From 138c943f6efc47c2c3363b9f0dbd40e2258224df Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 9 May 2018 15:42:43 +0200
Subject: [PATCH] Structure data model tweaks
---
src/mol-data/util/equivalence-classes.ts | 7 ++--
src/mol-geo/representation/structure/index.ts | 6 +--
src/mol-geo/representation/structure/point.ts | 4 +-
.../representation/structure/spacefill.ts | 4 +-
src/mol-geo/representation/structure/utils.ts | 8 ++--
src/mol-geo/theme/structure/color/index.ts | 4 +-
src/mol-geo/theme/structure/size/index.ts | 4 +-
.../structure/structure/structure.ts | 10 ++++-
src/mol-model/structure/structure/symmetry.ts | 39 +++++++++----------
src/mol-model/structure/structure/unit.ts | 15 ++++---
src/perf-tests/structure.ts | 9 ++++-
11 files changed, 59 insertions(+), 51 deletions(-)
diff --git a/src/mol-data/util/equivalence-classes.ts b/src/mol-data/util/equivalence-classes.ts
index e40456499..cfad84f04 100644
--- a/src/mol-data/util/equivalence-classes.ts
+++ b/src/mol-data/util/equivalence-classes.ts
@@ -17,6 +17,7 @@ class EquivalenceClassesImpl<K, V> {
return { id, keys, value };
}
+ // Return the group representative.
add(key: K, a: V) {
const hash = this.getHash(a);
if (this.byHash.has(hash)) {
@@ -25,16 +26,16 @@ class EquivalenceClassesImpl<K, V> {
const group = groups[i];
if (this.areEqual(a, group.value)) {
group.keys[group.keys.length] = key;
- return group.id;
+ return group.value;
}
}
const group = this.createGroup(key, a);
groups[groups.length] = group;
- return group.id;
+ return group.value;
} else {
const group = this.createGroup(key, a);
this.byHash.set(hash, [group]);
- return group.id;
+ return group.value;
}
}
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index 9caee1437..774ea8b07 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Structure, StructureSymmetry } from 'mol-model/structure';
+import { Structure, StructureSymmetry, Unit } from 'mol-model/structure';
import { Task } from 'mol-task'
import { RenderObject } from 'mol-gl/scene';
import { Representation, RepresentationProps } from '..';
@@ -14,7 +14,7 @@ import { Representation, RepresentationProps } from '..';
export interface UnitsRepresentation<P> {
renderObjects: ReadonlyArray<RenderObject>
- create: (group: StructureSymmetry.UnitGroup, props: P) => Task<void>
+ create: (group: Unit.SymmetryGroup, props: P) => Task<void>
update: (props: P) => Task<boolean>
}
@@ -26,7 +26,7 @@ export interface StructureRepresentation<P extends RepresentationProps = {}> ext
interface GroupRepresentation<T> {
repr: UnitsRepresentation<T>
- group: StructureSymmetry.UnitGroup
+ group: Unit.SymmetryGroup
}
export function StructureRepresentation<P>(reprCtor: () => UnitsRepresentation<P>): StructureRepresentation<P> {
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
index becee521f..5828e518c 100644
--- a/src/mol-geo/representation/structure/point.ts
+++ b/src/mol-geo/representation/structure/point.ts
@@ -7,7 +7,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createPointRenderObject, RenderObject, PointRenderObject } from 'mol-gl/scene'
-import { Unit, Element, StructureSymmetry } from 'mol-model/structure';
+import { Unit, Element } from 'mol-model/structure';
import { Task } from 'mol-task'
import { fillSerial } from 'mol-gl/renderable/util';
@@ -55,7 +55,7 @@ export default function Point(): UnitsRepresentation<PointProps> {
return {
renderObjects,
- create(group: StructureSymmetry.UnitGroup, props: PointProps = {}) {
+ create(group: Unit.SymmetryGroup, props: PointProps = {}) {
return Task.create('Point.create', async ctx => {
renderObjects.length = 0 // clear
curProps = { ...DefaultPointProps, ...props }
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 5dd62f7f9..1946f8103 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -10,7 +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 { Unit, Element, Queries, StructureSymmetry } from 'mol-model/structure';
+import { Unit, Element, Queries } from 'mol-model/structure';
import { UnitsRepresentation } from './index';
import { Task } from 'mol-task'
import { MeshBuilder } from '../../shape/mesh-builder';
@@ -77,7 +77,7 @@ export default function Spacefill(): UnitsRepresentation<SpacefillProps> {
return {
renderObjects,
- create(group: StructureSymmetry.UnitGroup, props: SpacefillProps = {}) {
+ create(group: Unit.SymmetryGroup, props: SpacefillProps = {}) {
return Task.create('Spacefill.create', async ctx => {
renderObjects.length = 0 // clear
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index 920159d1a..c7cd81d17 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { StructureSymmetry } from 'mol-model/structure';
+import { Unit } from 'mol-model/structure';
import { Mat4 } from 'mol-math/linear-algebra'
import { createUniformColor } from '../../util/color-data';
@@ -15,7 +15,7 @@ import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
-export function createTransforms({ units }: StructureSymmetry.UnitGroup) {
+export function createTransforms({ units }: Unit.SymmetryGroup) {
const unitCount = units.length
const transforms = new Float32Array(unitCount * 16)
for (let i = 0; i < unitCount; i++) {
@@ -24,7 +24,7 @@ export function createTransforms({ units }: StructureSymmetry.UnitGroup) {
return transforms
}
-export function createColors(group: StructureSymmetry.UnitGroup, vertexMap: VertexMap, props: ColorTheme) {
+export function createColors(group: Unit.SymmetryGroup, vertexMap: VertexMap, props: ColorTheme) {
switch (props.name) {
case 'atom-index':
return elementIndexColorData({ group, vertexMap })
@@ -39,7 +39,7 @@ export function createColors(group: StructureSymmetry.UnitGroup, vertexMap: Vert
}
}
-export function createSizes(group: StructureSymmetry.UnitGroup, vertexMap: VertexMap, props: SizeTheme) {
+export function createSizes(group: Unit.SymmetryGroup, vertexMap: VertexMap, props: SizeTheme) {
switch (props.name) {
case 'uniform':
return createUniformSize(props)
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index f03f0e9e5..9e0d0318d 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -4,11 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { StructureSymmetry } from 'mol-model/structure';
+import { Unit } from 'mol-model/structure';
import VertexMap from '../../../shape/vertex-map';
export interface StructureColorDataProps {
- group: StructureSymmetry.UnitGroup,
+ group: Unit.SymmetryGroup,
vertexMap: VertexMap
}
diff --git a/src/mol-geo/theme/structure/size/index.ts b/src/mol-geo/theme/structure/size/index.ts
index 325633c19..0c18ca93e 100644
--- a/src/mol-geo/theme/structure/size/index.ts
+++ b/src/mol-geo/theme/structure/size/index.ts
@@ -4,11 +4,11 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { StructureSymmetry } from 'mol-model/structure';
+import { Unit } from 'mol-model/structure';
import VertexMap from '../../../shape/vertex-map';
export interface StructureSizeDataProps {
- group: StructureSymmetry.UnitGroup,
+ group: Unit.SymmetryGroup,
vertexMap: VertexMap
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 8c7c500ab..c2a2ecd38 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -12,6 +12,7 @@ import { sortArray, sort, arraySwap, hash1 } from 'mol-data/util';
import Element from './element'
import Unit from './unit'
import { StructureLookup3D } from './util/lookup3d';
+import StructureSymmetry from './symmetry';
class Structure {
readonly unitMap: IntMap<Unit>;
@@ -184,6 +185,8 @@ namespace Structure {
const newUnits: Unit[] = [];
sortArray(this.ids);
+ const symmGroups = StructureSymmetry.UnitEquivalenceBuilder();
+
for (let i = 0, _i = this.ids.length; i < _i; i++) {
const id = this.ids[i];
const parent = this.parent.unitMap.get(id);
@@ -194,13 +197,16 @@ namespace Structure {
// if the length is the same, just copy the old unit.
if (unit.length === parent.elements.length) {
newUnits[newUnits.length] = parent;
+ symmGroups.add(parent.id, parent);
continue;
}
if (!this.isSorted && l > 1) sortArray(unit);
- // TODO: checking if two units are equal in the same symmetry group to reuse computed properties.
- newUnits[newUnits.length] = parent.getChild(SortedArray.ofSortedArray(unit));
+ let child = parent.getChild(SortedArray.ofSortedArray(unit));
+ const pivot = symmGroups.add(child.id, child);
+ if (child !== pivot) child = pivot.applyOperator(child.id, child.conformation.operator, true);
+ newUnits[newUnits.length] = child;
}
return create(newUnits);
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index b78827a9c..2bf71bda6 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -10,13 +10,9 @@ 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';
+import { EquivalenceClasses, hash2 } from 'mol-data/util';
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 function buildAssembly(structure: Structure, name: string) {
return Task.create('Build Symmetry', async ctx => {
const models = Structure.getModels(structure);
@@ -45,25 +41,26 @@ namespace StructureSymmetry {
});
}
- 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);
+ function hashUnit(u: Unit) {
+ return hash2(u.invariantId, SortedArray.hashCode(u.elements));
+ }
- 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));
+ function areUnitsEquivalent(a: Unit, b: Unit) {
+ return a.invariantId === b.invariantId && a.model.id === b.model.id && SortedArray.areEqual(a.elements, b.elements);
+ }
- for (const id of group) {
- const unit = s.unitMap.get(id);
- setGrouping.add(unit.id, unit);
- }
+ export function UnitEquivalenceBuilder() {
+ return EquivalenceClasses<number, Unit>(hashUnit, areUnitsEquivalent);
+ }
- 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)) });
- }
+ export function getTransformGroups(s: Structure): ReadonlyArray<Unit.SymmetryGroup> {
+ const groups = UnitEquivalenceBuilder();
+ for (const u of s.units) groups.add(u.id, u);
+
+ const ret: Unit.SymmetryGroup[] = [];
+ for (const eqUnits of groups.groups) {
+ const first = s.unitMap.get(eqUnits[0]);
+ ret.push({ elements: first.elements, units: eqUnits.map(id => s.unitMap.get(id)) });
}
return ret;
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 87bff5672..15a85c646 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -32,9 +32,8 @@ namespace Unit {
}
}
- export function applyOperator(id: number, unit: Unit, operator: SymmetryOperator): Unit {
- return create(id, unit.kind, unit.model, SymmetryOperator.compose(unit.conformation.operator, operator), unit.elements);
- }
+ // A group of units that differ only by symmetry operators.
+ export type SymmetryGroup = { readonly elements: SortedArray, readonly units: ReadonlyArray<Unit> }
export interface Base {
readonly id: number,
@@ -45,7 +44,7 @@ namespace Unit {
readonly conformation: SymmetryOperator.ArrayMapping,
getChild(elements: SortedArray): Unit,
- applyOperator(id: number, operator: SymmetryOperator): Unit,
+ applyOperator(id: number, operator: SymmetryOperator, dontCompose?: boolean /* = false */): Unit,
readonly lookup3d: Lookup3D
}
@@ -77,8 +76,8 @@ namespace Unit {
return new Atomic(this.id, this.invariantId, this.model, elements, this.conformation);
}
- applyOperator(id: number, operator: SymmetryOperator): Unit {
- const op = SymmetryOperator.compose(this.conformation.operator, operator);
+ applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
+ const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
return new Atomic(id, this.invariantId, this.model, this.elements, SymmetryOperator.createMapping(op, this.model.atomSiteConformation));
}
@@ -129,8 +128,8 @@ namespace Unit {
return createCoarse(this.id, this.invariantId, this.model, this.kind, this.sites, elements, this.conformation);
}
- applyOperator(id: number, operator: SymmetryOperator): Unit {
- const op = SymmetryOperator.compose(this.conformation.operator, operator);
+ applyOperator(id: number, operator: SymmetryOperator, dontCompose = false): Unit {
+ const op = dontCompose ? operator : SymmetryOperator.compose(this.conformation.operator, operator);
return createCoarse(id, this.invariantId, this.model, this.kind, this.sites, this.elements, SymmetryOperator.createMapping(op, this.sites));
}
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index dde9d8f73..d8e1037a9 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -292,8 +292,13 @@ export namespace PropertyAccess {
export async function testAssembly(id: string, s: Structure) {
console.time('assembly')
const a = await Run(StructureSymmetry.buildAssembly(s, '1'));
+ //const auth_comp_id = Q.props.residue.auth_comp_id;
+ //const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
+ //const alas = await query(q1, a);
+
console.timeEnd('assembly')
fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, a, true));
+ //fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, Selection.unionStructure(alas), true));
console.log('exported');
}
@@ -404,8 +409,8 @@ export namespace PropertyAccess {
//.add('test q', () => q1(structures[0]))
//.add('test q', () => q(structures[0]))
.add('test int', () => sumProperty(structures[0], l => col(l.element)))
- .add('test q1', async () => await q1(structures[0]))
- .add('test q3', async () => await q3(structures[0]))
+ .add('test q1', async () => await query(q1, structures[0]))
+ .add('test q3', async () => await query(q3, structures[0]))
// .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))
// .add('baseline', () => baseline(models[0]))
--
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