From e69b31bae7a7bc1e985c92ad351dba88f500be0b Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 19 Apr 2018 18:12:16 +0200
Subject: [PATCH] Removed old grid lookup
---
src/apps/structure-info/index.ts | 20 +-
src/mol-math/geometry/grid-lookup.ts | 291 ---------------------------
src/perf-tests/lookup3d.ts | 2 +-
3 files changed, 12 insertions(+), 301 deletions(-)
delete mode 100644 src/mol-math/geometry/grid-lookup.ts
diff --git a/src/apps/structure-info/index.ts b/src/apps/structure-info/index.ts
index 7a911acb4..6f6068173 100644
--- a/src/apps/structure-info/index.ts
+++ b/src/apps/structure-info/index.ts
@@ -26,7 +26,7 @@ async function getPdb(pdb: string) {
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 { label_atom_id } = atoms
const { label_comp_id, label_seq_id } = residues
@@ -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)} ${label_atom_id.value(aI)}`
}
+
function printBonds(model: Model) {
- const { count, offset, neighbor } = Model.bonds(model)
- for (let i = 0; i < count; ++i) {
- const start = offset[i];
- const end = offset[i + 1];
- for (let bI = start; bI < end; bI++) {
- console.log(`${atomLabel(model, i)} -- ${atomLabel(model, neighbor[bI])}`)
- }
- }
+ // TODO: do bonds again
+ // const { count, offset, neighbor } = Model.bonds(model)
+ // for (let i = 0; i < count; ++i) {
+ // const start = offset[i];
+ // const end = offset[i + 1];
+ // for (let bI = start; bI < end; bI++) {
+ // console.log(`${atomLabel(model, i)} -- ${atomLabel(model, neighbor[bI])}`)
+ // }
+ // }
}
async function run(pdb: string) {
diff --git a/src/mol-math/geometry/grid-lookup.ts b/src/mol-math/geometry/grid-lookup.ts
deleted file mode 100644
index 46660d95f..000000000
--- a/src/mol-math/geometry/grid-lookup.ts
+++ /dev/null
@@ -1,291 +0,0 @@
-// /*
-// * 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
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index cadc871cc..3875a8c13 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -6,7 +6,7 @@ import { Structure, Model } from 'mol-model/structure'
import { Run } from 'mol-task';
import { GridLookup3D } from 'mol-math/geometry';
-import { sortArray } from 'mol-data/util';
+// import { sortArray } from 'mol-data/util';
import { OrderedSet } from 'mol-data/int';
require('util.promisify').shim();
--
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