From a04ed8135db57ffe2e507cd77e35b5ca12b6eb3d Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 19 Apr 2018 16:22:27 +0200
Subject: [PATCH] refactoring grid lookup (step 3)
---
src/mol-math/geometry.ts | 12 +
src/mol-math/geometry/_spec/lookup3d.spec.ts | 51 ++
src/mol-math/geometry/common.ts | 15 +-
src/mol-math/geometry/grid-lookup.ts | 582 +++++++++---------
src/mol-math/geometry/lookup.ts | 0
src/mol-math/geometry/lookup3d/common.ts | 3 +-
src/mol-math/geometry/lookup3d/grid.ts | 118 ++--
src/mol-math/geometry/primitives/box3d.ts | 30 +-
src/mol-math/geometry/primitives/sphere3d.ts | 58 +-
src/mol-math/geometry/symmetry-operator.ts | 2 +-
.../structure/model/formats/mmcif/assembly.ts | 2 +-
src/mol-model/structure/model/model.ts | 31 +-
.../structure/model/properties/symmetry.ts | 2 +-
.../structure/model/utils/compute-bonds.ts | 506 +++++++--------
.../structure/structure/element/group.ts | 16 +-
.../structure/structure/structure.ts | 2 +-
src/mol-model/structure/structure/unit.ts | 2 +-
src/perf-tests/lookup3d.ts | 12 +-
18 files changed, 763 insertions(+), 681 deletions(-)
create mode 100644 src/mol-math/geometry.ts
create mode 100644 src/mol-math/geometry/_spec/lookup3d.spec.ts
delete mode 100644 src/mol-math/geometry/lookup.ts
diff --git a/src/mol-math/geometry.ts b/src/mol-math/geometry.ts
new file mode 100644
index 000000000..f8134ddd0
--- /dev/null
+++ b/src/mol-math/geometry.ts
@@ -0,0 +1,12 @@
+/*
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export * from './geometry/common'
+export * from './geometry/symmetry-operator'
+export * from './geometry/lookup3d/common'
+export * from './geometry/lookup3d/grid'
+export * from './geometry/primitives/box3d'
+export * from './geometry/primitives/sphere3d'
\ No newline at end of file
diff --git a/src/mol-math/geometry/_spec/lookup3d.spec.ts b/src/mol-math/geometry/_spec/lookup3d.spec.ts
new file mode 100644
index 000000000..af2c30a46
--- /dev/null
+++ b/src/mol-math/geometry/_spec/lookup3d.spec.ts
@@ -0,0 +1,51 @@
+/*
+* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+*
+* @author David Sehnal <david.sehnal@gmail.com>
+*/
+
+import { GridLookup3D } from '../../geometry';
+import { sortArray } from 'mol-data/util';
+import { OrderedSet } from 'mol-data/int';
+
+const xs = [0, 0, 1];
+const ys = [0, 1, 0];
+const zs = [0, 0, 0];
+const rs = [0, 0.5, 1/3];
+
+describe('GridLookup3d', () => {
+ it('basic', () => {
+ const grid = GridLookup3D({ x: xs, y: ys, z: zs, indices: OrderedSet.ofBounds(0, 3) });
+
+ let r = grid.find(0, 0, 0, 0);
+ expect(r.count).toBe(1);
+ expect(r.indices[0]).toBe(0);
+
+ r = grid.find(0, 0, 0, 1);
+ expect(r.count).toBe(3);
+ expect(sortArray(r.indices)).toEqual([0, 1, 2]);
+ });
+
+ it('radius', () => {
+ const grid = GridLookup3D({ x: xs, y: ys, z: zs, radius: [0, 0.5, 1 / 3], indices: OrderedSet.ofBounds(0, 3) });
+
+ let r = grid.find(0, 0, 0, 0);
+ expect(r.count).toBe(1);
+ expect(r.indices[0]).toBe(0);
+
+ r = grid.find(0, 0, 0, 0.5);
+ expect(r.count).toBe(2);
+ expect(sortArray(r.indices)).toEqual([0, 1]);
+ });
+
+ it('indexed', () => {
+ const grid = GridLookup3D({ x: xs, y: ys, z: zs, indices: OrderedSet.ofSingleton(1), radius: rs });
+
+ let r = grid.find(0, 0, 0, 0);
+ expect(r.count).toBe(0);
+
+ r = grid.find(0, 0, 0, 0.5);
+ expect(r.count).toBe(1);
+ expect(sortArray(r.indices)).toEqual([0]);
+ });
+});
\ No newline at end of file
diff --git a/src/mol-math/geometry/common.ts b/src/mol-math/geometry/common.ts
index 54d5b3b84..195224635 100644
--- a/src/mol-math/geometry/common.ts
+++ b/src/mol-math/geometry/common.ts
@@ -1,14 +1,17 @@
/*
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
+* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+*
+* @author David Sehnal <david.sehnal@gmail.com>
+*/
+
+import { OrderedSet } from 'mol-data/int'
export interface PositionData {
x: ArrayLike<number>,
y: ArrayLike<number>,
z: ArrayLike<number>,
- radius?: ArrayLike<number>,
// subset indices into the x/y/z/radius arrays
- indices?: ArrayLike<number>,
+ indices: OrderedSet,
+ // optional element radius
+ radius?: ArrayLike<number>
}
diff --git a/src/mol-math/geometry/grid-lookup.ts b/src/mol-math/geometry/grid-lookup.ts
index fa703c242..46660d95f 100644
--- a/src/mol-math/geometry/grid-lookup.ts
+++ b/src/mol-math/geometry/grid-lookup.ts
@@ -1,291 +1,291 @@
-/*
- * 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
+// /*
+// * 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/mol-math/geometry/lookup.ts b/src/mol-math/geometry/lookup.ts
deleted file mode 100644
index e69de29bb..000000000
diff --git a/src/mol-math/geometry/lookup3d/common.ts b/src/mol-math/geometry/lookup3d/common.ts
index 1b4212be1..a5a3e8d58 100644
--- a/src/mol-math/geometry/lookup3d/common.ts
+++ b/src/mol-math/geometry/lookup3d/common.ts
@@ -32,6 +32,5 @@ export interface Lookup3D {
// The result is mutated with each call to find.
find(x: number, y: number, z: number, radius: number): Result,
check(x: number, y: number, z: number, radius: number): boolean,
- boundingBox: Box3D,
- boundingSphere: Sphere3D
+ boundary: { box: Box3D, sphere: Sphere3D }
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/lookup3d/grid.ts b/src/mol-math/geometry/lookup3d/grid.ts
index b676904d0..b83bb4272 100644
--- a/src/mol-math/geometry/lookup3d/grid.ts
+++ b/src/mol-math/geometry/lookup3d/grid.ts
@@ -5,26 +5,47 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Result/*, Lookup3D*/ } from './common'
+import { Result, Lookup3D } from './common'
import { Box3D } from '../primitives/box3d';
import { Sphere3D } from '../primitives/sphere3d';
import { PositionData } from '../common';
import { Vec3 } from '../../linear-algebra';
+import { OrderedSet } from 'mol-data/int';
-// class GridLookup3D implements Lookup3D {
-// private result = Result.create();
-// private pivot = [0.1, 0.1, 0.1];
-// private radiusSq = 0.1;
-
-// find(x: number, y: number, z: number, radius: number): Result {
-// throw new Error("Method not implemented.");
-// }
-// check(x: number, y: number, z: number, radius: number): boolean {
-// throw new Error("Method not implemented.");
-// }
-// boundingBox: Box3D;
-// boundingSphere: Sphere3D;
-// }
+function GridLookup3D(data: PositionData): Lookup3D {
+ return new GridLookup3DImpl(data);
+}
+
+export { GridLookup3D }
+
+class GridLookup3DImpl implements Lookup3D {
+ private ctx: QueryContext;
+ boundary: Lookup3D['boundary'];
+
+ find(x: number, y: number, z: number, radius: number): Result {
+ this.ctx.x = x;
+ this.ctx.y = y;
+ this.ctx.z = z;
+ this.ctx.radius = radius;
+ this.ctx.isCheck = false;
+ query(this.ctx);
+ return this.ctx.result;
+ }
+ check(x: number, y: number, z: number, radius: number): boolean {
+ this.ctx.x = x;
+ this.ctx.y = y;
+ this.ctx.z = z;
+ this.ctx.radius = radius;
+ this.ctx.isCheck = true;
+ return query(this.ctx);
+ }
+
+ constructor(data: PositionData) {
+ const structure = build(data);
+ this.ctx = createContext(structure);
+ this.boundary = { box: structure.boundingBox, sphere: structure.boundingSphere };
+ }
+}
/**
* Adapted from https://github.com/arose/ngl
@@ -35,11 +56,11 @@ interface InputData {
x: ArrayLike<number>,
y: ArrayLike<number>,
z: ArrayLike<number>,
+ indices: OrderedSet,
radius?: ArrayLike<number>,
- indices: ArrayLike<number>
}
-interface SpatialHash {
+interface Grid3D {
size: number[],
min: number[],
grid: Uint32Array,
@@ -64,7 +85,7 @@ interface BuildState {
count: number
}
-function _build(state: BuildState): SpatialHash {
+function _build(state: BuildState): Grid3D {
const { expandedBox, size: [sX, sY, sZ], data: { x: px, y: py, z: pz, radius, indices }, count, delta } = state;
const n = sX * sY * sZ;
const { min: [minX, minY, minZ] } = expandedBox;
@@ -73,8 +94,8 @@ function _build(state: BuildState): SpatialHash {
let bucketCount = 0;
const grid = new Uint32Array(n);
const bucketIndex = new Int32Array(count);
- for (let t = 0, _t = indices.length; t < _t; t++) {
- const i = indices[t];
+ for (let t = 0, _t = OrderedSet.size(indices); t < _t; t++) {
+ const i = OrderedSet.getAt(indices, t);
const x = Math.floor((px[i] - minX) / delta[0]);
const y = Math.floor((py[i] - minY) / delta[1]);
const z = Math.floor((pz[i] - minZ) / delta[2]);
@@ -87,8 +108,8 @@ function _build(state: BuildState): SpatialHash {
}
if (radius) {
- for (let t = 0, _t = indices.length; t < _t; t++) {
- const i = indices[t];
+ for (let t = 0, _t = OrderedSet.size(indices); t < _t; t++) {
+ const i = OrderedSet.getAt(indices, t);
if (radius[i] > maxRadius) maxRadius = radius[i];
}
}
@@ -135,24 +156,22 @@ function _build(state: BuildState): SpatialHash {
}
}
-export function build(data: PositionData) {
+function build(data: PositionData) {
const boundingBox = Box3D.computeBounding(data);
+ // need to expand the grid bounds to avoid rounding errors
const expandedBox = Box3D.expand(boundingBox, Vec3.create(0.5, 0.5, 0.5));
const boundingSphere = Sphere3D.computeBounding(data);
-
- // TODO: specialized code that does not require the indices annotation?
- const indices = data.indices ? data.indices as number[] : new Int32Array(data.x.length) as any as number[];
- if (!data.indices) {
- for (let i = 0, _i = data.x.length; i < _i; i++) indices[i] = i;
- }
+ const { indices } = data;
const S = Vec3.sub(Vec3.zero(), expandedBox.max, expandedBox.min);
let delta, size;
- if (indices.length > 0) {
+ const elementCount = OrderedSet.size(indices);
+
+ if (elementCount > 0) {
// size of the box
// required "grid volume" so that each cell contains on average 32 elements.
- const V = Math.ceil(indices.length / 32);
+ const V = Math.ceil(elementCount / 32);
const f = Math.pow(V / (S[0] * S[1] * S[2]), 1 / 3);
size = [Math.ceil(S[0] * f), Math.ceil(S[1] * f), Math.ceil(S[2] * f)];
delta = [S[0] / size[0], S[1] / size[1], S[2] / size[2]];
@@ -175,19 +194,35 @@ export function build(data: PositionData) {
expandedBox,
boundingBox,
boundingSphere,
- count: indices.length,
+ count: elementCount,
delta
}
return _build(state);
}
-export function inSphere(structure: SpatialHash, x: number, y: number, z: number, radius: number): Result {
- const { min, size: [sX, sY, sZ], bucketOffset, bucketCounts, bucketArray, grid, data: { x: px, y: py, z: pz, indices }, delta } = structure;
- //const { radius: r, radiusSq: rSq, pivot: [x, y, z], isCheck, mask } = ctx;
- const r = radius, rSq = r * r;
+interface QueryContext {
+ structure: Grid3D,
+ x: number,
+ y: number,
+ z: number,
+ radius: number,
+ result: Result,
+ isCheck: boolean
+}
+
+function createContext(structure: Grid3D): QueryContext {
+ return { structure, x: 0.1, y: 0.1, z: 0.1, radius: 0.1, result: Result.create(), isCheck: false }
+}
+
+function query(ctx: QueryContext): boolean {
+ const { min, size: [sX, sY, sZ], bucketOffset, bucketCounts, bucketArray, grid, data: { x: px, y: py, z: pz, indices, radius }, delta, maxRadius } = ctx.structure;
+ const { radius: inputRadius, isCheck, x, y, z, result } = ctx;
+
+ const r = inputRadius + maxRadius;
+ const rSq = r * r;
- const result = Result.create();
+ Result.reset(result);
const loX = Math.max(0, Math.floor((x - r - min[0]) / delta[0]));
const loY = Math.max(0, Math.floor((y - r - min[1]) / delta[1]));
@@ -197,7 +232,7 @@ export function inSphere(structure: SpatialHash, x: number, y: number, z: number
const hiY = Math.min(sY - 1, Math.floor((y + r - min[1]) / delta[1]));
const hiZ = Math.min(sZ - 1, Math.floor((z + r - min[2]) / delta[2]));
- if (loX > hiX || loY > hiY || loZ > hiZ) return result;
+ if (loX > hiX || loY > hiY || loZ > hiZ) return false;
for (let ix = loX; ix <= hiX; ix++) {
for (let iy = loY; iy <= hiY; iy++) {
@@ -211,7 +246,7 @@ export function inSphere(structure: SpatialHash, x: number, y: number, z: number
const end = offset + count;
for (let i = offset; i < end; i++) {
- const idx = indices[bucketArray[i]];
+ const idx = OrderedSet.getAt(indices, bucketArray[i]);
const dx = px[idx] - x;
const dy = py[idx] - y;
@@ -219,12 +254,13 @@ export function inSphere(structure: SpatialHash, x: number, y: number, z: number
const distSq = dx * dx + dy * dy + dz * dz;
if (distSq <= rSq) {
- // if (isCheck) return true;
+ if (maxRadius > 0 && Math.sqrt(distSq) - radius![idx] > inputRadius) continue;
+ if (isCheck) return true;
Result.add(result, bucketArray[i], distSq);
}
}
}
}
}
- return result;
+ return result.count > 0;
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/primitives/box3d.ts b/src/mol-math/geometry/primitives/box3d.ts
index 0bdd9bd9d..21a579516 100644
--- a/src/mol-math/geometry/primitives/box3d.ts
+++ b/src/mol-math/geometry/primitives/box3d.ts
@@ -6,6 +6,7 @@
import { Vec3 } from '../../linear-algebra'
import { PositionData } from '../common'
+import { OrderedSet } from 'mol-data/int';
interface Box3D { min: Vec3, max: Vec3 }
@@ -15,28 +16,15 @@ namespace Box3D {
const max = [-Number.MAX_VALUE, -Number.MAX_VALUE, -Number.MAX_VALUE];
const { x, y, z, indices } = data;
-
- if (indices) {
- for (let t = 0, _t = indices.length; t < _t; t++) {
- const i = indices[t];
- 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]);
- }
- } else {
- for (let i = 0, _i = x.length; i < _i; 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]);
- }
+ for (let t = 0, _t = OrderedSet.size(indices); t < _t; t++) {
+ const i = OrderedSet.getAt(indices, t);
+ 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 { min: Vec3.create(min[0], min[1], min[2]), max: Vec3.create(max[0], max[1], max[2]) }
}
diff --git a/src/mol-math/geometry/primitives/sphere3d.ts b/src/mol-math/geometry/primitives/sphere3d.ts
index 701daf098..bd74a09a2 100644
--- a/src/mol-math/geometry/primitives/sphere3d.ts
+++ b/src/mol-math/geometry/primitives/sphere3d.ts
@@ -6,6 +6,7 @@
import { Vec3 } from '../../linear-algebra'
import { PositionData } from '../common'
+import { OrderedSet } from 'mol-data/int';
interface Sphere3D { center: Vec3, radius: number }
@@ -15,44 +16,25 @@ namespace Sphere3D {
let cx = 0, cy = 0, cz = 0;
let radiusSq = 0;
- if (indices) {
- for (let t = 0, _t = indices.length; t < _t; t++) {
- const i = indices[t];
- cx += x[i];
- cy += y[i];
- cz += z[i];
- }
-
- if (indices.length > 0) {
- cx /= indices.length;
- cy /= indices.length;
- cz /= indices.length;
- }
-
- for (let t = 0, _t = indices.length; t < _t; t++) {
- const i = indices[t];
- const dx = x[i] - cx, dy = y[i] - cy, dz = z[i] - cz;
- const d = dx * dx + dy * dy + dz * dz;
- if (d > radiusSq) radiusSq = d;
- }
- } else {
- for (let i = 0, _i = x.length; i < _i; i++) {
- cx += x[i];
- cy += y[i];
- cz += z[i];
- }
-
- if (x.length > 0) {
- cx /= x.length;
- cy /= x.length;
- cz /= x.length;
- }
-
- for (let i = 0, _i = x.length; i < _i; i++) {
- const dx = x[i] - cx, dy = y[i] - cy, dz = z[i] - cz;
- const d = dx * dx + dy * dy + dz * dz;
- if (d > radiusSq) radiusSq = d;
- }
+ const size = OrderedSet.size(indices);
+ for (let t = 0; t < size; t++) {
+ const i = OrderedSet.getAt(indices, t);
+ cx += x[i];
+ cy += y[i];
+ cz += z[i];
+ }
+
+ if (size > 0) {
+ cx /= size;
+ cy /= size;
+ cz /= size;
+ }
+
+ for (let t = 0; t < size; t++) {
+ const i = OrderedSet.getAt(indices, t);
+ const dx = x[i] - cx, dy = y[i] - cy, dz = z[i] - cz;
+ const d = dx * dx + dy * dy + dz * dz;
+ if (d > radiusSq) radiusSq = d;
}
return { center: Vec3.create(cx, cy, cz), radius: Math.sqrt(radiusSq) };
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index dcc83ade5..6b65fafd0 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -61,7 +61,7 @@ namespace SymmetryOperator {
}
}
-export default SymmetryOperator
+export { SymmetryOperator }
interface Projections { x(index: number): number, y(index: number): number, z(index: number): number }
diff --git a/src/mol-model/structure/model/formats/mmcif/assembly.ts b/src/mol-model/structure/model/formats/mmcif/assembly.ts
index 5d83ca871..a03ff07ae 100644
--- a/src/mol-model/structure/model/formats/mmcif/assembly.ts
+++ b/src/mol-model/structure/model/formats/mmcif/assembly.ts
@@ -5,7 +5,7 @@
*/
import { Mat4, Tensor } from 'mol-math/linear-algebra'
-import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
+import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import Format from '../../format'
import { Assembly, OperatorGroup, OperatorGroups } from '../../properties/symmetry'
import { Queries as Q } from '../../../query'
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index e6ed614f4..99a3877aa 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -5,16 +5,12 @@
*/
import UUID from 'mol-util/uuid'
-import GridLookup from 'mol-math/geometry/grid-lookup'
import Format from './format'
import Hierarchy from './properties/hierarchy'
import Conformation from './properties/conformation'
import Symmetry from './properties/symmetry'
-import Bonds from './properties/bonds'
import CoarseGrained from './properties/coarse-grained'
-import computeBonds from './utils/compute-bonds'
-
import from_gro from './formats/gro'
import from_mmCIF from './formats/mmcif'
@@ -38,8 +34,7 @@ interface Model extends Readonly<{
atomCount: number,
}> {
- '@spatialLookup'?: GridLookup,
- '@bonds'?: Bonds
+
} { }
namespace Model {
@@ -49,18 +44,18 @@ namespace Model {
case 'mmCIF': return from_mmCIF(format);
}
}
- export function spatialLookup(model: Model): GridLookup {
- if (model['@spatialLookup']) return model['@spatialLookup']!;
- const lookup = GridLookup(model.conformation);
- model['@spatialLookup'] = lookup;
- return lookup;
- }
- export function bonds(model: Model): Bonds {
- if (model['@bonds']) return model['@bonds']!;
- const bonds = computeBonds(model);
- model['@bonds'] = bonds;
- return bonds;
- }
+ // export function spatialLookup(model: Model): GridLookup {
+ // if (model['@spatialLookup']) return model['@spatialLookup']!;
+ // const lookup = GridLookup(model.conformation);
+ // model['@spatialLookup'] = lookup;
+ // return lookup;
+ // }
+ // export function bonds(model: Model): Bonds {
+ // if (model['@bonds']) return model['@bonds']!;
+ // const bonds = computeBonds(model);
+ // model['@bonds'] = bonds;
+ // return bonds;
+ // }
}
export default Model
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/symmetry.ts b/src/mol-model/structure/model/properties/symmetry.ts
index dfe599c2a..d459241b4 100644
--- a/src/mol-model/structure/model/properties/symmetry.ts
+++ b/src/mol-model/structure/model/properties/symmetry.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
+import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import { arrayFind } from 'mol-data/util'
import { Query } from '../../query'
import { Model } from '../../model'
diff --git a/src/mol-model/structure/model/utils/compute-bonds.ts b/src/mol-model/structure/model/utils/compute-bonds.ts
index 9b9170574..6db9047fd 100644
--- a/src/mol-model/structure/model/utils/compute-bonds.ts
+++ b/src/mol-model/structure/model/utils/compute-bonds.ts
@@ -1,253 +1,253 @@
-/**
- * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import Mask from 'mol-util/mask'
-import Model from '../model'
-import { BondType, ElementSymbol } from '../types'
-import Bonds from '../properties/bonds'
-import { StructConn, ComponentBondInfo } from '../formats/mmcif/bonds'
-
-export interface BondComputationParameters {
- maxHbondLength: number,
- forceCompute: boolean
-}
-
-// H,D,T are all mapped to H
-const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
-
-const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 1.9, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
-
-const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.3, 35: 1.3, 44: 1.05, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.55, 113: 1.59, 114: 1.36, 129: 1.45, 144: 1.6, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
-
-const __DefaultBondingRadius = 2.001;
-
-const MetalsSet = (function () {
- const metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
- const set = new Set<number>();
- for (const m of metals) {
- set.add(__ElementIndex[m]!);
- }
- return set;
-})();
-
-function pair(a: number, b: number) {
- if (a < b) return (a + b) * (a + b + 1) / 2 + b;
- else return (a + b) * (a + b + 1) / 2 + a;
-}
-
-function idx(e: ElementSymbol) {
- const i = __ElementIndex[e as any as string];
- if (i === void 0) return -1;
- return i;
-}
-
-function pairThreshold(i: number, j: number) {
- if (i < 0 || j < 0) return -1;
- const r = __ElementPairThresholds[pair(i, j)];
- if (r === void 0) return -1;
- return r;
-}
-
-function threshold(i: number) {
- if (i < 0) return __DefaultBondingRadius;
- const r = __ElementBondThresholds[i];
- if (r === void 0) return __DefaultBondingRadius;
- return r;
-}
-
-const H_ID = __ElementIndex['H']!;
-function isHydrogen(i: number) {
- return i === H_ID;
-}
-
-function computePerAtomBonds(atomA: number[], atomB: number[], _order: number[], _flags: number[], atomCount: number) {
- const bucketSizes = new Int32Array(atomCount);
- const bucketOffsets = new Int32Array(atomCount + 1) as any as number[];
- const bucketFill = new Int32Array(atomCount);
-
- for (const i of atomA) bucketSizes[i]++;
- for (const i of atomB) bucketSizes[i]++;
-
- let offset = 0;
- for (let i = 0; i < atomCount; i++) {
- bucketOffsets[i] = offset;
- offset += bucketSizes[i];
- }
- bucketOffsets[atomCount] = offset;
-
- const neighbor = new Int32Array(offset) as any as number[];
- const flags = new Uint16Array(offset) as any as number[];
- const order = new Int8Array(offset) as any as number[];
-
- for (let i = 0, _i = atomA.length; i < _i; i++) {
- const a = atomA[i], b = atomB[i], f = _flags[i], o = _order[i];
-
- const oa = bucketOffsets[a] + bucketFill[a];
- const ob = bucketOffsets[b] + bucketFill[b];
-
- neighbor[oa] = b;
- flags[oa] = f;
- order[oa] = o;
- bucketFill[a]++;
-
- neighbor[ob] = a;
- flags[ob] = f;
- order[ob] = o;
- bucketFill[b]++;
- }
-
- return {
- offsets: bucketOffsets,
- neighbor,
- flags,
- order
- };
-}
-
-function _computeBonds(model: Model, params: BondComputationParameters): Bonds {
- const MAX_RADIUS = 3;
-
- const { x, y, z } = model.conformation;
- const { atomCount } = model;
- const { residueKey } = model.hierarchy
- const { type_symbol, label_atom_id, label_alt_id } = model.hierarchy.atoms;
- const { label_comp_id } = model.hierarchy.residues;
- const query3d = Model.spatialLookup(model).find(Mask.always(atomCount));
-
- const structConn = model.sourceData.kind === 'mmCIF' ? StructConn.create(model) : void 0
- const component = model.sourceData.kind === 'mmCIF' ? ComponentBondInfo.create(model) : void 0
-
- const atomA: number[] = [];
- const atomB: number[] = [];
- const flags: number[] = [];
- const order: number[] = [];
-
- let lastResidue = -1;
- let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
-
- for (let aI = 0; aI < atomCount; aI++) {
- const raI = residueKey.value(aI);
- // const rowA = dataIndex[aI]; // TODO
- const rowA = aI;
-
- if (!params.forceCompute && raI !== lastResidue) {
- const resn = label_comp_id.value(rowA)!;
- if (!!component && component.entries.has(resn)) {
- componentMap = component.entries.get(resn)!.map;
- } else {
- componentMap = void 0;
- }
- }
- lastResidue = raI;
-
- const componentPairs = componentMap ? componentMap.get(label_atom_id.value(rowA)) : void 0;
-
- const aeI = idx(type_symbol.value(rowA)!);
-
- const { indices, count, squaredDistances } = query3d(x[aI], y[aI], z[aI], MAX_RADIUS);
- const isHa = isHydrogen(aeI);
- const thresholdA = threshold(aeI);
- const altA = label_alt_id.value(rowA);
- const metalA = MetalsSet.has(aeI);
- const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
-
- for (let ni = 0; ni < count; ni++) {
- const bI = indices[ni];
- if (bI <= aI) continue;
-
- // const rowB = dataIndex[bI]; // TODO
- const rowB = bI;
-
- const altB = label_alt_id.value(rowB);
- if (altA && altB && altA !== altB) continue;
-
- const beI = idx(type_symbol.value(rowB)!);
- const isMetal = metalA || MetalsSet.has(beI);
-
- const rbI = residueKey.value(bI);
- // handle "component dictionary" bonds.
- if (raI === rbI && componentPairs) {
- const e = componentPairs.get(label_atom_id.value(rowB)!);
- if (e) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
- order[order.length] = e.order;
- let flag = e.flags;
- if (isMetal) {
- if (flag | BondType.Flag.Covalent) flag ^= BondType.Flag.Covalent;
- flag |= BondType.Flag.MetallicCoordination;
- }
- flags[flags.length] = flag;
- }
- continue;
- }
-
- const isHb = isHydrogen(beI);
- if (isHa && isHb) continue;
-
- const dist = Math.sqrt(squaredDistances[ni]);
- if (dist === 0) continue;
-
- // handle "struct conn" bonds.
- if (structConnEntries && structConnEntries.length) {
- let added = false;
- for (const se of structConnEntries) {
- for (const p of se.partners) {
- if (p.atomIndex === bI) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
- flags[flags.length] = se.flags;
- order[order.length] = se.order;
- added = true;
- break;
- }
- }
- if (added) break;
- }
- if (added) continue;
- }
-
- if (isHa || isHb) {
- if (dist < params.maxHbondLength) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
- order[order.length] = 1;
- flags[flags.length] = BondType.Flag.Covalent | BondType.Flag.Computed; // TODO: check if correct
- }
- continue;
- }
-
- const thresholdAB = pairThreshold(aeI, beI);
- const pairingThreshold = thresholdAB > 0
- ? thresholdAB
- : beI < 0 ? thresholdA : Math.max(thresholdA, threshold(beI));
-
-
- if (dist <= pairingThreshold) {
- atomA[atomA.length] = aI;
- atomB[atomB.length] = bI;
- order[order.length] = 1;
- flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
- }
- }
- }
-
- const bonds = computePerAtomBonds(atomA, atomB, order, flags, atomCount);
- return {
- offset: bonds.offsets,
- neighbor: bonds.neighbor,
- flags: bonds.flags,
- order: bonds.order,
- count: atomA.length
- };
-}
-
-export default function computeBonds(model: Model, params?: Partial<BondComputationParameters>) {
- return _computeBonds(model, {
- maxHbondLength: (params && params.maxHbondLength) || 1.15,
- forceCompute: !!(params && params.forceCompute),
- });
-}
\ No newline at end of file
+// /**
+// * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
+
+// import Mask from 'mol-util/mask'
+// import Model from '../model'
+// import { BondType, ElementSymbol } from '../types'
+// import Bonds from '../properties/bonds'
+// import { StructConn, ComponentBondInfo } from '../formats/mmcif/bonds'
+
+// export interface BondComputationParameters {
+// maxHbondLength: number,
+// forceCompute: boolean
+// }
+
+// // H,D,T are all mapped to H
+// const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
+
+// const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 1.9, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
+
+// const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.3, 35: 1.3, 44: 1.05, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.55, 113: 1.59, 114: 1.36, 129: 1.45, 144: 1.6, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
+
+// const __DefaultBondingRadius = 2.001;
+
+// const MetalsSet = (function () {
+// const metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
+// const set = new Set<number>();
+// for (const m of metals) {
+// set.add(__ElementIndex[m]!);
+// }
+// return set;
+// })();
+
+// function pair(a: number, b: number) {
+// if (a < b) return (a + b) * (a + b + 1) / 2 + b;
+// else return (a + b) * (a + b + 1) / 2 + a;
+// }
+
+// function idx(e: ElementSymbol) {
+// const i = __ElementIndex[e as any as string];
+// if (i === void 0) return -1;
+// return i;
+// }
+
+// function pairThreshold(i: number, j: number) {
+// if (i < 0 || j < 0) return -1;
+// const r = __ElementPairThresholds[pair(i, j)];
+// if (r === void 0) return -1;
+// return r;
+// }
+
+// function threshold(i: number) {
+// if (i < 0) return __DefaultBondingRadius;
+// const r = __ElementBondThresholds[i];
+// if (r === void 0) return __DefaultBondingRadius;
+// return r;
+// }
+
+// const H_ID = __ElementIndex['H']!;
+// function isHydrogen(i: number) {
+// return i === H_ID;
+// }
+
+// function computePerAtomBonds(atomA: number[], atomB: number[], _order: number[], _flags: number[], atomCount: number) {
+// const bucketSizes = new Int32Array(atomCount);
+// const bucketOffsets = new Int32Array(atomCount + 1) as any as number[];
+// const bucketFill = new Int32Array(atomCount);
+
+// for (const i of atomA) bucketSizes[i]++;
+// for (const i of atomB) bucketSizes[i]++;
+
+// let offset = 0;
+// for (let i = 0; i < atomCount; i++) {
+// bucketOffsets[i] = offset;
+// offset += bucketSizes[i];
+// }
+// bucketOffsets[atomCount] = offset;
+
+// const neighbor = new Int32Array(offset) as any as number[];
+// const flags = new Uint16Array(offset) as any as number[];
+// const order = new Int8Array(offset) as any as number[];
+
+// for (let i = 0, _i = atomA.length; i < _i; i++) {
+// const a = atomA[i], b = atomB[i], f = _flags[i], o = _order[i];
+
+// const oa = bucketOffsets[a] + bucketFill[a];
+// const ob = bucketOffsets[b] + bucketFill[b];
+
+// neighbor[oa] = b;
+// flags[oa] = f;
+// order[oa] = o;
+// bucketFill[a]++;
+
+// neighbor[ob] = a;
+// flags[ob] = f;
+// order[ob] = o;
+// bucketFill[b]++;
+// }
+
+// return {
+// offsets: bucketOffsets,
+// neighbor,
+// flags,
+// order
+// };
+// }
+
+// function _computeBonds(model: Model, params: BondComputationParameters): Bonds {
+// const MAX_RADIUS = 3;
+
+// const { x, y, z } = model.conformation;
+// const { atomCount } = model;
+// const { residueKey } = model.hierarchy
+// const { type_symbol, label_atom_id, label_alt_id } = model.hierarchy.atoms;
+// const { label_comp_id } = model.hierarchy.residues;
+// const query3d = Model.spatialLookup(model).find(Mask.always(atomCount));
+
+// const structConn = model.sourceData.kind === 'mmCIF' ? StructConn.create(model) : void 0
+// const component = model.sourceData.kind === 'mmCIF' ? ComponentBondInfo.create(model) : void 0
+
+// const atomA: number[] = [];
+// const atomB: number[] = [];
+// const flags: number[] = [];
+// const order: number[] = [];
+
+// let lastResidue = -1;
+// let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
+
+// for (let aI = 0; aI < atomCount; aI++) {
+// const raI = residueKey.value(aI);
+// // const rowA = dataIndex[aI]; // TODO
+// const rowA = aI;
+
+// if (!params.forceCompute && raI !== lastResidue) {
+// const resn = label_comp_id.value(rowA)!;
+// if (!!component && component.entries.has(resn)) {
+// componentMap = component.entries.get(resn)!.map;
+// } else {
+// componentMap = void 0;
+// }
+// }
+// lastResidue = raI;
+
+// const componentPairs = componentMap ? componentMap.get(label_atom_id.value(rowA)) : void 0;
+
+// const aeI = idx(type_symbol.value(rowA)!);
+
+// const { indices, count, squaredDistances } = query3d(x[aI], y[aI], z[aI], MAX_RADIUS);
+// const isHa = isHydrogen(aeI);
+// const thresholdA = threshold(aeI);
+// const altA = label_alt_id.value(rowA);
+// const metalA = MetalsSet.has(aeI);
+// const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
+
+// for (let ni = 0; ni < count; ni++) {
+// const bI = indices[ni];
+// if (bI <= aI) continue;
+
+// // const rowB = dataIndex[bI]; // TODO
+// const rowB = bI;
+
+// const altB = label_alt_id.value(rowB);
+// if (altA && altB && altA !== altB) continue;
+
+// const beI = idx(type_symbol.value(rowB)!);
+// const isMetal = metalA || MetalsSet.has(beI);
+
+// const rbI = residueKey.value(bI);
+// // handle "component dictionary" bonds.
+// if (raI === rbI && componentPairs) {
+// const e = componentPairs.get(label_atom_id.value(rowB)!);
+// if (e) {
+// atomA[atomA.length] = aI;
+// atomB[atomB.length] = bI;
+// order[order.length] = e.order;
+// let flag = e.flags;
+// if (isMetal) {
+// if (flag | BondType.Flag.Covalent) flag ^= BondType.Flag.Covalent;
+// flag |= BondType.Flag.MetallicCoordination;
+// }
+// flags[flags.length] = flag;
+// }
+// continue;
+// }
+
+// const isHb = isHydrogen(beI);
+// if (isHa && isHb) continue;
+
+// const dist = Math.sqrt(squaredDistances[ni]);
+// if (dist === 0) continue;
+
+// // handle "struct conn" bonds.
+// if (structConnEntries && structConnEntries.length) {
+// let added = false;
+// for (const se of structConnEntries) {
+// for (const p of se.partners) {
+// if (p.atomIndex === bI) {
+// atomA[atomA.length] = aI;
+// atomB[atomB.length] = bI;
+// flags[flags.length] = se.flags;
+// order[order.length] = se.order;
+// added = true;
+// break;
+// }
+// }
+// if (added) break;
+// }
+// if (added) continue;
+// }
+
+// if (isHa || isHb) {
+// if (dist < params.maxHbondLength) {
+// atomA[atomA.length] = aI;
+// atomB[atomB.length] = bI;
+// order[order.length] = 1;
+// flags[flags.length] = BondType.Flag.Covalent | BondType.Flag.Computed; // TODO: check if correct
+// }
+// continue;
+// }
+
+// const thresholdAB = pairThreshold(aeI, beI);
+// const pairingThreshold = thresholdAB > 0
+// ? thresholdAB
+// : beI < 0 ? thresholdA : Math.max(thresholdA, threshold(beI));
+
+
+// if (dist <= pairingThreshold) {
+// atomA[atomA.length] = aI;
+// atomB[atomB.length] = bI;
+// order[order.length] = 1;
+// flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
+// }
+// }
+// }
+
+// const bonds = computePerAtomBonds(atomA, atomB, order, flags, atomCount);
+// return {
+// offset: bonds.offsets,
+// neighbor: bonds.neighbor,
+// flags: bonds.flags,
+// order: bonds.order,
+// count: atomA.length
+// };
+// }
+
+// export default function computeBonds(model: Model, params?: Partial<BondComputationParameters>) {
+// return _computeBonds(model, {
+// maxHbondLength: (params && params.maxHbondLength) || 1.15,
+// forceCompute: !!(params && params.forceCompute),
+// });
+// }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/element/group.ts b/src/mol-model/structure/structure/element/group.ts
index ff542066d..ec7544470 100644
--- a/src/mol-model/structure/structure/element/group.ts
+++ b/src/mol-model/structure/structure/element/group.ts
@@ -5,12 +5,15 @@
*/
import { OrderedSet } from 'mol-data/int'
+import { Lookup3D, GridLookup3D } from 'mol-math/geometry';
import Unit from '../unit'
interface ElementGroup {
elements: OrderedSet,
// Unique identifier of the group, usable as partial key for various "caches".
- key: number
+ key: number,
+
+ __lookup3d__?: Lookup3D
}
namespace ElementGroup {
@@ -61,6 +64,17 @@ namespace ElementGroup {
return createNew(set);
}
+ export function getLookup3d(unit: Unit, group: ElementGroup) {
+ if (group.__lookup3d__) return group.__lookup3d__;
+ if (Unit.isAtomic(unit)) {
+ const { x, y, z } = unit.model.conformation;
+ group.__lookup3d__ = GridLookup3D({ x, y, z, indices: group.elements });
+ return group.__lookup3d__;
+ }
+
+ throw 'not implemented';
+ }
+
let _id = 0;
function nextKey() {
const ret = _id;
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index b79ab2905..5f02951ce 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -6,7 +6,7 @@
import { OrderedSet, Iterator } from 'mol-data/int'
import { UniqueArray } from 'mol-data/generic'
-import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
+import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import { Model, Format } from '../model'
import Unit from './unit'
import ElementSet from './element/set'
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 73a503a2a..76accfeaf 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
+import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import ElementGroup from './element/group'
import { Model } from '../model'
diff --git a/src/perf-tests/lookup3d.ts b/src/perf-tests/lookup3d.ts
index 548fa35a1..3ccd9483f 100644
--- a/src/perf-tests/lookup3d.ts
+++ b/src/perf-tests/lookup3d.ts
@@ -5,8 +5,9 @@ import CIF from 'mol-io/reader/cif'
import { Structure, Model } from 'mol-model/structure'
import { Run } from 'mol-task';
-import { build, inSphere } from 'mol-math/geometry/lookup3d/grid';
+import { GridLookup3D } from 'mol-math/geometry';
import { sortArray } from 'mol-data/util';
+import { OrderedSet } from 'mol-data/int';
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
@@ -42,13 +43,14 @@ export async function readCIF(path: string) {
export async function test() {
const { mmcif } = await readCIF('e:/test/quick/1tqn_updated.cif');
- const data = build({ x: mmcif.atom_site.Cartn_x.toArray(), y: mmcif.atom_site.Cartn_y.toArray(), z: mmcif.atom_site.Cartn_z.toArray(),
- //indices: [0, 1, 2, 3]
+ const lookup = GridLookup3D({ x: mmcif.atom_site.Cartn_x.toArray(), y: mmcif.atom_site.Cartn_y.toArray(), z: mmcif.atom_site.Cartn_z.toArray(),
+ indices: OrderedSet.ofBounds(0, 4),
+ radius: [1, 1, 1, 1]
//indices: [1]
});
- console.log(data.boundingBox, data.boundingSphere);
+ console.log(lookup.boundary.box, lookup.boundary.sphere);
- const result = inSphere(data, -30.07, 8.178, -13.897, 10);
+ const result = lookup.find(-30.07, 8.178, -13.897, 1);
console.log(result.count, sortArray(result.indices));
}
--
GitLab