diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index 1e284a0a12b47738f2d32ca9dd550e07f9fbdbcd..c0e92f901c4d9955f900e78f03c193acf2ce28bc 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -17,7 +17,7 @@ import Spacefill, { SpacefillProps } from 'mol-geo/representation/structure/spac
import Point, { PointProps } from 'mol-geo/representation/structure/point'
import { Run } from 'mol-task'
-import { Symmetry, Structure, Model } from 'mol-model/structure'
+import { StructureSymmetry, Structure, Model } from 'mol-model/structure'
// import mcubes from './utils/mcubes'
import { getModelFromPdbId, getModelFromFile, log, Volume, getVolumeFromEmdId } from './utils'
@@ -110,7 +110,7 @@ export default class State {
let structure: Structure
const assemblies = model.symmetry.assemblies
if (assemblies.length) {
- structure = await Run(Symmetry.buildAssembly(Structure.ofModel(model), assembly || '1'), log, 500)
+ structure = await Run(StructureSymmetry.buildAssembly(Structure.ofModel(model), assembly || '1'), log, 500)
} else {
structure = Structure.ofModel(model)
}
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 5abea8553fa240cbdf5dd88df4a8a9c3b7ee11d0..8fde77fce22df99fac8d9a5cbc0718fe0ba312ca 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -10,7 +10,7 @@ require('util.promisify').shim();
// import { Table } from 'mol-data/db'
import CIF from 'mol-io/reader/cif'
-import { Model, Structure, Element, ElementSet, Unit, ElementGroup, Queries } from 'mol-model/structure'
+import { Model, Structure, Element, Unit, Queries } from 'mol-model/structure'
// import { Run, Progress } from 'mol-task'
import { OrderedSet } from 'mol-data/int';
import { Table } from 'mol-data/db';
@@ -41,31 +41,29 @@ export function atomLabel(model: Model, aI: number) {
export function printBonds(structure: Structure) {
- const { units, elements } = structure;
- const unitIds = ElementSet.unitIndices(elements);
+ // TODO
+ // for (const unit of structure.units) {
+ // const unit = units[OrderedSet.getAt(unitIds, i)];
+ // const group = ElementSet.groupFromUnitIndex(elements, OrderedSet.getAt(unitIds, i));
- for (let i = 0, _i = OrderedSet.size(unitIds); i < _i; i++) {
- const unit = units[OrderedSet.getAt(unitIds, i)];
- const group = ElementSet.groupFromUnitIndex(elements, OrderedSet.getAt(unitIds, i));
+ // const { count, offset, neighbor } = Unit.getGroupBonds(unit, group);
+ // const { model } = unit;
- const { count, offset, neighbor } = Unit.getGroupBonds(unit, group);
- const { model } = unit;
+ // if (!count) continue;
- if (!count) continue;
+ // for (let j = 0; j < offset.length - 1; ++j) {
+ // const start = offset[j];
+ // const end = offset[j + 1];
- for (let j = 0; j < offset.length - 1; ++j) {
- const start = offset[j];
- const end = offset[j + 1];
+ // if (end <= start) continue;
- if (end <= start) continue;
-
- const aI = ElementGroup.getAt(group, j);
- for (let _bI = start; _bI < end; _bI++) {
- const bI = ElementGroup.getAt(group, neighbor[_bI])
- console.log(`${atomLabel(model, aI)} -- ${atomLabel(model, bI)}`);
- }
- }
- }
+ // const aI = ElementGroup.getAt(group, j);
+ // for (let _bI = start; _bI < end; _bI++) {
+ // const bI = ElementGroup.getAt(group, neighbor[_bI])
+ // console.log(`${atomLabel(model, aI)} -- ${atomLabel(model, bI)}`);
+ // }
+ // }
+ // }
}
export function printSequence(model: Model) {
@@ -83,26 +81,23 @@ export function printSequence(model: Model) {
export function printUnits(structure: Structure) {
console.log('Units\n=============');
- const { elements, units } = structure;
- const unitIds = ElementSet.unitIndices(elements);
const l = Element.Location();
- for (let i = 0, _i = unitIds.length; i < _i; i++) {
- const unitId = unitIds[i];
- l.unit = units[unitId];
- const set = ElementSet.groupAt(elements, i).elements;
- const size = OrderedSet.size(set);
+ for (const unit of structure.units) {
+ l.unit = unit;
+ const elements = unit.elements;
+ const size = OrderedSet.size(elements);
if (Unit.isAtomic(l.unit)) {
- console.log(`Atomic unit ${unitId}: ${size} elements`);
+ console.log(`Atomic unit ${unit.id}: ${size} elements`);
} else if (Unit.isCoarse(l.unit)) {
- console.log(`Coarse unit ${unitId} (${Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians'}): ${size} elements.`);
+ console.log(`Coarse unit ${unit.id} (${Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians'}): ${size} elements.`);
const props = Queries.props.coarse_grained;
const seq = l.unit.model.sequence;
for (let j = 0, _j = Math.min(size, 10); j < _j; j++) {
- l.element = OrderedSet.getAt(set, j);
+ l.element = OrderedSet.getAt(elements, j);
const residues: string[] = [];
const start = props.seq_id_begin(l), end = props.seq_id_end(l);
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 274da6a077bbfdeedcf8449020d710e27647cfe0..9caee1437f431b73ac4359d70aadee7ad8f1c966 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -2,11 +2,10 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
-import { ElementGroup, ElementSet, Structure, Unit } from 'mol-model/structure';
-import { EquivalenceClasses } from 'mol-data/util';
-import { OrderedSet } from 'mol-data/int'
+import { Structure, StructureSymmetry } from 'mol-model/structure';
import { Task } from 'mol-task'
import { RenderObject } from 'mol-gl/scene';
import { Representation, RepresentationProps } from '..';
@@ -15,7 +14,7 @@ import { Representation, RepresentationProps } from '..';
export interface UnitsRepresentation<P> {
renderObjects: ReadonlyArray<RenderObject>
- create: (units: ReadonlyArray<Unit>, elementGroup: ElementGroup, props: P) => Task<void>
+ create: (group: StructureSymmetry.UnitGroup, props: P) => Task<void>
update: (props: P) => Task<boolean>
}
@@ -27,8 +26,7 @@ export interface StructureRepresentation<P extends RepresentationProps = {}> ext
interface GroupRepresentation<T> {
repr: UnitsRepresentation<T>
- units: Unit[]
- elementGroup: ElementGroup
+ group: StructureSymmetry.UnitGroup
}
export function StructureRepresentation<P>(reprCtor: () => UnitsRepresentation<P>): StructureRepresentation<P> {
@@ -39,40 +37,12 @@ export function StructureRepresentation<P>(reprCtor: () => UnitsRepresentation<P
renderObjects,
create(structure: Structure, props: P = {} as P) {
return Task.create('StructureRepresentation.create', async ctx => {
- const { elements, units } = structure;
- const uniqueGroups = EquivalenceClasses<number, { unit: Unit, group: ElementGroup }>(
- ({ unit, group }) => ElementGroup.hashCode(group),
- (a, b) => a.unit.model.id === b.unit.model.id && OrderedSet.areEqual(a.group.elements, b.group.elements)
- );
-
- // const uniqueTransformations = EquivalenceClasses<number, { unit: Unit, group: ElementGroup }>(
- // ({ unit, group }) => unit.operator.matrix.join(','),
- // (a, b) => Mat4.areEqual(a.unit.operator.matrix, b.unit.operator.matrix, EPSILON.Value)
- // );
-
- const unitIndices = ElementSet.unitIndices(elements);
- for (let i = 0, _i = unitIndices.length; i < _i; i++) {
- const unitIndex = unitIndices[i];
- const group = ElementSet.groupFromUnitIndex(elements, unitIndex);
- const unit = units[unitIndex]
- uniqueGroups.add(unitIndex, { unit, group });
- // uniqueTransformations.add(unitIndex, { unit, group });
- }
-
- // console.log({ uniqueGroups, uniqueTransformations })
-
- for (let i = 0, il = uniqueGroups.groups.length; i < il; i++) {
- const groupUnits: Unit[] = []
- const group = uniqueGroups.groups[i]
- // console.log('group', i)
- for (let j = 0, jl = group.length; j < jl; j++) {
- groupUnits.push(units[group[j]])
- }
- const elementGroup = ElementSet.groupFromUnitIndex(elements, group[0])
+ const groups = StructureSymmetry.getTransformGroups(structure);
+ for (let i = 0; i < groups.length; i++) {
+ const group = groups[i];
const repr = reprCtor()
- groupReprs.push({ repr, units: groupUnits, elementGroup })
- await ctx.update({ message: 'Building structure unit representations...', current: i, max: il });
- await ctx.runChild(repr.create(groupUnits, elementGroup, props));
+ groupReprs.push({ repr, group })
+ await ctx.runChild(repr.create(group, props), { message: 'Building structure unit representations...', current: i, max: groups.length });
renderObjects.push(...repr.renderObjects)
}
});
@@ -83,10 +53,10 @@ export function StructureRepresentation<P>(reprCtor: () => UnitsRepresentation<P
renderObjects.length = 0 // clear
for (let i = 0, il = groupReprs.length; i < il; ++i) {
const groupRepr = groupReprs[i]
- const { repr, units, elementGroup } = groupRepr
- await ctx.update({ message: 'Updating structure unit representations...', current: i, max: il });
- if (!await ctx.runChild(repr.update(props))) {
- await ctx.runChild(repr.create(units, elementGroup, props))
+ const { repr, group } = groupRepr
+ const state = { message: 'Updating structure unit representations...', current: i, max: il };
+ if (!await ctx.runChild(repr.update(props), state)) {
+ await ctx.runChild(repr.create(group, props), state)
}
renderObjects.push(...repr.renderObjects)
}
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
index 71f317e39c3a31e83cce6d0f63a3f25201406e29..becee521ffe39a131950a7aa6cffdb3e908e3f22 100644
--- a/src/mol-geo/representation/structure/point.ts
+++ b/src/mol-geo/representation/structure/point.ts
@@ -2,12 +2,12 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
import { ValueCell } from 'mol-util/value-cell'
import { createPointRenderObject, RenderObject, PointRenderObject } from 'mol-gl/scene'
-import { OrderedSet } from 'mol-data/int'
-import { Unit, ElementGroup, Element } from 'mol-model/structure';
+import { Unit, Element, StructureSymmetry } from 'mol-model/structure';
import { Task } from 'mol-task'
import { fillSerial } from 'mol-gl/renderable/util';
@@ -16,6 +16,7 @@ import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
import { createTransforms, createColors, createSizes } from './utils';
import { deepEqual } from 'mol-util';
+import { SortedArray } from 'mol-data/int';
export const DefaultPointProps = {
colorTheme: { name: 'instance-index' } as ColorTheme,
@@ -25,16 +26,17 @@ export const DefaultPointProps = {
}
export type PointProps = Partial<typeof DefaultPointProps>
-export function createPointVertices(unit: Unit, elementGroup: ElementGroup) {
- const elementCount = OrderedSet.size(elementGroup.elements)
+export function createPointVertices(unit: Unit) {
+ const elements = unit.elements
+ const elementCount = elements.length
const vertices = new Float32Array(elementCount * 3)
- const { x, y, z } = unit
+ const { x, y, z } = unit.conformation
const l = Element.Location()
l.unit = unit
for (let i = 0; i < elementCount; i++) {
- l.element = ElementGroup.getAt(elementGroup, i)
+ l.element = elements[i];
const i3 = i * 3
vertices[i3] = x(l.element)
vertices[i3 + 1] = y(l.element)
@@ -49,21 +51,21 @@ export default function Point(): UnitsRepresentation<PointProps> {
let curProps = DefaultPointProps
let _units: ReadonlyArray<Unit>
- let _elementGroup: ElementGroup
+ let _elements: SortedArray
return {
renderObjects,
- create(units: ReadonlyArray<Unit>, elementGroup: ElementGroup, props: PointProps = {}) {
+ create(group: StructureSymmetry.UnitGroup, props: PointProps = {}) {
return Task.create('Point.create', async ctx => {
renderObjects.length = 0 // clear
curProps = { ...DefaultPointProps, ...props }
- _units = units
- _elementGroup = elementGroup
+ _units = group.units
+ _elements = group.elements;
const { colorTheme, sizeTheme, alpha, visible } = curProps
- const elementCount = OrderedSet.size(elementGroup.elements)
- const unitCount = units.length
+ const elementCount = _elements.length
+ const unitCount = _units.length
const vertexMap = VertexMap.create(
elementCount,
@@ -73,16 +75,16 @@ export default function Point(): UnitsRepresentation<PointProps> {
)
await ctx.update('Computing point vertices');
- const vertices = createPointVertices(units[0], elementGroup)
+ const vertices = createPointVertices(_units[0])
await ctx.update('Computing point transforms');
- const transforms = createTransforms(units)
+ const transforms = createTransforms(group)
await ctx.update('Computing point colors');
- const color = createColors(units, elementGroup, vertexMap, colorTheme)
+ const color = createColors(group, vertexMap, colorTheme)
await ctx.update('Computing point sizes');
- const size = createSizes(units, elementGroup, vertexMap, sizeTheme)
+ const size = createSizes(group, vertexMap, sizeTheme)
points = createPointRenderObject({
objectId: 0,
@@ -106,7 +108,7 @@ export default function Point(): UnitsRepresentation<PointProps> {
},
update(props: PointProps) {
return Task.create('Point.update', async ctx => {
- if (!points || !_units || !_elementGroup) return false
+ if (!points || !_units || !_elements) return false
const newProps = { ...curProps, ...props }
if (deepEqual(curProps, newProps)) {
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 2d9b3c1a9e929f7cd1fb73458047ff008c5b8c7f..5dd62f7f91ec000627ad5ac33bcb99bb9b35c84e 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -2,6 +2,7 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
import { ValueCell } from 'mol-util/value-cell'
@@ -9,8 +10,7 @@ import { ValueCell } from 'mol-util/value-cell'
import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/scene'
// import { createColorTexture } from 'mol-gl/util';
import { Vec3, Mat4 } from 'mol-math/linear-algebra'
-import { OrderedSet } from 'mol-data/int'
-import { Unit, ElementGroup, Element, Queries } from 'mol-model/structure';
+import { Unit, Element, Queries, StructureSymmetry } from 'mol-model/structure';
import { UnitsRepresentation } from './index';
import { Task } from 'mol-task'
import { MeshBuilder } from '../../shape/mesh-builder';
@@ -28,9 +28,10 @@ export const DefaultSpacefillProps = {
}
export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
-function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: number) {
+function createSpacefillMesh(unit: Unit, detail: number) {
return Task.create('Sphere mesh', async ctx => {
- const elementCount = OrderedSet.size(elementGroup.elements)
+ const { elements } = unit;
+ const elementCount = elements.length;
const vertexCount = elementCount * icosahedronVertexCount(detail)
const meshBuilder = MeshBuilder.create(vertexCount)
@@ -47,12 +48,12 @@ function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: num
const v = Vec3.zero()
const m = Mat4.identity()
- const { x, y, z } = unit
+ const { x, y, z } = unit.conformation
const l = Element.Location()
l.unit = unit
for (let i = 0; i < elementCount; i++) {
- l.element = ElementGroup.getAt(elementGroup, i)
+ l.element = elements[i]
v[0] = x(l.element)
v[1] = y(l.element)
v[2] = z(l.element)
@@ -76,23 +77,23 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
return {
renderObjects,
- create(units: ReadonlyArray<Unit>, elementGroup: ElementGroup, props: SpacefillProps = {}) {
+ create(group: StructureSymmetry.UnitGroup, props: SpacefillProps = {}) {
return Task.create('Spacefill.create', async ctx => {
renderObjects.length = 0 // clear
const { detail, colorTheme, alpha, visible, doubleSided } = { ...DefaultSpacefillProps, ...props }
await ctx.update('Computing spacefill mesh');
- const mesh = await ctx.runChild(createSpacefillMesh(units[0], elementGroup, detail))
+ const mesh = await ctx.runChild(createSpacefillMesh(group.units[0], detail))
// console.log(mesh)
const vertexMap = VertexMap.fromMesh(mesh)
await ctx.update('Computing spacefill transforms');
- const transforms = createTransforms(units)
+ const transforms = createTransforms(group)
await ctx.update('Computing spacefill colors');
- const color = createColors(units, elementGroup, vertexMap, colorTheme)
+ const color = createColors(group, vertexMap, colorTheme)
spheres = createMeshRenderObject({
objectId: 0,
@@ -107,9 +108,9 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
transform: ValueCell.create(transforms),
index: mesh.indexBuffer,
- instanceCount: units.length,
+ instanceCount: group.units.length,
indexCount: mesh.triangleCount,
- elementCount: OrderedSet.size(elementGroup.elements),
+ elementCount: group.elements.length,
positionCount: mesh.vertexCount
})
renderObjects.push(spheres)
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index fba67c536e46e9447fd19b170299d25771b19996..920159d1a807b6435b58d590d1f5f0c9ae808092 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -2,9 +2,10 @@
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Unit, ElementGroup } from 'mol-model/structure';
+import { StructureSymmetry } from 'mol-model/structure';
import { Mat4 } from 'mol-math/linear-algebra'
import { createUniformColor } from '../../util/color-data';
@@ -14,35 +15,35 @@ import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
-export function createTransforms(units: ReadonlyArray<Unit>) {
+export function createTransforms({ units }: StructureSymmetry.UnitGroup) {
const unitCount = units.length
const transforms = new Float32Array(unitCount * 16)
for (let i = 0; i < unitCount; i++) {
- Mat4.toArray(units[i].operator.matrix, transforms, i * 16)
+ Mat4.toArray(units[i].conformation.operator.matrix, transforms, i * 16)
}
return transforms
}
-export function createColors(units: ReadonlyArray<Unit>, elementGroup: ElementGroup, vertexMap: VertexMap, props: ColorTheme) {
+export function createColors(group: StructureSymmetry.UnitGroup, vertexMap: VertexMap, props: ColorTheme) {
switch (props.name) {
case 'atom-index':
- return elementIndexColorData({ units, elementGroup, vertexMap })
+ return elementIndexColorData({ group, vertexMap })
case 'chain-id':
- return chainIdColorData({ units, elementGroup, vertexMap })
+ return chainIdColorData({ group, vertexMap })
case 'element-symbol':
- return elementSymbolColorData({ units, elementGroup, vertexMap })
+ return elementSymbolColorData({ group, vertexMap })
case 'instance-index':
- return instanceIndexColorData({ units, elementGroup, vertexMap })
+ return instanceIndexColorData({ group, vertexMap })
case 'uniform':
return createUniformColor(props)
}
}
-export function createSizes(units: ReadonlyArray<Unit>, elementGroup: ElementGroup, vertexMap: VertexMap, props: SizeTheme) {
+export function createSizes(group: StructureSymmetry.UnitGroup, vertexMap: VertexMap, props: SizeTheme) {
switch (props.name) {
case 'uniform':
return createUniformSize(props)
case 'vdw':
- return elementSizeData({ units, elementGroup, vertexMap })
+ return elementSizeData({ group, vertexMap })
}
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index fec2d8f8a7f5a6cb32cc67dede93663722406e89..95e305be302a3a1d0c86c2175cec389cde5d50b7 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ElementGroup, Unit, Queries, Element } from 'mol-model/structure';
+import { Unit, Queries, Element } from 'mol-model/structure';
import { StructureColorDataProps } from '.';
import { createAttributeOrElementColor } from '../../../util/color-data';
@@ -18,8 +18,8 @@ function createChainIdMap(unit: Unit) {
let count: number
let asym_id: Column<string>
if (Unit.isAtomic(unit)) {
- asym_id = unit.hierarchy.chains.label_asym_id
- count = unit.hierarchy.chains._rowCount
+ asym_id = unit.model.hierarchy.chains.label_asym_id
+ count = unit.model.hierarchy.chains._rowCount
} else if (Unit.isCoarse(unit)) {
asym_id = unit.sites.asym_id
count = unit.sites.count
@@ -39,7 +39,7 @@ function createChainIdMap(unit: Unit) {
}
export function chainIdColorData(props: StructureColorDataProps) {
- const { units, elementGroup, vertexMap } = props
+ const { group: { units, elements }, vertexMap } = props
const unit = units[0]
const { map, count } = createChainIdMap(unit)
@@ -59,7 +59,7 @@ export function chainIdColorData(props: StructureColorDataProps) {
return createAttributeOrElementColor(vertexMap, {
colorFn: (elementIdx: number) => {
- l.element = ElementGroup.getAt(elementGroup, elementIdx)
+ l.element = elements[elementIdx]
return scale.color(map.get(asym_id(l)) || 0)
},
vertexMap
diff --git a/src/mol-geo/theme/structure/color/element-index.ts b/src/mol-geo/theme/structure/color/element-index.ts
index b205043d46ffb5a1fee65485dc9f026644f7a2c6..f6540f95e3fff159b13f9f20908bba27152d83ec 100644
--- a/src/mol-geo/theme/structure/color/element-index.ts
+++ b/src/mol-geo/theme/structure/color/element-index.ts
@@ -6,13 +6,12 @@
import { ColorScale } from 'mol-util/color';
import { StructureColorDataProps } from '.';
-import { OrderedSet } from 'mol-data/int';
import { createElementInstanceColor } from '../../../util/color-data';
export function elementIndexColorData(props: StructureColorDataProps) {
- const { units, elementGroup, vertexMap } = props
+ const { group: { units, elements }, vertexMap } = props
const instanceCount = units.length
- const elementCount = OrderedSet.size(elementGroup.elements)
+ const elementCount = elements.length
const domain = [ 0, instanceCount * elementCount - 1 ]
const scale = ColorScale.create({ domain })
diff --git a/src/mol-geo/theme/structure/color/element-symbol.ts b/src/mol-geo/theme/structure/color/element-symbol.ts
index 432807d2bb4ee75947a70538afc9f93844591b97..815985b3347c57eb88bf4c47ad219939f2be1c7c 100644
--- a/src/mol-geo/theme/structure/color/element-symbol.ts
+++ b/src/mol-geo/theme/structure/color/element-symbol.ts
@@ -7,7 +7,6 @@
import { ElementSymbol } from 'mol-model/structure/model/types';
import { Color } from 'mol-util/color';
import { StructureColorDataProps } from '.';
-import { OrderedSet } from 'mol-data/int';
import { createAttributeOrElementColor } from '../../../util/color-data';
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
@@ -23,11 +22,11 @@ export function elementSymbolColor(element: ElementSymbol): Color {
}
export function elementSymbolColorData(props: StructureColorDataProps) {
- const { units, elementGroup, vertexMap } = props
+ const { group: { units, elements }, vertexMap } = props
const { type_symbol } = units[0].model.hierarchy.atoms
return createAttributeOrElementColor(vertexMap, {
colorFn: (elementIdx: number) => {
- const e = OrderedSet.getAt(elementGroup.elements, elementIdx)
+ const e = elements[elementIdx]
return elementSymbolColor(type_symbol.value(e))
},
vertexMap
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index 82d5b22a6c6535744d2c1000f5d0948bdace8311..f03f0e9e5ef9038ad699c0773d311955eb64fd38 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -4,12 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ElementGroup, Unit } from 'mol-model/structure';
+import { StructureSymmetry } from 'mol-model/structure';
import VertexMap from '../../../shape/vertex-map';
export interface StructureColorDataProps {
- units: ReadonlyArray<Unit>,
- elementGroup: ElementGroup,
+ group: StructureSymmetry.UnitGroup,
vertexMap: VertexMap
}
diff --git a/src/mol-geo/theme/structure/color/instance-index.ts b/src/mol-geo/theme/structure/color/instance-index.ts
index bd7d6f5775d05bf415f9e4df822f054086c4ad1c..ffae3b0861016c0901dac0e591150e26f114ae4f 100644
--- a/src/mol-geo/theme/structure/color/instance-index.ts
+++ b/src/mol-geo/theme/structure/color/instance-index.ts
@@ -9,7 +9,7 @@ import { StructureColorDataProps } from '.';
import { createInstanceColor } from '../../../util/color-data';
export function instanceIndexColorData(props: StructureColorDataProps) {
- const { units } = props
+ const { group: { units } } = props
const instanceCount = units.length
const domain = [ 0, instanceCount - 1 ]
diff --git a/src/mol-geo/theme/structure/size/element.ts b/src/mol-geo/theme/structure/size/element.ts
index d18238c1275ceb109c13febb5f31339805d593d4..8bf99acc04942e56183eeb840b458222ac3668ad 100644
--- a/src/mol-geo/theme/structure/size/element.ts
+++ b/src/mol-geo/theme/structure/size/element.ts
@@ -4,14 +4,15 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ElementGroup, Element, Unit, Queries } from 'mol-model/structure';
+import { Element, Unit, Queries } from 'mol-model/structure';
import { StructureSizeDataProps } from '.';
import { createAttributeSize } from '../../../util/size-data';
/** Create attribute data with the size of an element, i.e. vdw for atoms and radius for coarse spheres */
export function elementSizeData(props: StructureSizeDataProps) {
- const { units, elementGroup, vertexMap } = props
- const unit = units[0]
+ const { group, vertexMap } = props
+ const unit = group.units[0]
+ const elements = group.elements;
let radius: Element.Property<number>
if (Unit.isAtomic(unit)) {
radius = Queries.props.atom.vdw_radius
@@ -22,7 +23,7 @@ export function elementSizeData(props: StructureSizeDataProps) {
l.unit = unit
return createAttributeSize({
sizeFn: (elementIdx: number) => {
- l.element = ElementGroup.getAt(elementGroup, elementIdx)
+ l.element = elements[elementIdx]
return radius(l)
},
vertexMap
diff --git a/src/mol-geo/theme/structure/size/index.ts b/src/mol-geo/theme/structure/size/index.ts
index 22caed502febf7ab0dd05a25201fe1c960335f07..325633c19204e2f927acacf8f753dfe28ba11cfc 100644
--- a/src/mol-geo/theme/structure/size/index.ts
+++ b/src/mol-geo/theme/structure/size/index.ts
@@ -4,12 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ElementGroup, Unit } from 'mol-model/structure';
+import { StructureSymmetry } from 'mol-model/structure';
import VertexMap from '../../../shape/vertex-map';
export interface StructureSizeDataProps {
- units: ReadonlyArray<Unit>,
- elementGroup: ElementGroup,
+ group: StructureSymmetry.UnitGroup,
vertexMap: VertexMap
}
diff --git a/src/mol-model/structure/structure.ts b/src/mol-model/structure/structure.ts
index 0a3826b643d288bcd12f81ef695a288a68b07f5a..c57bb2a47cb40b67ac59da9cd567439d728d49c7 100644
--- a/src/mol-model/structure/structure.ts
+++ b/src/mol-model/structure/structure.ts
@@ -7,6 +7,6 @@
import Element from './structure/element'
import Structure from './structure/structure'
import Unit from './structure/unit'
-import Symmetry from './structure/symmetry'
+import StructureSymmetry from './structure/symmetry'
-export { Element, Structure, Unit, Symmetry }
\ No newline at end of file
+export { Element, Structure, Unit, StructureSymmetry }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 35f92e9d687e733aa2750e2de9e0e93d1cd79fd9..b78827a9c7a7c4f1aec81c47c438b3f560ad5df0 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -8,37 +8,66 @@ import Structure from './structure'
import { Selection } from '../query'
import { ModelSymmetry } from '../model'
import { Task } from 'mol-task';
+import { SortedArray } from 'mol-data/int';
+import Unit from './unit';
+import { EquivalenceClasses } from 'mol-data/util';
-namespace Symmetry {
- export const buildAssembly = buildAssemblyImpl;
-}
+namespace StructureSymmetry {
+ // Units that have the same elements but differ with operator only.
+ export type UnitGroup = { readonly elements: SortedArray, readonly units: ReadonlyArray<Unit> }
+ export type TransformGroups = ReadonlyArray<UnitGroup>
-export default Symmetry;
+ export function buildAssembly(structure: Structure, name: string) {
+ return Task.create('Build Symmetry', async ctx => {
+ const models = Structure.getModels(structure);
+ if (models.length !== 1) throw new Error('Can only build assemblies from structures based on 1 model.');
-function buildAssemblyImpl(structure: Structure, name: string) {
- return Task.create('Build Symmetry', async ctx => {
- const models = Structure.getModels(structure);
- if (models.length !== 1) throw new Error('Can only build assemblies from structures based on 1 model.');
+ const assembly = ModelSymmetry.findAssembly(models[0], name);
+ if (!assembly) throw new Error(`Assembly '${name}' is not defined.`);
- const assembly = ModelSymmetry.findAssembly(models[0], name);
- if (!assembly) throw new Error(`Assembly '${name}' is not defined.`);
+ const assembler = Structure.Builder();
- const assembler = Structure.Builder();
+ for (const g of assembly.operatorGroups) {
+ const selection = await ctx.runChild(g.selector(structure));
+ if (Selection.structureCount(selection) === 0) {
+ continue;
+ }
+ const { units } = Selection.unionStructure(selection);
- for (const g of assembly.operatorGroups) {
- const selection = await ctx.runChild(g.selector(structure));
- if (Selection.structureCount(selection) === 0) {
- continue;
+ for (const oper of g.operators) {
+ for (const unit of units) {
+ assembler.addWithOperator(unit, oper);
+ }
+ }
}
- const { units } = Selection.unionStructure(selection);
- for (const oper of g.operators) {
- for (const unit of units) {
- assembler.addWithOperator(unit, oper);
- }
+ return assembler.getStructure();
+ });
+ }
+
+ export function getTransformGroups(s: Structure): StructureSymmetry.TransformGroups {
+ // group everything by the "invariantId"
+ const invariantGroups = EquivalenceClasses<number, Unit>(u => u.invariantId, (a, b) => a.invariantId === b.invariantId && a.model.id === b.model.id);
+ for (const u of s.units) invariantGroups.add(u.id, u);
+
+ const ret: UnitGroup[] = [];
+ // group everything by the "element array"
+ for (const group of invariantGroups.groups) {
+ const setGrouping = EquivalenceClasses<number, Unit>(u => SortedArray.hashCode(u.elements), (a, b) => SortedArray.areEqual(a.elements, b.elements));
+
+ for (const id of group) {
+ const unit = s.unitMap.get(id);
+ setGrouping.add(unit.id, unit);
+ }
+
+ for (const eqUnits of setGrouping.groups) {
+ const first = s.unitMap.get(eqUnits[0]);
+ ret.push({ elements: first.elements, units: eqUnits.map(id => s.unitMap.get(id)) });
}
}
- return assembler.getStructure();
- });
-}
\ No newline at end of file
+ return ret;
+ }
+}
+
+export default StructureSymmetry;
\ No newline at end of file
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 65608d08b1f7812b80e3387900899d95650192c9..dde9d8f7316ab84ee47203382f29479ff66b9ef9 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,7 +11,7 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, Element, Selection, Symmetry, Query } from 'mol-model/structure'
+import { Structure, Model, Queries as Q, Element, Selection, StructureSymmetry, Query } from 'mol-model/structure'
//import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
@@ -291,7 +291,7 @@ export namespace PropertyAccess {
export async function testAssembly(id: string, s: Structure) {
console.time('assembly')
- const a = await Run(Symmetry.buildAssembly(s, '1'));
+ const a = await Run(StructureSymmetry.buildAssembly(s, '1'));
console.timeEnd('assembly')
fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, a, true));
console.log('exported');