From a8d43028399b03dc0f6a7efbc0f21c4f275c1af1 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 11 Jun 2018 15:25:37 +0200
Subject: [PATCH] sort mmCIF atom_site
---
src/mol-data/util/_spec/buckets.spec.ts | 12 +++++--
src/mol-data/util/buckets.ts | 25 ++++++++++++---
.../structure/model/formats/mmcif.ts | 3 ++
.../structure/model/formats/mmcif/sort.ts | 32 +++++++++++++++++++
4 files changed, 65 insertions(+), 7 deletions(-)
create mode 100644 src/mol-model/structure/model/formats/mmcif/sort.ts
diff --git a/src/mol-data/util/_spec/buckets.spec.ts b/src/mol-data/util/_spec/buckets.spec.ts
index 2207a53f9..64046ce37 100644
--- a/src/mol-data/util/_spec/buckets.spec.ts
+++ b/src/mol-data/util/_spec/buckets.spec.ts
@@ -18,16 +18,24 @@ describe('buckets', () => {
it('full range', () => {
const xs = [1, 1, 2, 2, 3, 1];
const range = createRangeArray(0, xs.length - 1);
- const bs = makeBuckets(range, i => xs[i]);
+ const bs = makeBuckets(range, i => xs[i], false);
expect(reorder(range, xs)).toEqual([1, 1, 1, 2, 2, 3]);
expect(Array.from(bs)).toEqual([0, 3, 5, 6]);
});
+ it('sort', () => {
+ const xs = [3, 1, 2, 1, 2, 3];
+ const range = createRangeArray(0, xs.length - 1);
+ makeBuckets(range, i => xs[i], true);
+
+ expect(reorder(range, xs)).toEqual([1, 1, 2, 2, 3, 3]);
+ });
+
it('subrange', () => {
const xs = [2, 1, 2, 1, 2, 3, 1];
const range = createRangeArray(0, xs.length - 1);
- const bs = makeBuckets(range, i => xs[i], 1, 5);
+ const bs = makeBuckets(range, i => xs[i], false, 1, 5);
expect(reorder(range, xs)).toEqual([2, 1, 1, 2, 2, 3, 1]);
expect(Array.from(bs)).toEqual([1, 3, 5]);
diff --git a/src/mol-data/util/buckets.ts b/src/mol-data/util/buckets.ts
index 58a747e9d..33bbc3d79 100644
--- a/src/mol-data/util/buckets.ts
+++ b/src/mol-data/util/buckets.ts
@@ -5,11 +5,12 @@
*/
type Bucket = {
+ key: any,
count: number,
offset: number
}
-function _makeBuckets(indices: Helpers.ArrayLike<number>, getKey: (i: number) => any, start: number, end: number) {
+function _makeBuckets(indices: Helpers.ArrayLike<number>, getKey: (i: number) => any, sort: boolean, start: number, end: number) {
const buckets = new Map<any, Bucket>();
const bucketList: Bucket[] = [];
@@ -21,7 +22,7 @@ function _makeBuckets(indices: Helpers.ArrayLike<number>, getKey: (i: number) =>
buckets.get(key)!.count++;
if (prevKey !== key) isBucketed = false;
} else {
- const bucket: Bucket = { count: 1, offset: i };
+ const bucket: Bucket = { key, count: 1, offset: i };
buckets.set(key, bucket);
bucketList[bucketList.length] = bucket;
}
@@ -31,11 +32,25 @@ function _makeBuckets(indices: Helpers.ArrayLike<number>, getKey: (i: number) =>
const bucketOffsets = new Int32Array(bucketList.length + 1);
bucketOffsets[bucketList.length] = end;
- if (isBucketed) {
+ let sorted = true;
+ if (sort) {
+ for (let i = 1, _i = bucketList.length; i < _i; i++) {
+ if (bucketList[i - 1].key > bucketList[i].key) {
+ sorted = false;
+ break;
+ }
+ }
+ }
+
+ if (isBucketed && sorted) {
for (let i = 0; i < bucketList.length; i++) bucketOffsets[i] = bucketList[i].offset;
return bucketOffsets;
}
+ if (sort && !sorted) {
+ bucketList.sort((x, y) => x.key <= y.key ? -1 : 1);
+ }
+
let offset = 0;
for (let i = 0; i < bucketList.length; i++) {
const b = bucketList[i];
@@ -64,11 +79,11 @@ function _makeBuckets(indices: Helpers.ArrayLike<number>, getKey: (i: number) =>
* Reorders indices so that the same keys are next to each other, [start, end)
* Returns the offsets of buckets. So that [offsets[i], offsets[i + 1]) determines the range.
*/
-export function makeBuckets<T>(indices: Helpers.ArrayLike<number>, getKey: (i: number) => string | number, start?: number, end?: number): ArrayLike<number> {
+export function makeBuckets<T>(indices: Helpers.ArrayLike<number>, getKey: (i: number) => string | number, sort: boolean, start?: number, end?: number): ArrayLike<number> {
const s = start || 0;
const e = typeof end === 'undefined' ? indices.length : end;
if (e - s <= 0) throw new Error('Can only bucket non-empty collections.');
- return _makeBuckets(indices, getKey, s, e);
+ return _makeBuckets(indices, getKey, sort, s, e);
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index a5c8c5008..f83a449f0 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -23,6 +23,7 @@ import { getSequence } from './mmcif/sequence';
import mmCIF_Format = Format.mmCIF
import { Task } from 'mol-task';
import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
+import { sortAtomSite } from './mmcif/sort';
function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
@@ -196,6 +197,8 @@ function buildModels(format: mmCIF_Format): Task<ReadonlyArray<Model>> {
let modelStart = 0;
while (modelStart < atomCount) {
const bounds = findModelBounds(format, modelStart);
+
+ // const indices = await sortAtomSite(ctx, format.data.atom_site, 0, Interval.end(bounds));
const model = createModel(format, bounds, models.length > 0 ? models[models.length - 1] : void 0);
models.push(model);
modelStart = Interval.end(bounds);
diff --git a/src/mol-model/structure/model/formats/mmcif/sort.ts b/src/mol-model/structure/model/formats/mmcif/sort.ts
new file mode 100644
index 000000000..aa071aedb
--- /dev/null
+++ b/src/mol-model/structure/model/formats/mmcif/sort.ts
@@ -0,0 +1,32 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
+import { createRangeArray, makeBuckets } from 'mol-data/util';
+import { Column } from 'mol-data/db';
+import { RuntimeContext } from 'mol-task';
+
+export async function sortAtomSite(ctx: RuntimeContext, atom_site: mmCIF_Database['atom_site'], start: number, end: number) {
+ const indices = createRangeArray(start, end - 1);
+
+ const { label_entity_id, label_asym_id, label_seq_id } = atom_site;
+ const entityBuckets = makeBuckets(indices, label_entity_id.value, false);
+ if (ctx.shouldUpdate) await ctx.update();
+ for (let ei = 0, _eI = entityBuckets.length - 1; ei < _eI; ei++) {
+ const chainBuckets = makeBuckets(indices, label_asym_id.value, false, entityBuckets[ei], entityBuckets[ei + 1]);
+ for (let cI = 0, _cI = chainBuckets.length - 1; cI < _cI; cI++) {
+ const aI = chainBuckets[cI];
+ // are we in HETATM territory?
+ if (label_seq_id.valueKind(aI) !== Column.ValueKind.Present) continue;
+
+ makeBuckets(indices, label_seq_id.value, true, aI, chainBuckets[cI + 1]);
+ if (ctx.shouldUpdate) await ctx.update();
+ }
+ if (ctx.shouldUpdate) await ctx.update();
+ }
+
+ return indices;
+}
\ No newline at end of file
--
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