From dd0ad070c819aa8ba316b487f04696c0ef88aa91 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 7 Jun 2018 13:16:23 +0200
Subject: [PATCH] Induce IntGraph subgraph
---
src/helpers.d.ts | 1 +
src/mol-data/int/_spec/sorted-array.spec.ts | 4 ++
src/mol-data/int/impl/sorted-array.ts | 35 +++++++++-
src/mol-data/int/sorted-array.ts | 4 +-
src/mol-data/util/array.ts | 24 +++++++
src/mol-math/graph.ts | 2 +-
src/mol-math/graph/_spec/int-graph.spec.ts | 11 ++-
.../graph/{int/graph.ts => int-graph.ts} | 67 +++++++++++++++----
.../structure/structure/unit/bonds/data.ts | 1 +
.../structure/unit/bonds/inter-compute.ts | 1 +
.../structure/unit/bonds/inter-data.ts | 1 +
.../structure/structure/unit/rings/compute.ts | 2 +-
12 files changed, 135 insertions(+), 18 deletions(-)
rename src/mol-math/graph/{int/graph.ts => int-graph.ts} (61%)
create mode 100644 src/mol-model/structure/structure/unit/bonds/data.ts
create mode 100644 src/mol-model/structure/structure/unit/bonds/inter-compute.ts
create mode 100644 src/mol-model/structure/structure/unit/bonds/inter-data.ts
diff --git a/src/helpers.d.ts b/src/helpers.d.ts
index 3dbdd2dc7..69dca2592 100644
--- a/src/helpers.d.ts
+++ b/src/helpers.d.ts
@@ -13,4 +13,5 @@ declare module Helpers {
export type NumberArray = TypedArray | number[]
export type UintArray = Uint8Array | Uint16Array | Uint32Array | number[]
export type ValueOf<T> = T[keyof T]
+ export type ArrayCtor<T> = { new(size: number): { [i: number]: T, length: number } }
}
\ No newline at end of file
diff --git a/src/mol-data/int/_spec/sorted-array.spec.ts b/src/mol-data/int/_spec/sorted-array.spec.ts
index 2cd82af32..c5ca33cf5 100644
--- a/src/mol-data/int/_spec/sorted-array.spec.ts
+++ b/src/mol-data/int/_spec/sorted-array.spec.ts
@@ -59,6 +59,10 @@ describe('sortedArray', () => {
compareArrays(SortedArray.deduplicate(SortedArray.ofSortedArray([1, 2, 3])), [1, 2, 3]);
});
+ it('indicesOf', () => {
+ compareArrays(SortedArray.indicesOf(SortedArray.ofSortedArray([10, 11, 12]), SortedArray.ofSortedArray([10, 12, 14])), [0, 2]);
+ })
+
// console.log(Interval.findPredecessorIndexInInterval(Interval.ofBounds(0, 3), 2, Interval.ofBounds(0, 3)))
// console.log(SortedArray.findPredecessorIndexInInterval(SortedArray.ofSortedArray([0, 1, 2]), 2, Interval.ofBounds(0, 3)))
});
\ No newline at end of file
diff --git a/src/mol-data/int/impl/sorted-array.ts b/src/mol-data/int/impl/sorted-array.ts
index 4a5476c16..09b787726 100644
--- a/src/mol-data/int/impl/sorted-array.ts
+++ b/src/mol-data/int/impl/sorted-array.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { sortArray, hash3, hash4 } from '../../util'
+import { sortArray, hash3, hash4, createRangeArray } from '../../util'
import Interval from '../interval'
type Nums = ArrayLike<number>
@@ -289,6 +289,39 @@ export function deduplicate(xs: Nums) {
return ret;
}
+export function indicesOf(a: Nums, b: Nums): Nums {
+ if (a === b) return ofSortedArray(createRangeArray(0, a.length - 1));
+
+ const { startI: sI, startJ: sJ, endI, endJ } = getSuitableIntersectionRange(a, b);
+ let i = sI, j = sJ;
+ let commonCount = 0;
+ while (i < endI && j < endJ) {
+ const x = a[i], y = b[j];
+ if (x < y) { i++; }
+ else if (x > y) { j++; }
+ else { i++; j++; commonCount++; }
+ }
+
+ const lenA = a.length;
+ // no common elements
+ if (!commonCount) return Empty;
+ // A is subset of B ==> A
+ if (commonCount === lenA) return ofSortedArray(createRangeArray(0, a.length - 1));
+
+ const indices = new Int32Array(commonCount);
+ let offset = 0;
+ i = sI;
+ j = sJ;
+ while (i < endI && j < endJ) {
+ const x = a[i], y = b[j];
+ if (x < y) { i++; }
+ else if (x > y) { j++; }
+ else { indices[offset++] = i; i++; j++; }
+ }
+
+ return ofSortedArray(indices);
+}
+
const _maxIntRangeRet = { startI: 0, startJ: 0, endI: 0, endJ: 0 };
// for small sets, just gets the whole range, for large sets does a bunch of binary searches
function getSuitableIntersectionRange(a: Nums, b: Nums) {
diff --git a/src/mol-data/int/sorted-array.ts b/src/mol-data/int/sorted-array.ts
index 928e383dd..2c92aa329 100644
--- a/src/mol-data/int/sorted-array.ts
+++ b/src/mol-data/int/sorted-array.ts
@@ -41,7 +41,9 @@ namespace SortedArray {
export const findPredecessorIndexInInterval: (array: SortedArray, x: number, bounds: Interval) => number = Impl.findPredecessorIndexInInterval as any;
export const findRange: (array: SortedArray, min: number, max: number) => Interval = Impl.findRange as any;
- export const deduplicate: (arrat: SortedArray) => SortedArray = Impl.deduplicate as any;
+ export const deduplicate: (array: SortedArray) => SortedArray = Impl.deduplicate as any;
+ /** Returns indices of xs in the array. E.g. indicesOf([10, 11, 12], [10, 12]) ==> [0, 2] */
+ export const indicesOf: (array: SortedArray, xs: SortedArray) => SortedArray = Impl.indicesOf as any;
}
interface SortedArray extends ArrayLike<number> { '@type': 'int-sorted-array' }
diff --git a/src/mol-data/util/array.ts b/src/mol-data/util/array.ts
index 93707e797..94311c38c 100644
--- a/src/mol-data/util/array.ts
+++ b/src/mol-data/util/array.ts
@@ -22,4 +22,28 @@ export function iterableToArray<T>(it: IterableIterator<T>): T[] {
ret[ret.length] = value;
}
return ret;
+}
+
+/** Fills the array so that array[0] = start and array[array.length - 1] = end */
+export function createRangeArray(start: number, end: number, ctor?: Helpers.ArrayCtor<number>) {
+ const len = end - start + 1;
+ const array = ctor ? new ctor(len) : new Int32Array(len);
+ for (let i = 0; i < len; i++) {
+ array[i] = i + start;
+ }
+ return array;
+}
+
+export function arrayPickIndices<T>(array: ArrayLike<T>, indices: ArrayLike<number>) {
+ const ret = new (arrayGetCtor(array))(indices.length);
+ for (let i = 0, _i = indices.length; i < _i; i++) {
+ ret[i] = array[indices[i]];
+ }
+ return ret;
+}
+
+export function arrayGetCtor<T>(data: ArrayLike<T>): Helpers.ArrayCtor<T> {
+ const ret = (data as any).constructor;
+ if (!ret) throw new Error('data does not define a constructor and it should');
+ return ret;
}
\ No newline at end of file
diff --git a/src/mol-math/graph.ts b/src/mol-math/graph.ts
index ce0429662..f152b30c2 100644
--- a/src/mol-math/graph.ts
+++ b/src/mol-math/graph.ts
@@ -4,4 +4,4 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-export * from './graph/int/graph'
\ No newline at end of file
+export * from './graph/int-graph'
\ No newline at end of file
diff --git a/src/mol-math/graph/_spec/int-graph.spec.ts b/src/mol-math/graph/_spec/int-graph.spec.ts
index 3d75dddb0..25319d118 100644
--- a/src/mol-math/graph/_spec/int-graph.spec.ts
+++ b/src/mol-math/graph/_spec/int-graph.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { IntGraph } from '../int/graph';
+import { IntGraph } from '../int-graph';
describe('IntGraph', () => {
const vc = 3;
@@ -28,9 +28,16 @@ describe('IntGraph', () => {
});
it('triangle-propAndEdgeIndex', () => {
- const prop = graph.prop;
+ const prop = graph.edgeProps.prop;
expect(prop[graph.getEdgeIndex(0, 1)]).toBe(10);
expect(prop[graph.getEdgeIndex(1, 2)]).toBe(11);
expect(prop[graph.getEdgeIndex(2, 0)]).toBe(12);
});
+
+ it('induce', () => {
+ const induced = IntGraph.induceByVertices(graph, [1, 2]);
+ expect(induced.vertexCount).toBe(2);
+ expect(induced.edgeCount).toBe(1);
+ expect(induced.edgeProps.prop[induced.getEdgeIndex(0, 1)]).toBe(11);
+ })
});
\ No newline at end of file
diff --git a/src/mol-math/graph/int/graph.ts b/src/mol-math/graph/int-graph.ts
similarity index 61%
rename from src/mol-math/graph/int/graph.ts
rename to src/mol-math/graph/int-graph.ts
index fb50ee13f..f6576942c 100644
--- a/src/mol-math/graph/int/graph.ts
+++ b/src/mol-math/graph/int-graph.ts
@@ -1,3 +1,5 @@
+import { arrayPickIndices } from 'mol-data/util';
+
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
@@ -12,12 +14,13 @@
*
* Edge properties are indexed same as in the arrays a and b.
*/
-type IntGraph<EdgeProperties extends object = { }> = {
+interface IntGraph<EdgeProps extends IntGraph.EdgePropsBase = {}> {
readonly offset: ArrayLike<number>,
readonly a: ArrayLike<number>,
readonly b: ArrayLike<number>,
readonly vertexCount: number,
readonly edgeCount: number,
+ readonly edgeProps: Readonly<EdgeProps>
/**
* Get the edge index between i-th and j-th vertex.
@@ -28,11 +31,14 @@ type IntGraph<EdgeProperties extends object = { }> = {
*/
getEdgeIndex(i: number, j: number): number,
getVertexEdgeCount(i: number): number
-} & EdgeProperties
+}
namespace IntGraph {
- class Impl implements IntGraph<any> {
+ export type EdgePropsBase = { [name: string]: ArrayLike<any> }
+
+ class IntGraphImpl implements IntGraph<any> {
readonly vertexCount: number;
+ readonly edgeProps: object;
getEdgeIndex(i: number, j: number): number {
let a, b;
@@ -48,18 +54,14 @@ namespace IntGraph {
return this.offset[i + 1] - this.offset[i];
}
- constructor(public offset: ArrayLike<number>, public a: ArrayLike<number>, public b: ArrayLike<number>, public edgeCount: number, props?: any) {
+ constructor(public offset: ArrayLike<number>, public a: ArrayLike<number>, public b: ArrayLike<number>, public edgeCount: number, edgeProps?: any) {
this.vertexCount = offset.length - 1;
- if (props) {
- for (const p of Object.keys(props)) {
- (this as any)[p] = props[p];
- }
- }
+ this.edgeProps = edgeProps || {};
}
}
- export function create<EdgeProps extends object = { }>(offset: ArrayLike<number>, a: ArrayLike<number>, b: ArrayLike<number>, edgeCount: number, edgeProps?: EdgeProps): IntGraph<EdgeProps> {
- return new Impl(offset, a, b, edgeCount, edgeProps) as IntGraph<EdgeProps>;
+ export function create<EdgeProps extends IntGraph.EdgePropsBase = {}>(offset: ArrayLike<number>, a: ArrayLike<number>, b: ArrayLike<number>, edgeCount: number, edgeProps?: EdgeProps): IntGraph<EdgeProps> {
+ return new IntGraphImpl(offset, a, b, edgeCount, edgeProps) as IntGraph<EdgeProps>;
}
export class EdgeBuilder {
@@ -75,7 +77,7 @@ namespace IntGraph {
a: Int32Array;
b: Int32Array;
- createGraph<EdgeProps extends object = { }>(edgeProps?: EdgeProps) {
+ createGraph<EdgeProps extends IntGraph.EdgePropsBase = {}>(edgeProps?: EdgeProps) {
return create(this.offsets, this.a, this.b, this.edgeCount, edgeProps);
}
@@ -132,6 +134,47 @@ namespace IntGraph {
this.b = new Int32Array(offset);
}
}
+
+ export function induceByVertices<P extends IntGraph.EdgePropsBase>(graph: IntGraph<P>, vertexIndices: ArrayLike<number>): IntGraph<P> {
+ const { b, offset, vertexCount, edgeProps } = graph;
+ const vertexMap = new Int32Array(vertexCount);
+ for (let i = 0, _i = vertexIndices.length; i < _i; i++) vertexMap[vertexIndices[i]] = i + 1;
+
+ let newEdgeCount = 0;
+ for (let i = 0; i < vertexCount; i++) {
+ if (vertexMap[i] === 0) continue;
+ for (let j = offset[i], _j = offset[i + 1]; j < _j; j++) {
+ if (b[j] > i && vertexMap[b[j]] !== 0) newEdgeCount++;
+ }
+ }
+
+ const newOffsets = new Int32Array(vertexIndices.length + 1);
+ const edgeIndices = new Int32Array(2 * newEdgeCount);
+ const newA = new Int32Array(2 * newEdgeCount);
+ const newB = new Int32Array(2 * newEdgeCount);
+ let eo = 0, vo = 0;
+ for (let i = 0; i < vertexCount; i++) {
+ if (vertexMap[i] === 0) continue;
+ const aa = vertexMap[i] - 1;
+ for (let j = offset[i], _j = offset[i + 1]; j < _j; j++) {
+ const bb = vertexMap[b[j]];
+ if (bb === 0) continue;
+
+ newA[eo] = aa;
+ newB[eo] = bb - 1;
+ edgeIndices[eo] = j;
+ eo++;
+ }
+ newOffsets[++vo] = eo;
+ }
+
+ const newEdgeProps: P = {} as any;
+ for (const key of Object.keys(edgeProps)) {
+ newEdgeProps[key] = arrayPickIndices(edgeProps[key], edgeIndices);
+ }
+
+ return create(newOffsets, newA, newB, newEdgeCount, newEdgeProps);
+ }
}
export { IntGraph }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/data.ts b/src/mol-model/structure/structure/unit/bonds/data.ts
new file mode 100644
index 000000000..0ffdd02fc
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/bonds/data.ts
@@ -0,0 +1 @@
+// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
new file mode 100644
index 000000000..0ffdd02fc
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -0,0 +1 @@
+// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-data.ts b/src/mol-model/structure/structure/unit/bonds/inter-data.ts
new file mode 100644
index 000000000..0ffdd02fc
--- /dev/null
+++ b/src/mol-model/structure/structure/unit/bonds/inter-data.ts
@@ -0,0 +1 @@
+// TODO
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit/rings/compute.ts b/src/mol-model/structure/structure/unit/rings/compute.ts
index a76cd6e47..3a8359412 100644
--- a/src/mol-model/structure/structure/unit/rings/compute.ts
+++ b/src/mol-model/structure/structure/unit/rings/compute.ts
@@ -148,7 +148,7 @@ function addRing(state: State, a: number, b: number) {
function findRings(state: State, from: number) {
const { bonds, startVertex, endVertex, visited, queue, pred } = state;
- const { b: neighbor, flags: bondFlags, offset } = bonds;
+ const { b: neighbor, edgeProps: { flags: bondFlags }, offset } = bonds;
visited[from] = 1;
queue[0] = from;
let head = 0, size = 1;
--
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