import { createMeshRenderObject, MeshRenderObject } from 'mol-gl/render-object';
import { ValueCell, defaults } from 'mol-util';
import { Mat4 } from 'mol-math/linear-algebra';
-import { createUniformColor } from '../../util/color-data';
+import { createValueColor } from '../../util/color-data';
import { getMeshData } from '../../util/mesh-data';
import { RenderableState, MeshValues } from 'mol-gl/renderable';
import { PickingId } from '../../util/picking';
@@ -65,7 +65,7 @@ export default function SurfaceVisual(): VolumeVisual<SurfaceProps> {
}
const instanceCount = 1
- const color = createUniformColor({ value: 0x7ec0ee })
+ const color = createValueColor(0x7ec0ee)
const marker = createEmptyMarkers()
const values: MeshValues = {
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index d703aa303..c0bc8e83f 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -4,11 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit, StructureProperties, StructureElement } from 'mol-model/structure';
+import { Unit, StructureProperties, StructureElement, Link } from 'mol-model/structure';
-import { StructureColorDataProps } from '.';
-import { ColorData, createElementColor, createUniformColor } from '../../../util/color-data';
-import { ColorScale } from 'mol-util/color';
+import { ColorData, createElementColor } from '../../../util/color-data';
+import { ColorScale, Color } from 'mol-util/color';
+import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
function getAsymId(unit: Unit): StructureElement.Property<string> {
switch (unit.kind) {
@@ -18,54 +18,28 @@ function getAsymId(unit: Unit): StructureElement.Property<string> {
case Unit.Kind.Gaussians:
return StructureProperties.coarse.asym_id
}
- throw new Error('unhandled unit kind')
}
-export function chainIdColorData(props: StructureColorDataProps, locationFn: (l: StructureElement, renderElementIdx: number) => void, colorData?: ColorData) {
- const { group: { units }, elementCount } = props
- const unit = units[0]
-
- const map = unit.model.properties.asymIdSerialMap
- const count = map.size
-
- const domain = [ 0, count - 1 ]
- const scale = ColorScale.create({ domain })
- const asym_id = getAsymId(unit)
-
+export function chainIdColorData(locationIt: LocationIterator, colorData?: ColorData) {
const l = StructureElement.create()
- l.unit = unit
- return createElementColor({
- colorFn: (renderElementIdx: number) => {
- locationFn(l, renderElementIdx)
+ function colorFn(locationValue: LocationValue): Color {
+ const { location } = locationValue
+ if (StructureElement.isLocation(location)) {
+ const map = location.unit.model.properties.asymIdSerialMap
+ const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
+ const asym_id = getAsymId(location.unit)
+ return scale.color(map.get(asym_id(location)) || 0)
+ } else if (Link.isLocation(location)) {
+ const map = location.aUnit.model.properties.asymIdSerialMap
+ const scale = ColorScale.create({ domain: [ 0, map.size - 1 ] })
+ const asym_id = getAsymId(location.aUnit)
+ l.unit = location.aUnit
+ l.element = location.aUnit.elements[location.aIndex]
return scale.color(map.get(asym_id(l)) || 0)
- },
- elementCount
- }, colorData)
-}
-
-export function chainIdElementColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const elements = props.group.units[0].elements
- function locationFn(l: StructureElement, renderElementIdx: number) {
- l.element = elements[renderElementIdx]
+ }
+ return 0
}
- return chainIdColorData(props, locationFn, colorData)
-}
-export function chainIdLinkColorData(props: StructureColorDataProps, colorData?: ColorData): ColorData {
- const unit = props.group.units[0]
- const elements = unit.elements
- let locationFn: (l: StructureElement, renderElementIdx: number) => void
- switch (unit.kind) {
- case Unit.Kind.Atomic:
- const { a } = unit.links
- locationFn = (l: StructureElement, renderElementIdx: number) => {
- l.element = elements[a[renderElementIdx]]
- }
- return chainIdColorData(props, locationFn, colorData)
- case Unit.Kind.Spheres:
- case Unit.Kind.Gaussians:
- // no chainId link color for coarse units, return uniform grey color
- return createUniformColor({ value: 0xCCCCCC }, colorData)
- }
+ return createElementColor(locationIt, colorFn, colorData)
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element-index.ts b/src/mol-geo/theme/structure/color/element-index.ts
index 510e0a4d5..7cd06ef40 100644
--- a/src/mol-geo/theme/structure/color/element-index.ts
+++ b/src/mol-geo/theme/structure/color/element-index.ts
@@ -5,18 +5,17 @@
*/
import { ColorScale } from 'mol-util/color';
-import { StructureColorDataProps } from '.';
import { createElementInstanceColor, ColorData } from '../../../util/color-data';
+import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
-export function elementIndexColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const { group: { units }, elementCount } = props
- const instanceCount = units.length
+export function elementIndexColorData(locationIt: LocationIterator, colorData?: ColorData) {
+ const { elementCount, instanceCount } = locationIt
const domain = [ 0, instanceCount * elementCount - 1 ]
const scale = ColorScale.create({ domain })
- return createElementInstanceColor({
- colorFn: (instanceIdx, elementIdx) => scale.color(instanceIdx * elementCount + elementIdx),
- instanceCount,
- elementCount
- }, colorData)
+ return createElementInstanceColor(
+ locationIt,
+ (value: LocationValue) => scale.color(value.instanceIndex * elementCount + value.elementIndex),
+ colorData
+ )
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element-symbol.ts b/src/mol-geo/theme/structure/color/element-symbol.ts
index eebb514d9..5c99412f6 100644
--- a/src/mol-geo/theme/structure/color/element-symbol.ts
+++ b/src/mol-geo/theme/structure/color/element-symbol.ts
@@ -6,8 +6,9 @@
import { ElementSymbol } from 'mol-model/structure/model/types';
import { Color } from 'mol-util/color';
-import { StructureColorDataProps } from '.';
import { createElementColor, ColorData } from '../../../util/color-data';
+import { StructureElement, Unit, Link } from 'mol-model/structure';
+import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
export const ElementSymbolColors: { [k: string]: Color } = {
@@ -21,14 +22,22 @@ export function elementSymbolColor(element: ElementSymbol): Color {
return c === void 0 ? DefaultElementSymbolColor : c
}
-export function elementSymbolColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const { group: { units, elements }, elementCount } = props
- const { type_symbol } = units[0].model.atomicHierarchy.atoms
- return createElementColor({
- colorFn: (elementIdx: number) => {
- const e = elements[elementIdx]
- return elementSymbolColor(type_symbol.value(e))
- },
- elementCount
- }, colorData)
+export function elementSymbolColorData(locationIt: LocationIterator, colorData?: ColorData) {
+ function colorFn(locationValue: LocationValue): Color {
+ const { location } = locationValue
+ if (StructureElement.isLocation(location)) {
+ if (Unit.isAtomic(location.unit)) {
+ const { type_symbol } = location.unit.model.atomicHierarchy.atoms
+ return elementSymbolColor(type_symbol.value(location.element))
+ }
+ } else if (Link.isLocation(location)) {
+ if (Unit.isAtomic(location.aUnit)) {
+ const { type_symbol } = location.aUnit.model.atomicHierarchy.atoms
+ return elementSymbolColor(type_symbol.value(location.aUnit.elements[location.aIndex]))
+ }
+ }
+ return DefaultElementSymbolColor
+ }
+
+ return createElementColor(locationIt, colorFn, colorData)
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index 41645f276..05e8c3200 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -12,6 +12,6 @@ export interface StructureColorDataProps {
}
export { elementIndexColorData } from './element-index'
-export { chainIdElementColorData } from './chain-id'
+export { chainIdColorData } from './chain-id'
export { elementSymbolColorData } from './element-symbol'
export { instanceIndexColorData } from './instance-index'
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/instance-index.ts b/src/mol-geo/theme/structure/color/instance-index.ts
index bc79c2c22..ca40a1d00 100644
--- a/src/mol-geo/theme/structure/color/instance-index.ts
+++ b/src/mol-geo/theme/structure/color/instance-index.ts
@@ -5,17 +5,17 @@
*/
import { ColorScale } from 'mol-util/color';
-import { StructureColorDataProps } from '.';
import { createInstanceColor, ColorData } from '../../../util/color-data';
+import { LocationIterator, LocationValue } from '../../../representation/structure/visual/util/location-iterator';
-export function instanceIndexColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const { group: { units } } = props
- const instanceCount = units.length
-
+export function instanceIndexColorData(locationIt: LocationIterator, colorData?: ColorData) {
+ const { instanceCount } = locationIt
const domain = [ 0, instanceCount - 1 ]
const scale = ColorScale.create({ domain })
- return createInstanceColor({
- colorFn: scale.color,
- instanceCount
- }, colorData)
+
+ function colorFn(locationValue: LocationValue) {
+ return scale.color(locationValue.instanceIndex)
+ }
+
+ return createInstanceColor(locationIt, colorFn, colorData)
}
\ 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 4aa569851..7b207d8db 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -7,8 +7,8 @@
import { ValueCell } from 'mol-util';
import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
import { Color } from 'mol-util/color';
-import VertexMap from '../shape/vertex-map';
import { Vec2, Vec3 } from 'mol-math/linear-algebra';
+import { LocationIterator, LocationValue, NullLocationValue } from '../representation/structure/visual/util/location-iterator';
export type ColorType = 'uniform' | 'attribute' | 'instance' | 'element' | 'elementInstance'
@@ -20,6 +20,8 @@ export type ColorData = {
dColorType: ValueCell<string>,
}
+export type LocationColor = (locationValue: LocationValue) => Color
+
const emptyColorTexture = { array: new Uint8Array(3), width: 1, height: 1 }
function createEmptyColorTexture() {
return {
@@ -28,21 +30,16 @@ function createEmptyColorTexture() {
}
}
-export interface UniformColorProps {
- value: Color
-}
-
-/** Creates color uniform */
-export function createUniformColor(props: UniformColorProps, colorData?: ColorData): ColorData {
+export function createValueColor(value: Color, colorData?: ColorData): ColorData {
if (colorData) {
- ValueCell.update(colorData.uColor, Color.toRgbNormalized(props.value) as Vec3)
+ ValueCell.update(colorData.uColor, Color.toRgbNormalized(value) as Vec3)
if (colorData.dColorType.ref.value !== 'uniform') {
ValueCell.update(colorData.dColorType, 'uniform')
}
return colorData
} else {
return {
- uColor: ValueCell.create(Color.toRgbNormalized(props.value) as Vec3),
+ uColor: ValueCell.create(Color.toRgbNormalized(value) as Vec3),
aColor: ValueCell.create(new Float32Array(0)),
...createEmptyColorTexture(),
dColorType: ValueCell.create('uniform'),
@@ -50,39 +47,44 @@ export function createUniformColor(props: UniformColorProps, colorData?: ColorDa
}
}
-export interface AttributeColorProps {
- colorFn: (elementIdx: number) => Color
- vertexMap: VertexMap
+/** Creates color uniform */
+export function createUniformColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
+ return createValueColor(colorFn(NullLocationValue), colorData)
}
-/** Creates color attribute with color for each element (i.e. shared across instances/units) */
-export function createAttributeColor(props: AttributeColorProps, colorData?: ColorData): ColorData {
- const { colorFn, vertexMap } = props
- const { idCount, offsetCount, offsets } = vertexMap
- const colors = new Float32Array(idCount * 3);
- for (let i = 0, il = offsetCount - 1; i < il; ++i) {
- const start = offsets[i]
- const end = offsets[i + 1]
- const hexColor = colorFn(i)
- for (let i = start, il = end; i < il; ++i) {
- Color.toArrayNormalized(hexColor, colors, i * 3)
- }
- }
- if (colorData) {
- ValueCell.update(colorData.aColor, colors)
- if (colorData.dColorType.ref.value !== 'attribute') {
- ValueCell.update(colorData.dColorType, 'attribute')
- }
- return colorData
- } else {
- return {
- uColor: ValueCell.create(Vec3.zero()),
- aColor: ValueCell.create(colors),
- ...createEmptyColorTexture(),
- dColorType: ValueCell.create('attribute'),
- }
- }
-}
+// export interface AttributeColorProps {
+// colorFn: (elementIdx: number) => Color
+// vertexMap: VertexMap
+// }
+
+// /** Creates color attribute with color for each element (i.e. shared across instances/units) */
+// export function createAttributeColor(props: AttributeColorProps, colorData?: ColorData): ColorData {
+// const { colorFn, vertexMap } = props
+// const { idCount, offsetCount, offsets } = vertexMap
+// const colors = new Float32Array(idCount * 3);
+// for (let i = 0, il = offsetCount - 1; i < il; ++i) {
+// const start = offsets[i]
+// const end = offsets[i + 1]
+// const hexColor = colorFn(i)
+// for (let i = start, il = end; i < il; ++i) {
+// Color.toArrayNormalized(hexColor, colors, i * 3)
+// }
+// }
+// if (colorData) {
+// ValueCell.update(colorData.aColor, colors)
+// if (colorData.dColorType.ref.value !== 'attribute') {
+// ValueCell.update(colorData.dColorType, 'attribute')
+// }
+// return colorData
+// } else {
+// return {
+// uColor: ValueCell.create(Vec3.zero()),
+// aColor: ValueCell.create(colors),
+// ...createEmptyColorTexture(),
+// dColorType: ValueCell.create('attribute'),
+// }
+// }
+// }
export function createTextureColor(colors: TextureImage, type: ColorType, colorData?: ColorData): ColorData {
if (colorData) {
@@ -103,53 +105,38 @@ export function createTextureColor(colors: TextureImage, type: ColorType, colorD
}
}
-export interface InstanceColorProps {
- colorFn: (instanceIdx: number) => Color
- instanceCount: number
-}
-
/** Creates color texture with color for each instance/unit */
-export function createInstanceColor(props: InstanceColorProps, colorData?: ColorData): ColorData {
- const { colorFn, instanceCount} = props
+export function createInstanceColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
+ const { instanceCount} = locationIt
const colors = colorData && colorData.tColor.ref.value.array.length >= instanceCount * 3 ? colorData.tColor.ref.value : createTextureImage(instanceCount, 3)
- for (let i = 0; i < instanceCount; i++) {
- Color.toArray(colorFn(i), colors.array, i * 3)
+ while (locationIt.hasNext && !locationIt.isNextNewInstance) {
+ const value = locationIt.move()
+ Color.toArray(colorFn(value), colors.array, value.index * 3)
+ locationIt.skipInstance()
}
return createTextureColor(colors, 'instance', colorData)
}
-export interface ElementColorProps {
- colorFn: (elementIdx: number) => Color
- elementCount: number
-}
-
/** Creates color texture with color for each element (i.e. shared across instances/units) */
-export function createElementColor(props: ElementColorProps, colorData?: ColorData): ColorData {
- const { colorFn, elementCount } = props
+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)
- for (let i = 0, il = elementCount; i < il; ++i) {
- Color.toArray(colorFn(i), colors.array, i * 3)
+ while (locationIt.hasNext && !locationIt.isNextNewInstance) {
+ const value = locationIt.move()
+ // console.log(value)
+ Color.toArray(colorFn(value), colors.array, value.elementIndex * 3)
}
return createTextureColor(colors, 'element', colorData)
}
-export interface ElementInstanceColorProps {
- colorFn: (instanceIdx: number, elementIdx: number) => Color
- instanceCount: number,
- elementCount: number
-}
-
/** Creates color texture with color for each element instance (i.e. for each unit) */
-export function createElementInstanceColor(props: ElementInstanceColorProps, colorData?: ColorData): ColorData {
- const { colorFn, instanceCount, elementCount } = props
+export function createElementInstanceColor(locationIt: LocationIterator, colorFn: LocationColor, colorData?: ColorData): ColorData {
+ const { elementCount, instanceCount } = locationIt
const count = instanceCount * elementCount
const colors = colorData && colorData.tColor.ref.value.array.length >= count * 3 ? colorData.tColor.ref.value : createTextureImage(count, 3)
- let colorOffset = 0
- for (let i = 0; i < instanceCount; i++) {
- for (let j = 0, jl = elementCount; j < jl; ++j) {
- Color.toArray(colorFn(i, j), colors.array, colorOffset)
- colorOffset += 3
- }
+ while (locationIt.hasNext && !locationIt.isNextNewInstance) {
+ const value = locationIt.move()
+ Color.toArray(colorFn(value), colors.array, value.index * 3)
}
return createTextureColor(colors, 'elementInstance', colorData)
}
\ 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 52e7cfe07..c314659a2 100644
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -11,7 +11,7 @@ import { Vec3, Mat4 } from 'mol-math/linear-algebra';
import { ValueCell } from 'mol-util';
import Renderer from '../renderer';
-import { createUniformColor } from 'mol-geo/util/color-data';
+import { createValueColor } from 'mol-geo/util/color-data';
import { createUniformSize } from 'mol-geo/util/size-data';
import { createContext } from '../webgl/context';
import { RenderableState } from '../renderable';
@@ -47,7 +47,7 @@ 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 color = createUniformColor({ value: 0xFF0000 })
+ const color = createValueColor(0xFF0000)
const size = createUniformSize({ value: 1 })
const marker = createEmptyMarkers()
diff --git a/src/mol-model/location.ts b/src/mol-model/location.ts
new file mode 100644
index 000000000..c3361122a
--- /dev/null
+++ b/src/mol-model/location.ts
@@ -0,0 +1,17 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StructureElement } from './structure'
+import { Link } from './structure/structure/unit/links'
+
+/** A null value Location */
+export const NullLocation = { kind: 'null-location' as 'null-location' }
+export type NullLocation = typeof NullLocation
+export function isNullLocation(x: any): x is NullLocation {
+ return !!x && x.kind === 'null-location';
+}
+
+export type Location = StructureElement | Link.Location | NullLocation
\ No newline at end of file
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index c235548f9..37a679c9c 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -14,7 +14,7 @@ export function isEveryLoci(x: any): x is EveryLoci {
return !!x && x.kind === 'every-loci';
}
-/** A Loci that that is empty */
+/** A Loci that is empty */
export const EmptyLoci = { kind: 'empty-loci' as 'empty-loci' }
export type EmptyLoci = typeof EmptyLoci
export function isEmptyLoci(x: any): x is EmptyLoci {
diff --git a/src/mol-model/structure/structure/element.ts b/src/mol-model/structure/structure/element.ts
index f8e35caff..cae429e50 100644
--- a/src/mol-model/structure/structure/element.ts
+++ b/src/mol-model/structure/structure/element.ts
@@ -9,13 +9,16 @@ import Unit from './unit'
import { ElementIndex } from '../model';
interface StructureElement<U = Unit> {
+ readonly kind: 'element-location',
unit: U,
/** Index into element (atomic/coarse) properties of unit.model */
element: ElementIndex
}
namespace StructureElement {
- export function create(unit?: Unit, element?: ElementIndex): StructureElement { return { unit: unit as any, element: element || (0 as ElementIndex) }; }
+ export function create(unit?: Unit, element?: ElementIndex): StructureElement {
+ return { kind: 'element-location', unit: unit as any, element: element || (0 as ElementIndex) };
+ }
// TODO: when nominal types are available, make this indexed by UnitIndex
export type Set = SortedArray<ElementIndex>
@@ -58,6 +61,10 @@ namespace StructureElement {
export function isLoci(x: any): x is Loci {
return !!x && x.kind === 'element-loci';
}
+
+ export function isLocation(x: any): x is StructureElement {
+ return !!x && x.kind === 'element-location';
+ }
}
export default StructureElement
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/links.ts b/src/mol-model/structure/structure/unit/links.ts
index 20345c1bf..c7ff8e0a7 100644
--- a/src/mol-model/structure/structure/unit/links.ts
+++ b/src/mol-model/structure/structure/unit/links.ts
@@ -1,10 +1,11 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Unit } from '../../structure'
+import { Unit, StructureElement } from '../../structure'
export * from './links/data'
export * from './links/intra-compute'
@@ -12,12 +13,21 @@ export * from './links/inter-compute'
namespace Link {
export interface Location {
- readonly aUnit: Unit,
+ readonly kind: 'link-location',
+ aUnit: Unit,
/** Index into aUnit.elements */
- readonly aIndex: number,
- readonly bUnit: Unit,
+ aIndex: StructureElement.UnitIndex,
+ bUnit: Unit,
/** Index into bUnit.elements */
- readonly bIndex: number,
+ bIndex: StructureElement.UnitIndex,
+ }
+
+ export function Location(aUnit?: Unit, aIndex?: StructureElement.UnitIndex, bUnit?: Unit, bIndex?: StructureElement.UnitIndex): Location {
+ return { kind: 'link-location', aUnit: aUnit as any, aIndex: aIndex as any, bUnit: bUnit as any, bIndex: bIndex as any };
+ }
+
+ export function isLocation(x: any): x is Location {
+ return !!x && x.kind === 'link-location';
}
export interface Loci {
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 427399122..c88e165ec 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -78,7 +78,7 @@ export class Stage {
// this.loadPdbid('1hrv') // viral assembly
// this.loadPdbid('1rb8') // virus
// this.loadPdbid('1blu') // metal coordination
- // this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
+ this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
// this.loadPdbid('2np2') // dna
@@ -105,7 +105,7 @@ export class Stage {
// this.loadPdbid('2fnc') // contains maltotriose
// this.loadPdbid('4zs9') // contains raffinose
// this.loadPdbid('2yft') // contains kestose
- this.loadPdbid('2b5t') // contains large carbohydrate polymer
+ // this.loadPdbid('2b5t') // contains large carbohydrate polymer
// this.loadPdbid('1b5f') // contains carbohydrate with alternate locations
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
// this.loadMmcifUrl(`../../examples/1cbs_updated.cif`)
--
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