From a2bf489017f28f5d2863c159883ef85577c60b7f Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Mon, 25 May 2020 03:52:35 +0200
Subject: [PATCH] fix bond ordering when creating structure from Topology
---
src/mol-model/structure/model/model.ts | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 68033af3b..0f490fc5c 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -120,16 +120,26 @@ export namespace Model {
return _trajectoryFromModelAndCoordinates(model, coordinates).trajectory;
}
+ function invertIndex(xs: ArrayLike<number>) {
+ const ret = new Int32Array(xs.length);
+ for (let i = 0, _i = xs.length; i < _i; i++) {
+ ret[xs[i]] = i;
+ }
+ return ret;
+ }
+
export function trajectoryFromTopologyAndCoordinates(topology: Topology, coordinates: Coordinates): Task<Trajectory> {
return Task.create('Create Trajectory', async ctx => {
const model = (await createModels(topology.basic, topology.sourceData, ctx))[0];
if (!model) throw new Error('found no model');
const { trajectory, srcIndexArray } = _trajectoryFromModelAndCoordinates(model, coordinates);
+ // TODO: cache the inverted index somewhere?
+ const invertedIndex = srcIndexArray ? invertIndex(srcIndexArray) : void 0;
const pairs = srcIndexArray
? {
- indexA: Column.ofIntArray(Column.mapToArray(topology.bonds.indexA, i => srcIndexArray[i], Int32Array)),
- indexB: Column.ofIntArray(Column.mapToArray(topology.bonds.indexB, i => srcIndexArray[i], Int32Array)),
+ indexA: Column.ofIntArray(Column.mapToArray(topology.bonds.indexA, i => invertedIndex![i], Int32Array)),
+ indexB: Column.ofIntArray(Column.mapToArray(topology.bonds.indexB, i => invertedIndex![i], Int32Array)),
order: topology.bonds.order
}
: topology.bonds;
--
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