diff --git a/src/mol-data/structure/query/generators.ts b/src/mol-data/structure/query/generators.ts
index 0479437b9281dbc2bccdc17bfe12f1588a888ce3..a4ca33bd5ccf1c1e5707ad138fcbcf36d66df35a 100644
--- a/src/mol-data/structure/query/generators.ts
+++ b/src/mol-data/structure/query/generators.ts
@@ -5,8 +5,9 @@
*/
import Query from './query'
+import Selection from './selection'
import * as P from './properties'
-import { AtomSet, Atom } from '../structure'
+import { Structure, AtomSet, Atom } from '../structure'
import { OrderedSet, Segmentation } from 'mol-base/collections/integer'
export interface AtomGroupsSpec {
@@ -40,7 +41,7 @@ function atomGroupsLinear(atomTest: Atom.Predicate): Query {
const { atoms, units } = structure;
const unitIds = AtomSet.unitIds(atoms);
const l = Atom.Location();
- const builder = AtomSet.Builder(atoms);
+ const builder = AtomSet.LinearBuilder(atoms);
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
@@ -55,7 +56,7 @@ function atomGroupsLinear(atomTest: Atom.Predicate): Query {
builder.commitUnit(unitId);
}
- return { units, atoms: builder.getSet() };
+ return Structure.create(units, builder.getSet());
};
}
@@ -64,7 +65,7 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
const { atoms, units } = structure;
const unitIds = AtomSet.unitIds(atoms);
const l = Atom.Location();
- const builder = AtomSet.Builder(atoms);
+ const builder = AtomSet.LinearBuilder(atoms);
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
@@ -98,16 +99,60 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
builder.commitUnit(unitId);
}
- return { units, atoms: builder.getSet() };
+ return Structure.create(units, builder.getSet());
};
}
+class LinearGroupingBuilder {
+ private builders: AtomSet.Builder[] = [];
+ private builderMap: { [key: string]: AtomSet.Builder } = Object.create(null);
+
+ add(key: any, unit: number, atom: number) {
+ let b = this.builderMap[key];
+ if (!b) {
+ b = AtomSet.LinearBuilder(this.structure.atoms);
+ this.builders[this.builders.length] = b;
+ this.builderMap[key] = b;
+ }
+ b.add(unit, atom);
+ }
+
+ private allSingletons() {
+ for (let i = 0, _i = this.builders.length; i < _i; i++) {
+ if (this.builders[i].atomCount > 1) return false;
+ }
+ return true;
+ }
+
+ private singletonStructure(): Structure {
+ const atoms: Atom[] = Atom.createEmptyArray(this.builders.length);
+ for (let i = 0, _i = this.builders.length; i < _i; i++) {
+ atoms[i] = this.builders[i].singleton();
+ }
+ return Structure.create(this.structure.units, AtomSet.create(atoms));
+ }
+
+ private fullSelection() {
+ const ret: Structure[] = [];
+ for (let i = 0, _i = this.builders.length; i < _i; i++) {
+ ret[i] = Structure.create(this.structure.units, this.builders[i].getSet());
+ }
+ return ret;
+ }
+
+ getSelection(): Selection {
+ const len = this.builders.length;
+ if (len === 0) return Selection.Empty;
+ if (len === 1) return Structure.create(this.structure.units, this.builders[0].getSet());
+ if (this.allSingletons()) return this.singletonStructure();
+ return this.fullSelection();
+ }
+
+ constructor(private structure: Structure) { }
+}
+
function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomGroupsSpec): Query {
return structure => {
throw 'nyi'
};
-}
-
-// class LinearGroupingBuilder {
-
-// }
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-data/structure/query/selection.ts b/src/mol-data/structure/query/selection.ts
index 48f96ec4913b3c54ae091a98ffdb564c968d57e7..57700f93130819e001a66dd4ebb1b7f051426fee 100644
--- a/src/mol-data/structure/query/selection.ts
+++ b/src/mol-data/structure/query/selection.ts
@@ -27,20 +27,20 @@ namespace Selection {
if (!sel.length) return Structure.Empty;
const sets = [];
for (let i = 0, _i = sel.length; i < _i; i++) sets[sets.length] = sel[i].atoms;
- return { units: unionUnits(sel), atoms: AtomSet.unionMany(sets) };
+ return Structure.create(unionUnits(sel), AtomSet.unionMany(sets));
}
export function structures(sel: Selection): Iterator<Structure> {
if (isStructure(sel)) {
const units = sel.units;
- return Iterator.map<Atom, Structure>(AtomSet.atoms(sel.atoms), atoms => ({ units, atoms }));
+ return Iterator.map<Atom, Structure>(AtomSet.atoms(sel.atoms), atoms => Structure.create(units, atoms));
}
return Iterator.Array(sel);
}
export function getAt(sel: Selection, i: number): Structure {
if (isStructure(sel)) {
- return { units: sel.units, atoms: AtomSet.atomGetAt(sel.atoms, i) };
+ return Structure.create(sel.units, AtomSet.atomGetAt(sel.atoms, i));
}
return sel[i];
}
diff --git a/src/mol-data/structure/structure/atom.ts b/src/mol-data/structure/structure/atom.ts
index cdc5b1302c2922ff7efdd4c8d14824547853b360..2a5b1c0192e1f407224187ac47a5fc0515339d96 100644
--- a/src/mol-data/structure/structure/atom.ts
+++ b/src/mol-data/structure/structure/atom.ts
@@ -20,6 +20,8 @@ namespace Atom {
export const areEqual: (a: Atom, b: Atom) => boolean = Tuple.areEqual;
export const hashCode: (a: Atom) => number = Tuple.hashCode;
+ export function createEmptyArray(n: number): Atom[] { return new Float64Array(n) as any; }
+
/** All the information required to access atom properties */
export interface Location { unit: Unit, atom: number }
export function Location(): Location { return { unit: {} as any, atom: 0 }; }
diff --git a/src/mol-data/structure/structure/atom/set.ts b/src/mol-data/structure/structure/atom/set.ts
index 93a2177949c73603dce5ba069718101c90ecb1e4..6abe38108e98014014ece3185f83d18554de0560 100644
--- a/src/mol-data/structure/structure/atom/set.ts
+++ b/src/mol-data/structure/structure/atom/set.ts
@@ -7,7 +7,7 @@
import { OrderedSet, SortedArray, Iterator } from 'mol-base/collections/integer'
import Atom from '../atom'
import * as Impl from './set/impl'
-import createBuilder from './set/builder'
+import createBuilder, { Builder as AtomSetBuilder } from './set/builder'
/** A map-like representation of grouped atom set */
namespace AtomSet {
@@ -38,8 +38,9 @@ namespace AtomSet {
export const intersect: (a: AtomSet, b: AtomSet) => AtomSet = Impl.intersect as any;
export const subtract: (a: AtomSet, b: AtomSet) => AtomSet = Impl.subtract as any;
- export function SortedBuilder(parent: AtomSet) { return createBuilder(parent, true); }
- export function Builder(parent: AtomSet) { return createBuilder(parent, false); }
+ export type Builder = AtomSetBuilder
+ export function LinearBuilder(parent: AtomSet): Builder { return createBuilder(parent, true); }
+ export function UnsortedBuilder(parent: AtomSet): Builder { return createBuilder(parent, false); }
// TODO: bounding sphere
// TODO: distance, areWithIn?
diff --git a/src/mol-data/structure/structure/atom/set/builder.ts b/src/mol-data/structure/structure/atom/set/builder.ts
index 2d51dc9c5f7ae2a574695d52ebc84e06854065d7..bf756939e99e700d0e504770b1d3f11eb41177b2 100644
--- a/src/mol-data/structure/structure/atom/set/builder.ts
+++ b/src/mol-data/structure/structure/atom/set/builder.ts
@@ -5,14 +5,17 @@
*/
import AtomSet from '../set'
+import Atom from '../../atom'
import { OrderedSet } from 'mol-base/collections/integer'
import { sortArray } from 'mol-base/collections/sort'
-class Builder {
+export class Builder {
private keys: number[] = [];
private units: number[][] = Object.create(null);
private currentUnit: number[] = [];
+ atomCount = 0;
+
add(u: number, a: number) {
const unit = this.units[u];
if (!!unit) { unit[unit.length] = a; }
@@ -20,10 +23,11 @@ class Builder {
this.units[u] = [a];
this.keys[this.keys.length] = u;
}
+ this.atomCount++;
}
beginUnit() { this.currentUnit = this.currentUnit.length > 0 ? [] : this.currentUnit; }
- addToUnit(a: number) { this.currentUnit[this.currentUnit.length] = a; }
+ addToUnit(a: number) { this.currentUnit[this.currentUnit.length] = a; this.atomCount++; }
commitUnit(u: number) {
if (this.currentUnit.length === 0) return;
this.keys[this.keys.length] = u;
@@ -53,6 +57,11 @@ class Builder {
return allEqual ? this.parent : AtomSet.create(sets);
}
+ singleton(): Atom {
+ const u = this.keys[0];
+ return Atom.create(u, this.units[u][0]);
+ }
+
constructor(private parent: AtomSet, private sorted: boolean) { }
}
diff --git a/src/mol-data/structure/structure/atom/set/impl.ts b/src/mol-data/structure/structure/atom/set/impl.ts
index dbb0974826fc6cd440ec8fcdddc85350f596b741..8c0f2bcd4dfec8e3a2f57ecc92436254b19c2470 100644
--- a/src/mol-data/structure/structure/atom/set/impl.ts
+++ b/src/mol-data/structure/structure/atom/set/impl.ts
@@ -467,7 +467,7 @@ function unionN(sets: ArrayLike<AtomSetImpl>, eCount: { count: number }) {
eCount.count = countE;
if (!countN) return Empty;
if (countN === sets.length) return ofAtoms(sets as ArrayLike<Atom>);
- const packed = new Float64Array(countN);
+ const packed = Atom.createEmptyArray(countN);
let offset = 0;
for (let i = 0, _i = sets.length; i < _i; i++) {
const s = sets[i];
diff --git a/src/mol-data/structure/structure/structure.ts b/src/mol-data/structure/structure/structure.ts
index 8917e842b52a194f47f93176d566fc9eb484be2d..be0df65b59761a024b43690ce74350d164e62a40 100644
--- a/src/mol-data/structure/structure/structure.ts
+++ b/src/mol-data/structure/structure/structure.ts
@@ -18,6 +18,10 @@ interface Structure extends Readonly<{
namespace Structure {
export const Empty = { units: {}, atoms: AtomSet.Empty };
+ export function create(units: Structure['units'], atoms: AtomSet): Structure {
+ return { units, atoms };
+ }
+
export function ofData(format: Format) {
const models = Model.create(format);
return models.map(ofModel);
@@ -50,7 +54,7 @@ namespace Structure {
addUnit(unit: Unit) { this.units[unit.id] = unit; }
addAtoms(unitId: number, atoms: OrderedSet) { this.atoms[unitId] = atoms; this.atomCount += OrderedSet.size(atoms); }
- getStructure(): Structure { return this.atomCount > 0 ? { units: this.units, atoms: AtomSet.create(this.atoms) } : Empty; }
+ getStructure(): Structure { return this.atomCount > 0 ? Structure.create(this.units, AtomSet.create(this.atoms)) : Empty; }
}
export function Builder(): Builder { return new BuilderImpl(); }
diff --git a/src/perf-tests/sets.ts b/src/perf-tests/sets.ts
index 9a3461414e8b1da7e4ed2323c85c6e6a501fd517..76d8c03c7b003c8bd6ae9d38b65ab4ea8b9bb8fb 100644
--- a/src/perf-tests/sets.ts
+++ b/src/perf-tests/sets.ts
@@ -200,7 +200,7 @@ export namespace Union {
export namespace Build {
function createSorted() {
- const b = AtomSet.SortedBuilder(AtomSet.Empty);
+ const b = AtomSet.LinearBuilder(AtomSet.Empty);
for (let i = 0; i < 10; i++) {
for (let j = 0; j < 1000; j++) {
b.add(i, j);
@@ -210,7 +210,7 @@ export namespace Build {
}
function createByUnit() {
- const b = AtomSet.SortedBuilder(AtomSet.Empty);
+ const b = AtomSet.LinearBuilder(AtomSet.Empty);
for (let i = 0; i < 10; i++) {
b.beginUnit();
for (let j = 0; j < 1000; j++) {
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 23300ac6a0e8545075ea87e8e25ee39a79e2f987..331b46ebfee5b7c745474826cfbe178e2fb1f3c9 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -236,7 +236,7 @@ export namespace PropertyAccess {
export async function run() {
const { structures, models } = await readCIF('./examples/1cbs_full.bcif');
- //const { structures, models } = await readCIF('e:/test/quick/3j3q_full.bcif');
+ //const { structures, models } = await readCIF('e:/test/quick/1jj2_full.bcif');
//const { structures, models } = await readCIF('e:/test/quick/3j3q_updated.cif');
console.log('parsed');