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Commit e69b31ba authored by David Sehnal's avatar David Sehnal
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Removed old grid lookup

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src/apps/structure-info/index.ts
+ 11
− 9
View file @ e69b31ba
...@@ -26,7 +26,7 @@ async function getPdb(pdb: string) { ...@@ -26,7 +26,7 @@ async function getPdb(pdb: string) {
return CIF.schema.mmCIF(parsed.result.blocks[0]) return CIF.schema.mmCIF(parsed.result.blocks[0])
} }
function atomLabel(model: Model, aI: number) { export function atomLabel(model: Model, aI: number) {
const { atoms, residues, chains, residueSegments, chainSegments } = model.hierarchy const { atoms, residues, chains, residueSegments, chainSegments } = model.hierarchy
const { label_atom_id } = atoms const { label_atom_id } = atoms
const { label_comp_id, label_seq_id } = residues const { label_comp_id, label_seq_id } = residues
...@@ -36,15 +36,17 @@ function atomLabel(model: Model, aI: number) { ...@@ -36,15 +36,17 @@ function atomLabel(model: Model, aI: number) {
return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}` return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`
} }
function printBonds(model: Model) { function printBonds(model: Model) {
const { count, offset, neighbor } = Model.bonds(model) // TODO: do bonds again
for (let i = 0; i < count; ++i) { // const { count, offset, neighbor } = Model.bonds(model)
const start = offset[i]; // for (let i = 0; i < count; ++i) {
const end = offset[i + 1]; // const start = offset[i];
for (let bI = start; bI < end; bI++) { // const end = offset[i + 1];
console.log(`${atomLabel(model, i)} -- ${atomLabel(model, neighbor[bI])}`) // for (let bI = start; bI < end; bI++) {
} // console.log(`${atomLabel(model, i)} -- ${atomLabel(model, neighbor[bI])}`)
} // }
// }
} }
async function run(pdb: string) { async function run(pdb: string) {
......
src/mol-math/geometry/grid-lookup.ts deleted 100644 → 0
+ 0
− 291
View file @ 0b038559
// /*
// * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
// *
// * @author David Sehnal <david.sehnal@gmail.com>
// * @author Alexander Rose <alexander.rose@weirdbyte.de>
// */
// // TODO: 3d grid lookup (use single cell for small sets), make bounding sphere part of the structure
// // TODO: assign radius to points?
// /**
// * A "masked" 3D spatial lookup structure.
// */
// import Mask from 'mol-util/mask'
// export type FindFunc = (x: number, y: number, z: number, radius: number) => Result
// export type CheckFunc = (x: number, y: number, z: number, radius: number) => boolean
// export interface Result {
// readonly count: number,
// readonly indices: number[],
// readonly squaredDistances: number[]
// }
// export interface Positions { x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number> }
// interface GridLookup { find: (mask: Mask) => FindFunc, check: (mask: Mask) => CheckFunc }
// function GridLookup(positions: Positions): GridLookup {
// const tree = build(createInputData(positions));
// return {
// find(mask) {
// const ctx = QueryContext.create(tree, mask, false);
// return function (x: number, y: number, z: number, radius: number) {
// QueryContext.update(ctx, x, y, z, radius);
// nearest(ctx);
// return ctx.buffer;
// }
// },
// check(mask) {
// const ctx = QueryContext.create(tree, mask, true);
// return function (x: number, y: number, z: number, radius: number) {
// QueryContext.update(ctx, x, y, z, radius);
// return nearest(ctx);
// }
// }
// }
// }
// interface InputData {
// bounds: Box3D,
// count: number,
// positions: Positions
// }
// interface Box3D {
// min: number[],
// max: number[]
// }
// namespace Box3D {
// export function createInfinite(): Box3D {
// return {
// min: [Number.MAX_VALUE, Number.MAX_VALUE, Number.MAX_VALUE],
// max: [-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE]
// }
// }
// }
// /**
// * Query context. Handles the actual querying.
// */
// interface QueryContext<T> {
// structure: T,
// pivot: number[],
// radius: number,
// radiusSq: number,
// buffer: QueryContext.Buffer,
// mask: Mask,
// isCheck: boolean
// }
// namespace QueryContext {
// export interface Buffer extends Result {
// count: number;
// indices: any[];
// squaredDistances: number[];
// }
// export function add<T>(ctx: QueryContext<T>, distSq: number, index: number) {
// const buffer = ctx.buffer;
// buffer.squaredDistances[buffer.count] = distSq;
// buffer.indices[buffer.count++] = index;
// }
// function resetBuffer(buffer: Buffer) { buffer.count = 0; }
// function createBuffer(): Buffer {
// return {
// indices: [],
// count: 0,
// squaredDistances: []
// }
// }
// /**
// * Query the tree and store the result to this.buffer. Overwrites the old result.
// */
// export function update<T>(ctx: QueryContext<T>, x: number, y: number, z: number, radius: number) {
// ctx.pivot[0] = x;
// ctx.pivot[1] = y;
// ctx.pivot[2] = z;
// ctx.radius = radius;
// ctx.radiusSq = radius * radius;
// resetBuffer(ctx.buffer);
// }
// export function create<T>(structure: T, mask: Mask, isCheck: boolean): QueryContext<T> {
// return {
// structure,
// buffer: createBuffer(),
// pivot: [0.1, 0.1, 0.1],
// radius: 1.1,
// radiusSq: 1.1 * 1.1,
// mask,
// isCheck
// }
// }
// }
// function createInputData(positions: { x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number> }): InputData {
// const { x, y, z } = positions;
// const bounds = Box3D.createInfinite();
// const count = x.length;
// const { min, max } = bounds;
// for (let i = 0; i < count; i++) {
// min[0] = Math.min(x[i], min[0]);
// min[1] = Math.min(y[i], min[1]);
// min[2] = Math.min(z[i], min[2]);
// max[0] = Math.max(x[i], max[0]);
// max[1] = Math.max(y[i], max[1]);
// max[2] = Math.max(z[i], max[2]);
// }
// return { positions, bounds, count };
// }
// /**
// * Adapted from https://github.com/arose/ngl
// * MIT License Copyright (C) 2014+ Alexander Rose
// */
// interface SpatialHash {
// size: number[],
// min: number[],
// grid: Uint32Array,
// bucketOffset: Uint32Array,
// bucketCounts: Int32Array,
// bucketArray: Int32Array,
// positions: Positions
// }
// interface State {
// size: number[],
// positions: Positions,
// bounds: Box3D,
// count: number
// }
// const enum Constants { Exp = 3 }
// function nearest(ctx: QueryContext<SpatialHash>): boolean {
// const { min: [minX, minY, minZ], size: [sX, sY, sZ], bucketOffset, bucketCounts, bucketArray, grid, positions: { x: px, y: py, z: pz } } = ctx.structure;
// const { radius: r, radiusSq: rSq, pivot: [x, y, z], isCheck, mask } = ctx;
// const loX = Math.max(0, (x - r - minX) >> Constants.Exp);
// const loY = Math.max(0, (y - r - minY) >> Constants.Exp);
// const loZ = Math.max(0, (z - r - minZ) >> Constants.Exp);
// const hiX = Math.min(sX, (x + r - minX) >> Constants.Exp);
// const hiY = Math.min(sY, (y + r - minY) >> Constants.Exp);
// const hiZ = Math.min(sZ, (z + r - minZ) >> Constants.Exp);
// for (let ix = loX; ix <= hiX; ix++) {
// for (let iy = loY; iy <= hiY; iy++) {
// for (let iz = loZ; iz <= hiZ; iz++) {
// const bucketIdx = grid[(((ix * sY) + iy) * sZ) + iz];
// if (bucketIdx > 0) {
// const k = bucketIdx - 1;
// const offset = bucketOffset[k];
// const count = bucketCounts[k];
// const end = offset + count;
// for (let i = offset; i < end; i++) {
// const idx = bucketArray[i];
// if (!mask.has(idx)) continue;
// const dx = px[idx] - x;
// const dy = py[idx] - y;
// const dz = pz[idx] - z;
// const distSq = dx * dx + dy * dy + dz * dz;
// if (distSq <= rSq) {
// if (isCheck) return true;
// QueryContext.add(ctx, distSq, idx)
// }
// }
// }
// }
// }
// }
// return ctx.buffer.count > 0;
// }
// function _build(state: State): SpatialHash {
// const { bounds, size: [sX, sY, sZ], positions: { x: px, y: py, z: pz }, count } = state;
// const n = sX * sY * sZ;
// const { min: [minX, minY, minZ] } = bounds;
// let bucketCount = 0;
// const grid = new Uint32Array(n);
// const bucketIndex = new Int32Array(count);
// for (let i = 0; i < count; i++) {
// const x = (px[i] - minX) >> Constants.Exp;
// const y = (py[i] - minY) >> Constants.Exp;
// const z = (pz[i] - minZ) >> Constants.Exp;
// const idx = (((x * sY) + y) * sZ) + z;
// if ((grid[idx] += 1) === 1) {
// bucketCount += 1
// }
// bucketIndex[i] = idx;
// }
// const bucketCounts = new Int32Array(bucketCount);
// for (let i = 0, j = 0; i < n; i++) {
// const c = grid[i];
// if (c > 0) {
// grid[i] = j + 1;
// bucketCounts[j] = c;
// j += 1;
// }
// }
// const bucketOffset = new Uint32Array(count);
// for (let i = 1; i < count; ++i) {
// bucketOffset[i] += bucketOffset[i - 1] + bucketCounts[i - 1];
// }
// const bucketFill = new Int32Array(bucketCount);
// const bucketArray = new Int32Array(count);
// for (let i = 0; i < count; i++) {
// const bucketIdx = grid[bucketIndex[i]]
// if (bucketIdx > 0) {
// const k = bucketIdx - 1;
// bucketArray[bucketOffset[k] + bucketFill[k]] = i;
// bucketFill[k] += 1;
// }
// }
// return {
// size: state.size,
// bucketArray,
// bucketCounts,
// bucketOffset,
// grid,
// min: state.bounds.min,
// positions: state.positions
// }
// }
// function build({ positions, bounds, count }: InputData): SpatialHash {
// const size = [
// ((bounds.max[0] - bounds.min[0]) >> Constants.Exp) + 1,
// ((bounds.max[1] - bounds.min[1]) >> Constants.Exp) + 1,
// ((bounds.max[2] - bounds.min[2]) >> Constants.Exp) + 1
// ];
// const state: State = {
// size,
// positions,
// bounds,
// count
// }
// return _build(state);
// }
// export default GridLookup;
\ No newline at end of file
src/perf-tests/lookup3d.ts
+ 1
− 1
View file @ e69b31ba
...@@ -6,7 +6,7 @@ import { Structure, Model } from 'mol-model/structure' ...@@ -6,7 +6,7 @@ import { Structure, Model } from 'mol-model/structure'
import { Run } from 'mol-task'; import { Run } from 'mol-task';
import { GridLookup3D } from 'mol-math/geometry'; import { GridLookup3D } from 'mol-math/geometry';
import { sortArray } from 'mol-data/util'; // import { sortArray } from 'mol-data/util';
import { OrderedSet } from 'mol-data/int'; import { OrderedSet } from 'mol-data/int';
require('util.promisify').shim(); require('util.promisify').shim();
......
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