How to use uniqueArrayBuilder method in fast-check-monorepo

Best JavaScript code snippet using fast-check-monorepo

modifiers.ts

Source:modifiers.ts Github

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1/*2 * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.3 *4 * @author David Sehnal <david.sehnal@gmail.com>5 */6import Environment from '../environment'7import Expression from '../expression'8import Context from '../context'9import AtomSet from '../../data/atom-set'10import AtomSelection from '../../data/atom-selection'11import { UniqueArrayBuilder, sortAsc, FastSet, FastMap } from '../../../utils/collections'12import Mask from '../../../utils/mask'13import { Model, Bonds } from '../../../structure/data'14import ElementAddress from '../../data/element-address'15import BondAddress from '../../data/bond-address'16import { defaultBondTest, testBond, BondTest, maxAtomValueInSelection } from './common'17import AtomSetIt = AtomSet.Iterator18type Selection = Expression<AtomSelection>19export function queryEach(env: Environment, selection: Selection, query: Selection): AtomSelection {20 const builder = AtomSelection.uniqueBuilder();21 for (const atomSet of AtomSelection.atomSets(selection(env))){22 const ctx = Context.ofAtomSet(env.context, atomSet);23 for (const mappedAtomSet of AtomSelection.atomSets(query(Environment(ctx)))) {24 builder.add(mappedAtomSet);25 }26 }27 return builder.getSelection();28}29export function intersectBy(env: Environment, selection: Selection, by: Selection): AtomSelection {30 const mask = AtomSelection.getMask(by(env));31 const builder = AtomSelection.uniqueBuilder();32 const it = AtomSetIt();33 for (const atomSet of AtomSelection.atomSets(selection(env))) {34 let count = 0;35 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {36 if (mask.has(a)) count++;37 }38 if (!count) continue;39 const intersection = new Int32Array(count);40 let offset = 0;41 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {42 if (mask.has(a)) intersection[offset++] = a;43 }44 builder.add(AtomSet(intersection));45 }46 return builder.getSelection();47}48export function exceptBy(env: Environment, selection: Selection, by: Selection): AtomSelection {49 const mask = AtomSelection.getMask(by(env));50 const builder = AtomSelection.uniqueBuilder();51 const it = AtomSetIt();52 for (const atomSet of AtomSelection.atomSets(selection(env))) {53 let count = 0;54 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {55 if (!mask.has(a)) count++;56 }57 if (!count) continue;58 const complement = new Int32Array(count);59 let offset = 0;60 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {61 if (!mask.has(a)) complement[offset++] = a;62 }63 builder.add(AtomSet(complement));64 }65 return builder.getSelection();66}67export function unionBy(env: Environment, selection: Selection, by: Selection): AtomSelection {const atomCount = env.context.model.atoms.count;68 const atomSets = AtomSelection.atomSets(selection(env));69 const glue = by(env);70 const occurenceCount = new Int32Array(atomCount);71 const it = AtomSetIt();72 for (const atomSet of atomSets) {73 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {74 occurenceCount[a]++;75 }76 }77 let totalOccurences = 0;78 const occurentOffsets = new Int32Array(atomCount);79 let offset = 0;80 for (const oc of occurenceCount as any as number[]) {81 occurentOffsets[offset++] = totalOccurences;82 totalOccurences += oc;83 }84 let setIndex = 0;85 const atomMap = new Int32Array(totalOccurences);86 const atomFill = new Int32Array(atomCount);87 for (const atomSet of atomSets) {88 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {89 offset = occurentOffsets[a] + atomFill[a];90 atomFill[a]++;91 atomMap[offset] = setIndex;92 }93 setIndex++;94 }95 const builder = AtomSelection.uniqueBuilder();96 for (const glueSet of AtomSelection.atomSets(glue)) {97 const toGlue = UniqueArrayBuilder<number>();98 for (let a = AtomSetIt.start(it, glueSet); !it.done; a = it.next().value) {99 const o = occurentOffsets[a];100 for (let i = 0, _i = occurenceCount[a]; i < _i; i++) {101 const key = atomMap[o + i];102 UniqueArrayBuilder.add(toGlue, key, key);103 }104 }105 const indices = UniqueArrayBuilder<number>();106 for (const atomSetIndex of toGlue.array) {107 for (let a = AtomSetIt.start(it, atomSets[atomSetIndex]); !it.done; a = it.next().value) {108 UniqueArrayBuilder.add(indices, a, a);109 }110 }111 builder.add(AtomSet(sortAsc(indices.array)));112 }113 return builder.getSelection();114}115export function union(env: Environment, selection: Selection): AtomSelection {116 const sel = selection(env);117 if (!AtomSelection.atomSets(sel).length) return AtomSelection.empty;118 return AtomSelection([AtomSet(AtomSelection.getAtomIndices(selection(env)))]);119}120export interface ClusterParams {121 selection: Selection,122 minDist?: Expression<number>,123 maxDist: Expression<number>,124 minSize?: Expression<number>,125 maxSize?: Expression<number>126}127interface ClusterCtx {128 minDist: number,129 maxDist: number,130 minSize: number,131 maxSize: number,132 selection: AtomSelection,133 builder: AtomSelection.Builder,134 model: Model135}136function clusterAround(ctx: ClusterCtx, a: AtomSet, included: number[], candidates: number[]) {137 const depth = included.length;138 if (depth >= ctx.minSize) {139 ctx.builder.add(a);140 }141 if (depth >= ctx.maxSize || depth >= candidates.length) {142 return;143 }144 const { minDist, maxDist } = ctx;145 const atomSets = AtomSelection.atomSets(ctx.selection);146 const lastIncluded = included[included.length - 1];147 for (const bI of candidates) {148 if (bI <= lastIncluded) continue;149 const b = atomSets[bI];150 let canInclude = true;151 for (const iI of included) {152 const dist = AtomSet.distance(ctx.model, b, atomSets[iI]);153 if (dist < minDist || dist > maxDist) {154 canInclude = false;155 break;156 }157 }158 if (!canInclude) continue;159 included.push(bI);160 clusterAround(ctx, AtomSet.union(a, b), included, candidates);161 included.pop();162 }163}164function _cluster(ctx: ClusterCtx) {165 let i = 0;166 const lookup = AtomSelection.lookup3d(ctx.model, ctx.selection);167 for (const atomSet of AtomSelection.atomSets(ctx.selection)) {168 const candidates = lookup.queryAtomSet(atomSet, ctx.maxDist);169 sortAsc(candidates);170 clusterAround(ctx, atomSet, [i], candidates);171 i++;172 }173}174export function cluster(env: Environment, params: ClusterParams): AtomSelection {175 const cCtx: ClusterCtx = {176 selection: params.selection(env),177 minDist: (params.minDist && params.minDist(env)) || 0,178 maxDist: (params.maxDist && params.maxDist(env)),179 minSize: Math.max((params.minSize && params.minSize(env)) || 2, 2),180 maxSize: (params.maxSize && params.maxSize(env)) || Number.POSITIVE_INFINITY,181 builder: AtomSelection.linearBuilder(),182 model: env.context.model183 };184 _cluster(cCtx);185 return cCtx.builder.getSelection();186}187export interface IncludeSurroundingsParams {188 selection: Selection,189 radius: Expression<number>,190 atomRadius?: Expression<number>,191 wholeResidues?: Expression<boolean>192}193interface IncludeSurroundingsContext {194 env: Environment,195 selection: AtomSelection,196 radius: number,197 atomRadius: Expression<number>,198 wholeResidues: boolean199}200function _zeroRadius(env: Environment) { return 0; }201function includeSurroundingsNoRadius(ctx: IncludeSurroundingsContext) {202 const { env, selection, radius: r, wholeResidues } = ctx;203 const { model, mask } = env.context;204 const findWithin = Model.spatialLookup(model).find(mask);205 const { x, y, z } = model.positions;206 const { residueIndex } = model.atoms;207 const { atomOffset } = model.residues;208 const builder = AtomSelection.uniqueBuilder();209 const includedResides = FastSet.create<number>();210 const it = AtomSetIt();211 for (const atomSet of AtomSelection.atomSets(selection)) {212 const atoms = UniqueArrayBuilder<number>();213 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {214 const { count, indices } = findWithin(x[a], y[a], z[a], r);215 for (let i = 0, _i = count; i < _i; i++) {216 const b = indices[i];217 if (wholeResidues) {218 const rI = residueIndex[b];219 if (includedResides.has(rI)) continue;220 includedResides.add(rI);221 for (let j = atomOffset[rI], _j = atomOffset[rI + 1]; j < _j; j++) {222 if (!mask.has(j)) continue;223 UniqueArrayBuilder.add(atoms, j, j);224 }225 } else {226 UniqueArrayBuilder.add(atoms, b, b);227 }228 }229 }230 builder.add(AtomSet(sortAsc(atoms.array)));231 }232 return builder.getSelection();233}234function includeSurroundingsWithRadius(ctx: IncludeSurroundingsContext) {235 const { env, selection, radius, wholeResidues, atomRadius } = ctx;236 const { model, mask } = env.context;237 const findWithin = Model.spatialLookup(model).find(mask);238 const { x, y, z } = model.positions;239 const { residueIndex } = model.atoms;240 const { atomOffset } = model.residues;241 const builder = AtomSelection.uniqueBuilder();242 const includedResides = FastSet.create<number>();243 const maxSelectionAtomRadius = maxAtomValueInSelection(env, selection, atomRadius);244 Environment.lockSlot(env, 'element');245 const element = env.slots.element;246 let maxStructureAtomRadius = 0;247 for (let i = 0, _i = model.atoms.count; i < _i; i++) {248 if (!mask.has(i)) continue;249 ElementAddress.setAtom(model, element, i);250 const r = atomRadius(env);251 if (r > maxStructureAtomRadius) maxStructureAtomRadius = r;252 }253 const extendedRadius = radius + maxSelectionAtomRadius + maxStructureAtomRadius;254 const it = AtomSetIt();255 for (const atomSet of AtomSelection.atomSets(selection)) {256 const atoms = UniqueArrayBuilder<number>();257 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {258 const { count, indices, squaredDistances } = findWithin(x[a], y[a], z[a], extendedRadius);259 ElementAddress.setAtom(model, element, a);260 const rA = atomRadius(env);261 for (let i = 0, _i = count; i < _i; i++) {262 const b = indices[i];263 ElementAddress.setAtom(model, element, b);264 const rB = atomRadius(env);265 if (Math.sqrt(squaredDistances[i]) - rA - rB > radius) continue;266 if (wholeResidues) {267 const rI = residueIndex[b];268 if (includedResides.has(rI)) continue;269 includedResides.add(rI);270 for (let j = atomOffset[rI], _j = atomOffset[rI + 1]; j < _j; j++) {271 if (!mask.has(j)) continue;272 UniqueArrayBuilder.add(atoms, j, j);273 }274 } else {275 UniqueArrayBuilder.add(atoms, b, b);276 }277 }278 }279 builder.add(AtomSet(sortAsc(atoms.array)));280 }281 Environment.unlockSlot(env, 'element');282 return builder.getSelection();283}284export function includeSurroundings(env: Environment, params: IncludeSurroundingsParams): AtomSelection {285 const ctx: IncludeSurroundingsContext = {286 env,287 selection: params.selection(env),288 radius: params.radius(env),289 atomRadius: params.atomRadius || _zeroRadius,290 wholeResidues: params.wholeResidues ? params.wholeResidues(env) : false291 };292 if (ctx.atomRadius === _zeroRadius) {293 return includeSurroundingsNoRadius(ctx);294 } else {295 return includeSurroundingsWithRadius(ctx);296 }297}298interface ExpandConnectedCtx {299 env: Environment,300 model: Model,301 bonds: Bonds,302 mask: Mask,303 slot: BondAddress,304 test: BondTest,305 it: AtomSetIt306}307function _expandFrontierAtoms({ env, mask, bonds, test, slot }: ExpandConnectedCtx, frontier: number[], atoms: UniqueArrayBuilder<number>) {308 const newFrontier: number[] = [];309 const { neighbor, offset: bondAtomOffset, order, flags } = bonds;310 for (const a of frontier) {311 const start = bondAtomOffset[a], end = bondAtomOffset[a + 1];312 for (let i = start; i < end; i++) {313 const b = neighbor[i];314 if (mask.has(b) && testBond(env, slot, a, b, order[i], flags[i], test) && UniqueArrayBuilder.add(atoms, b, b)) newFrontier[newFrontier.length] = b;315 }316 }317 return newFrontier;318}319function _expandAtoms(ctx: ExpandConnectedCtx, atomSet: AtomSet, numLayers: number) {320 if (!numLayers) return atomSet;321 const result = UniqueArrayBuilder<number>();322 let frontier: number[] = [];323 const { it } = ctx;324 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {325 frontier[frontier.length] = a;326 }327 for (const a of frontier) UniqueArrayBuilder.add(result, a, a);328 for (let i = 0; i < numLayers; i++) {329 frontier = _expandFrontierAtoms(ctx, frontier, result);330 }331 sortAsc(result.array);332 return AtomSet(result.array);333}334function _expandFrontierResidues({ env, model, mask, bonds, test, slot }: ExpandConnectedCtx, frontier: number[], residues: UniqueArrayBuilder<number>) {335 const newFrontier: number[] = [];336 const { neighbor, offset: bondAtomOffset, order, flags } = bonds;337 const { atomOffset } = model.residues;338 const { residueIndex } = model.atoms;339 for (const rI of frontier) {340 for (let a = atomOffset[rI], _a = atomOffset[rI + 1]; a < _a; a++) {341 if (!mask.has(a)) continue;342 const start = bondAtomOffset[a], end = bondAtomOffset[a + 1];343 for (let i = start; i < end; i++) {344 const b = neighbor[i];345 if (!mask.has(b)) continue;346 const r = residueIndex[b];347 if (testBond(env, slot, a, b, order[i], flags[i], test) && UniqueArrayBuilder.add(residues, r, r)) newFrontier[newFrontier.length] = r;348 }349 }350 }351 return newFrontier;352}353function _expandResidues(ctx: ExpandConnectedCtx, atomSet: AtomSet, numLayers: number) {354 if (!numLayers) return atomSet;355 const { atomOffset } = ctx.model.residues;356 const { residueIndex } = ctx.model.atoms;357 const residues = UniqueArrayBuilder<number>();358 let frontier: number[] = [];359 const { mask, it } = ctx360 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {361 const rI = residueIndex[a];362 if (UniqueArrayBuilder.add(residues, rI, rI)) frontier[frontier.length] = rI;363 }364 for (let i = 0; i < numLayers; i++) {365 frontier = _expandFrontierResidues(ctx, frontier, residues);366 }367 sortAsc(residues.array);368 const atoms: number[] = [];369 for (let rI of residues.array) {370 for (let a = atomOffset[rI], _a = atomOffset[rI + 1]; a < _a; a++) {371 if (mask.has(a)) atoms[atoms.length] = a;372 }373 }374 return AtomSet(atoms);375}376export interface IncludeConnectedParams {377 selection: Selection,378 bondTest?: Expression<boolean>,379 layerCount?: Expression<number>,380 wholeResidues?: Expression<boolean>381}382export function includeConnected(env: Environment, { selection, layerCount, wholeResidues, bondTest }: IncludeConnectedParams): AtomSelection {383 const src = selection(env);384 const { model, mask } = env.context;385 const bonds = Model.bonds(model);386 const numLayers = Math.max(0, layerCount ? layerCount(env) : 1);387 const asResidues = !!wholeResidues && !!wholeResidues(env);388 const test = bondTest || defaultBondTest;389 const builder = AtomSelection.uniqueBuilder();390 Environment.lockSlot(env, 'bond');391 const ctx: ExpandConnectedCtx = {392 env,393 bonds,394 model,395 mask,396 slot: env.slots.bond,397 test,398 it: AtomSetIt()399 };400 for (const atomSet of AtomSelection.atomSets(src)) {401 if (asResidues) builder.add(_expandResidues(ctx, atomSet, numLayers));402 else builder.add(_expandAtoms(ctx, atomSet, numLayers));403 }404 Environment.unlockSlot(env, 'bond');405 return builder.getSelection();406}407export function expandProperty(env: Environment, selection: Selection, property: Expression<any>): AtomSelection {408 const { context } = env;409 const src = selection(env);410 const propertyToSetMap: FastMap<any, UniqueArrayBuilder<number>> = FastMap.create();411 Environment.lockSlot(env, 'element');412 const element = env.slots.element;413 let index = 0;414 const sets: number[][] = [];415 const it = AtomSetIt();416 for (const atomSet of AtomSelection.atomSets(src)) {417 for (let a = AtomSetIt.start(it, atomSet); !it.done; a = it.next().value) {418 ElementAddress.setAtom(context.model, element, a);419 const p = property(env);420 if (propertyToSetMap.has(p)) UniqueArrayBuilder.add(propertyToSetMap.get(p)!, index, index);421 else {422 const ub = UniqueArrayBuilder<number>();423 UniqueArrayBuilder.add(ub, index, index);424 propertyToSetMap.set(p, ub);425 }426 }427 sets[index] = [];428 index++;429 }430 const { mask } = context;431 for (let i = 0, _i = context.model.atoms.count; i < _i; i++) {432 if (!mask.has(i)) continue;433 ElementAddress.setAtom(context.model, element, i);434 const p = property(env);435 if (!propertyToSetMap.has(p)) continue;436 for (const setIndex of propertyToSetMap.get(p)!.array) sets[setIndex].push(i);437 }438 Environment.unlockSlot(env, 'element');439 const builder = AtomSelection.uniqueBuilder();440 for (const set of sets) builder.add(AtomSet(set));441 return builder.getSelection();...

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atom-set.ts

Source:atom-set.ts Github

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1/*2 * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.3 *4 * @author David Sehnal <david.sehnal@gmail.com>5 */6import { sortAsc, UniqueArrayBuilder } from '../../utils/collections'7import { Model } from '../../structure/data'8import Mask from '../../utils/mask'9type AtomSet = number | ArrayAtomSet10function AtomSet(indices: number | ArrayLike<number>): AtomSet {11 if (typeof indices === 'number') return indices;12 if (indices.length === 1) return indices[0];13 return ArrayAtomSet(indices as ReadonlyArray<number>);14}15interface ArrayAtomSet {16 atomIndices: ReadonlyArray<number>17 hashCodeComputed: boolean,18 hashCode: number,19 //hierarchy: { residueIndices: number[], chainIndices: number[], entityIndices: number[] } | undefined,20 boundingSphere: { center: [number, number, number], radius: number } | undefined21}22function ArrayAtomSet(indices: ArrayLike<number>): ArrayAtomSet {23 return {24 atomIndices: indices as ReadonlyArray<number>,25 hashCode: 0,26 hashCodeComputed: false,27 boundingSphere: void 028 };29}30namespace AtomSet {31 export interface Iterator {32 [Symbol.iterator](): Iterator,33 done: boolean;34 value: number;35 next(): { done: boolean, value: number }36 reset(atomSet: AtomSet): Iterator;37 }38 class IteratorImpl implements Iterator {39 done = true;40 value = 0;41 private atomSet: AtomSet = void 0 as any;42 private index: number = -1;43 private length: number = 0;44 [Symbol.iterator]() { return this };45 next() {46 const index = ++this.index;47 if (typeof this.atomSet === 'number') {48 this.done = this.index > 0;49 } else {50 if (index >= this.length) {51 this.done = true;52 } else {53 this.value = this.atomSet.atomIndices[index];54 }55 }56 return this;57 }58 reset(atomSet: AtomSet) {59 if (typeof atomSet === 'number') {60 this.value = atomSet;61 this.length = 1;62 } else {63 const ind = atomSet.atomIndices;64 this.value = ind[0];65 this.length = ind.length;66 }67 this.done = false;68 this.atomSet = atomSet;69 this.index = -1;70 return this;71 }72 }73 export function Iterator(): Iterator { return new IteratorImpl(); }74 export namespace Iterator {75 export function start(it: Iterator, atomSet: AtomSet) { return it.reset(atomSet).next().value; }76 }77 export function count(a: AtomSet) {78 return typeof a === 'number' ? 1 : a.atomIndices.length;79 }80 export function toIndices(a: AtomSet): ReadonlyArray<number> {81 return typeof a === 'number' ? [a] : a.atomIndices;82 }83 export function getMask(a: AtomSet) {84 return typeof a === 'number' ? Mask.singleton(a) : Mask.ofUniqueIndices(a.atomIndices);85 }86 const itA = Iterator(), itB = Iterator();87 export function areEqual(a: AtomSet, b: AtomSet) {88 const cnt = count(a);89 if (cnt !== count(b)) return false;90 Iterator.start(itA, a);91 Iterator.start(itB, b);92 for (let i = 0; i < cnt; i++) {93 if (itA.value !== itB.value) return false;94 itA.next();95 itB.next();96 }97 return true;98 }99 export function ofUnsortedIndices(indices: number[]): AtomSet {100 return AtomSet(sortAsc(indices));101 }102 export function atomDistanceSq(x: number[], y: number[], z: number[], i: number, j: number) {103 const dx = x[i] - x[j], dy = y[i] - y[j], dz = z[i] - z[j];104 return dx * dx + dy * dy + dz * dz;105 }106 function computeHashCode(atomSet: ArrayAtomSet) {107 let code = 23;108 for (const i of atomSet.atomIndices) {109 code = (31 * code + i) | 0;110 }111 atomSet.hashCode = code;112 atomSet.hashCodeComputed = true;113 return code;114 }115 export function hashCode(atomSet: AtomSet) {116 if (typeof atomSet === 'number') return atomSet;117 if (atomSet.hashCodeComputed) return atomSet.hashCode!;118 return computeHashCode(atomSet);119 }120 export function hierarchy(model: Model, atomSet: AtomSet) {121 const residueIndices = UniqueArrayBuilder<number>();122 const chainIndices = UniqueArrayBuilder<number>();123 const entityIndices = UniqueArrayBuilder<number>();124 const rIndices = model.atoms.residueIndex;125 const cIndices = model.residues.chainIndex;126 const eIndices = model.chains.entityIndex;127 const it = Iterator();128 for (let i = Iterator.start(it, atomSet); !it.done; i = it.next().value) { UniqueArrayBuilder.add(residueIndices, rIndices[i], rIndices[i]); }129 for (const i of residueIndices.array) { UniqueArrayBuilder.add(chainIndices, cIndices[i], cIndices[i]); }130 for (const i of chainIndices.array) { UniqueArrayBuilder.add(entityIndices, eIndices[i], eIndices[i]); }131 return { residueIndices: residueIndices.array, chainIndices: chainIndices.array, entityIndices: entityIndices.array };132 }133 function computeBoundingSphere(model: Model, atomSet: ArrayAtomSet) {134 const { x, y, z } = model.positions;135 if (atomSet.atomIndices.length === 1) {136 const i = atomSet.atomIndices[0];137 atomSet.boundingSphere = { center: [x[i], y[i], z[i]], radius: 0 };138 return atomSet.boundingSphere;139 }140 const center: [number, number, number] = [0, 0, 0];141 for (const i of atomSet.atomIndices) {142 center[0] += x[i];143 center[1] += y[i];144 center[2] += z[i];145 }146 center[0] *= 1 / atomSet.atomIndices.length;147 center[1] *= 1 / atomSet.atomIndices.length;148 center[2] *= 1 / atomSet.atomIndices.length;149 let radius = 0;150 for (const i of atomSet.atomIndices) {151 const dx = center[0] - x[i], dy = center[1] - y[i], dz = center[2] - z[i];152 radius = Math.max(dx * dx + dy * dy + dz * dz, radius);153 }154 atomSet.boundingSphere = { center, radius };155 return atomSet.boundingSphere;156 }157 export function boundingSphere(model: Model, atomSet: AtomSet) {158 if (typeof atomSet === 'number') {159 const { x, y, z } = model.positions;160 return { center: [x[atomSet], y[atomSet], z[atomSet]], radius: 0 };161 }162 if (atomSet.boundingSphere) return atomSet.boundingSphere;163 return computeBoundingSphere(model, atomSet);164 }165 export function distance(model: Model, a: AtomSet, b: AtomSet) {166 if (a === b) return 0;167 let distSq = Number.POSITIVE_INFINITY;168 const { x, y, z } = model.positions;169 for (let i = Iterator.start(itA, a); !itA.done; i = itA.next().value) {170 for (let j = Iterator.start(itB, b); !itB.done; j = itB.next().value) {171 const d = atomDistanceSq(x, y, z, i, j);172 if (d < distSq) distSq = d;173 }174 }175 return Math.sqrt(distSq);176 }177 export function areWithin(model: Model, a: AtomSet, b: AtomSet, maxDistance: number) {178 if (a === b) return true;179 const dSq = maxDistance * maxDistance;180 const { x, y, z } = model.positions;181 for (let i = Iterator.start(itA, a); !itA.done; i = itA.next().value) {182 for (let j = Iterator.start(itB, b); !itB.done; j = itB.next().value) {183 if (atomDistanceSq(x, y, z, i, j) <= dSq) return true;184 }185 }186 return false;187 }188 export function union(a: AtomSet, b: AtomSet): AtomSet {189 const la = count(a), lb = count(b);190 let i = 0, j = 0, resultSize = 0;191 Iterator.start(itA, a);192 Iterator.start(itB, b);193 while (i < la && j < lb) {194 const x = itA.value, y = itB.value;195 resultSize++;196 if (x < y) { itA.next(); i++; }197 else if (x > y) { itB.next(); j++; }198 else { i++; j++; itA.next(); itB.next(); }199 }200 resultSize += Math.max(la - i, lb - j);201 const indices = new Int32Array(resultSize);202 let offset = 0;203 i = 0;204 j = 0;205 Iterator.start(itA, a);206 Iterator.start(itB, b);207 while (i < la && j < lb) {208 const x = itA.value, y = itB.value;209 resultSize++;210 if (x < y) { indices[offset++] = x; i++; itA.next(); }211 else if (x > y) { indices[offset++] = y; j++; itB.next(); }212 else { indices[offset++] = x; i++; j++; itA.next(); itB.next(); }213 }214 for (; i < la; i++) { indices[offset++] = itA.value; itA.next(); }215 for (; j < lb; j++) { indices[offset++] = itB.value; itB.next(); }216 return AtomSet(indices);217 }218}...

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collections.ts

Source:collections.ts Github

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1/*2 * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.3 *4 * @author David Sehnal <david.sehnal@gmail.com>5 */6export interface UniqueArrayBuilder<T> { _keys: any, array: T[] }7export function UniqueArrayBuilder<T>(): UniqueArrayBuilder<T> { return { _keys: Object.create(null), array: [] } }8export namespace UniqueArrayBuilder {9 export function add<T>({ _keys, array }: UniqueArrayBuilder<T>, key: string | number, value: any) {10 if (_keys[key] === 1) return false;11 _keys[key] = 1;12 array.push(value);13 return true;14 }15}16function _ascSort(a: number, b: number) {17 return a - b;18}19export function sortAsc<T extends ArrayLike<number>>(array: T): T {20 Array.prototype.sort.call(array, _ascSort);21 return array;22}23/**24 * An "object" based implementation of map that supports string and numeric keys25 * which should be ok for most use cases in LiteMol.26 *27 * The type limitation is on purpose to prevent using the type in places that are28 * not appropriate.29 */30export interface FastMap<K extends string | number, V> {31 readonly size: number;32 set(key: K, v: V): void;33 get(key: K): V | undefined;34 delete(key: K): boolean;35 has(key: K): boolean;36 clear(): void;37 /**38 * Iterate over the collection.39 * Optional "context" object can be supplied that is passed to the callback.40 *41 * Enumerates only values that are not undefined.42 */43 forEach<Context>(f: (value: V, key: K, ctx?: Context) => void, ctx?: Context): void;44}45/**46 * An "object" based implementation of set that supports string and numeric values47 * which should be ok for most use cases in LiteMol.48 *49 * The type limitation is on purpose to prevent using the type in places that are50 * not appropriate.51 */52export interface FastSet<T extends string | number> {53 readonly size: number;54 add(key: T): boolean;55 delete(key: T): boolean;56 has(key: T): boolean;57 clear(): void;58 /**59 * Iterate over the collection.60 * Optional "context" object can be supplied that is passed to the callback.61 */62 forEach<Context>(f: (key: T, ctx?: Context) => boolean | any, ctx?: Context): void;63}64function createMapObject() {65 const map = Object.create(null);66 // to cause deoptimization as we don't want to create hidden classes67 map['__'] = void 0;68 delete map['__'];69 return map;70}71type MapData = { data: any, size: number }72export namespace FastMap {73 function forEach(data: any, f: (value: any, key: any, ctx: any) => void, ctx: any) {74 for (const key of Object.keys(data)) {75 const v = data[key];76 if (v === void 0) continue;77 f(v, key, ctx);78 }79 }80 const fastMap = {81 set(this: MapData, key: string | number, v: any) {82 if (this.data[key] === void 0 && v !== void 0) {83 this.size++;84 }85 this.data[key] = v;86 },87 get(this: MapData, key: string | number) {88 return this.data[key];89 },90 delete(this: MapData, key: string | number) {91 if (this.data[key] === void 0) return false;92 delete this.data[key];93 this.size--;94 return true;95 },96 has(this: MapData, key: string | number) {97 return this.data[key] !== void 0;98 },99 clear(this: MapData) {100 this.data = createMapObject();101 this.size = 0;102 },103 forEach(this: MapData, f: (k: string | number, v: number, ctx?: any) => void, ctx?: any) {104 forEach(this.data, f, ctx !== void 0 ? ctx : void 0);105 }106 };107 /**108 * Creates an empty map.109 */110 export function create<K extends string | number, V>(): FastMap<K, V> {111 const ret = Object.create(fastMap) as any;112 ret.data = createMapObject();113 ret.size = 0;114 return ret;115 }116 /**117 * Create a map from an array of the form [[key, value], ...]118 */119 export function ofArray<K extends string | number, V>(data: [K, V][]) {120 const ret = create<K, V>();121 for (const xs of data) {122 ret.set(xs[0] as K, xs[1] as V);123 }124 return ret;125 }126 /**127 * Create a map from an object of the form { key: value, ... }128 */129 export function ofObject<V>(data: { [key: string]: V }) {130 const ret = create<string, V>();131 for (const key of Object.keys(data)) {132 const v = data[key];133 ret.set(key, v);134 }135 return ret;136 }137}138export namespace FastSet {139 function forEach(data: any, f: (k: string | number, ctx: any) => boolean | void, ctx: any) {140 for (const p of Object.keys(data)) {141 if (data[p] !== null) continue;142 if (f(p, ctx) === false) break;143 }144 }145 /**146 * Uses null for present values.147 */148 const fastSet = {149 add(this: MapData, key: string | number) {150 if (this.data[key] === null) return false;151 this.data[key] = null;152 this.size++;153 return true;154 },155 delete(this: MapData, key: string | number) {156 if (this.data[key] !== null) return false;157 delete this.data[key];158 this.size--;159 return true;160 },161 has(this: MapData, key: string | number) {162 return this.data[key] === null;163 },164 clear(this: MapData) {165 this.data = createMapObject();166 this.size = 0;167 },168 forEach(this: MapData, f: (k: string | number, ctx: any) => void, ctx?: any) {169 forEach(this.data, f, ctx !== void 0 ? ctx : void 0);170 }171 };172 /**173 * Create an empty set.174 */175 export function create<T extends string | number>(): FastSet<T> {176 const ret = Object.create(fastSet) as any;177 ret.data = createMapObject();178 ret.size = 0;179 return ret;180 }181 /**182 * Create a set of an "array like" sequence.183 */184 export function ofArray<T extends string | number>(xs: ArrayLike<T>) {185 const ret = create<T>();186 for (let i = 0, l = xs.length; i < l; i++) {187 ret.add(xs[i]);188 }189 return ret;190 }191 export function isSubset<T extends string | number>(a: FastSet<T>, b: FastSet<T>) {192 const _ctx = { b, count: 0 };193 a.forEach((e, ctx) => {194 if (!ctx!.b.has(e)) return false;195 ctx!.count++;196 }, _ctx);197 return _ctx.count === a.size;198 }...

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Using AI Code Generation

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1const { uniqueArrayBuilder } = require("fast-check-monorepo");2console.log(uniqueArrayBuilder(10));3{4 "scripts": {5 },6 "dependencies": {7 }8}

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Using AI Code Generation

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1const { uniqueArrayBuilder } = require('fast-check-monorepo');2const array = uniqueArrayBuilder().build();3console.log(array);4{5 "scripts": {6 },7 "dependencies": {8 }9}10const array = uniqueArrayBuilder({minSize: 1, maxSize: 5, minUniqueItems: 1, maxUniqueItems: 5}).build();11The uniqueArrayBuilder() method can also be used to build an array of a specific type. For example, the following code will build an array of strings:12const array = uniqueArrayBuilder().of(string()).build();13The uniqueArrayBuilder() method can also be used to build an array of a specific type and with a specific set of settings. For example, the following code will build an array of strings with a minimum size of 1, a maximum size of 5, a minimum of 1 unique item, and a maximum of 5 unique items:14const array = uniqueArrayBuilder({minSize: 1, maxSize: 5, minUniqueItems: 1, maxUniqueItems: 5}).of(string()).build();15The uniqueArrayBuilder() method can also be used to build an array of

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Using AI Code Generation

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1const { uniqueArrayBuilder } = require('fast-check-monorepo');2const { uniqueArrayBuilder } = require('fast-check');3const uniqueArray = uniqueArrayBuilder(100);4console.log(uniqueArray(10));5const { uniqueArrayBuilder } = require('fast-check');6const uniqueArray = uniqueArrayBuilder(100);7console.log(uniqueArray(10));

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Using AI Code Generation

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1const uniqueArrayBuilder = require('fast-check-monorepo/dist/lib/check/arbitrary/uniqueArrayBuilder').uniqueArrayBuilder;2const uniqueArrayBuilder1 = require('fast-check-monorepo').uniqueArrayBuilder;3const fc = require('fast-check');4const { uniqueArrayBuilder } = require('fast-check-monorepo');5console.log('uniqueArrayBuilder: ', uniqueArrayBuilder);6const uniqueArrayArb = uniqueArrayBuilder(fc.integer(), 0, 1);7fc.assert(fc.property(uniqueArrayArb, (uniqueArray) => {8 const uniqueArraySet = new Set(uniqueArray);9 return uniqueArray.length === uniqueArraySet.size;10}));11console.log('uniqueArrayBuilder: ', uniqueArrayBuilder);12const uniqueArrayArb1 = uniqueArrayBuilder1(fc.integer(), 0, 1);13fc.assert(fc.property(uniqueArrayArb1, (uniqueArray) => {14 const uniqueArraySet = new Set(uniqueArray);15 return uniqueArray.length === uniqueArraySet.size;16}));17console.log('uniqueArrayBuilder: ', uniqueArrayBuilder);18const uniqueArrayArb2 = uniqueArrayBuilder(fc.integer(), 0, 1);19fc.assert(fc.property(uniqueArrayArb2, (uniqueArray) => {20 const uniqueArraySet = new Set(uniqueArray);21 return uniqueArray.length === uniqueArraySet.size;22}));

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Using AI Code Generation

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1const { uniqueArrayBuilder } = require('fast-check');2const { array } = require('fast-check');3const uniqueArray = uniqueArrayBuilder(array);4console.log(uniqueArray().generate());5at Object.<anonymous> (C:\Users\test.js:3:26)6at Module._compile (internal/modules/cjs/loader.js:1137:30)7at Object.Module._extensions..js (internal/modules/cjs/loader.js:1157:10)8at Module.load (internal/modules/cjs/loader.js:986:32)9at Function.Module._load (internal/modules/cjs/loader.js:879:14)10at Function.executeUserEntryPoint [as runMain] (internal/modules/run_main.js:71:12)11const { uniqueArrayBuilder } = require('fast-check-monorepo');12const { array } = require('fast-check-monorepo');13const uniqueArray = uniqueArrayBuilder(array);

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Using AI Code Generation

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1const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;2const uniqueArray = uniqueArrayBuilder(array, array.length);3const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;4const uniqueArray = uniqueArrayBuilder(array, array.length);5const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;6const uniqueArray = uniqueArrayBuilder(array, array.length);7const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;8const uniqueArray = uniqueArrayBuilder(array, array.length);9const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;10const uniqueArray = uniqueArrayBuilder(array, array.length);11const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;12const uniqueArray = uniqueArrayBuilder(array, array.length);13const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;14const uniqueArray = uniqueArrayBuilder(array, array.length);15const uniqueArrayBuilder = require("fast-check-monorepo").uniqueArrayBuilder;16const uniqueArray = uniqueArrayBuilder(array, array.length);17const uniqueArrayBuilder = require("fast

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