diff --git a/CHANGELOG.md b/CHANGELOG.md
index 73d64332859fff29877d2c48885f3ff40b10ecd9..e613e3a4a6c6e582715f0f9981f20fb9599c3368 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add glTF (GLB) and STL support to ``geo-export`` extension.
- Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
+- Fix #178: ``IndexPairBonds`` for non-single residue structures (bug due to atom reordering).
## [v2.0.5] - 2021-04-26
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 5dcc9a97fa064837b752b610bc6ac795c69b80d0..8de466ac0a7b88cc6903f791feba3806ff79d9f6 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -131,32 +131,14 @@ export namespace Model {
return new ArrayTrajectory(_trajectoryFromModelAndCoordinates(model, coordinates).trajectory);
}
- export 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 models = await createModels(topology.basic, topology.sourceData, ctx);
if (models.frameCount === 0) throw new Error('found no model');
const model = models.representative;
- 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 => invertedIndex![i], Int32Array)),
- indexB: Column.ofIntArray(Column.mapToArray(topology.bonds.indexB, i => invertedIndex![i], Int32Array)),
- order: topology.bonds.order
- }
- : topology.bonds;
-
- const bondData = { pairs, count: model.atomicHierarchy.atoms._rowCount };
+ const { trajectory } = _trajectoryFromModelAndCoordinates(model, coordinates);
+
+ const bondData = { pairs: topology.bonds, count: model.atomicHierarchy.atoms._rowCount };
const indexPairBonds = IndexPairBonds.fromData(bondData);
let index = 0;
@@ -176,6 +158,25 @@ export namespace Model {
return center;
}
+ function invertIndex(xs: Column<number>) {
+ const invertedIndex = new Int32Array(xs.rowCount);
+ let isIdentity = false;
+ for (let i = 0, _i = xs.rowCount; i < _i; i++) {
+ const x = xs.value(i);
+ if (x !== i) isIdentity = false;
+ invertedIndex[x] = i;
+ }
+ return { isIdentity, invertedIndex: invertedIndex as unknown as ArrayLike<ElementIndex> };
+ }
+
+ const InvertedAtomSrcIndexProp = '__InvertedAtomSrcIndex__';
+ export function getInvertedAtomSourceIndex(model: Model): { isIdentity: boolean, invertedIndex: ArrayLike<ElementIndex> } {
+ if (model._staticPropertyData[InvertedAtomSrcIndexProp]) return model._staticPropertyData[InvertedAtomSrcIndexProp];
+ const index = invertIndex(model.atomicHierarchy.atomSourceIndex);
+ model._staticPropertyData[InvertedAtomSrcIndexProp] = index;
+ return index;
+ }
+
const TrajectoryInfoProp = '__TrajectoryInfo__';
export type TrajectoryInfo = { readonly index: number, readonly size: number }
export const TrajectoryInfo = {
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
index 1a30fcce4e9b310e6d31b94406efff2079d0d813..77221dc1694e5a932be9a1dd5c246e770f87a1eb 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -19,6 +19,7 @@ import { IndexPairBonds } from '../../../../../mol-model-formats/structure/prope
import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
import { StructConn } from '../../../../../mol-model-formats/structure/property/bonds/struct_conn';
import { equalEps } from '../../../../../mol-math/linear-algebra/3d/common';
+import { Model } from '../../../model';
const MAX_RADIUS = 4;
@@ -48,7 +49,10 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const hasOccupancy = occupancyA.isDefined && occupancyB.isDefined;
const structConn = unitA.model === unitB.model && StructConn.Provider.get(unitA.model);
- const indexPairs = unitA.model === unitB.model && IndexPairBonds.Provider.get(unitA.model);
+ const indexPairs = !props.forceCompute && unitA.model === unitB.model && IndexPairBonds.Provider.get(unitA.model);
+
+ const { atomSourceIndex: sourceIndex } = unitA.model.atomicHierarchy;
+ const { invertedIndex } = indexPairs ? Model.getInvertedAtomSourceIndex(unitB.model) : { invertedIndex: void 0 };
const structConnExhaustive = unitA.model === unitB.model && StructConn.isExhaustive(unitA.model);
@@ -70,8 +74,10 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
if (!props.forceCompute && indexPairs) {
const { order, distance, flag } = indexPairs.edgeProps;
- for (let i = indexPairs.offset[aI], il = indexPairs.offset[aI + 1]; i < il; ++i) {
- const bI = indexPairs.b[i];
+
+ const srcA = sourceIndex.value(aI);
+ for (let i = indexPairs.offset[srcA], il = indexPairs.offset[srcA + 1]; i < il; ++i) {
+ const bI = invertedIndex![indexPairs.b[i]];
const _bI = SortedArray.indexOf(unitB.elements, bI) as StructureElement.UnitIndex;
if (_bI < 0) continue;
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 81f20fbcba73d25c7265130a1d0397d30f440725..673858e1593d5403c450dc776d99c11df70bba5f 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -51,6 +51,9 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const atomCount = unit.elements.length;
const { edgeProps } = indexPairs;
+ const { atomSourceIndex: sourceIndex } = unit.model.atomicHierarchy;
+ const { invertedIndex } = Model.getInvertedAtomSourceIndex(unit.model);
+
const atomA: StructureElement.UnitIndex[] = [];
const atomB: StructureElement.UnitIndex[] = [];
const flags: number[] = [];
@@ -60,8 +63,10 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const aI = atoms[_aI];
const isHa = type_symbol.value(aI) === 'H';
- for (let i = indexPairs.offset[aI], il = indexPairs.offset[aI + 1]; i < il; ++i) {
- const bI = indexPairs.b[i];
+ const srcA = sourceIndex.value(aI);
+
+ for (let i = indexPairs.offset[srcA], il = indexPairs.offset[srcA + 1]; i < il; ++i) {
+ const bI = invertedIndex[indexPairs.b[i]];
if (aI >= bI) continue;
const _bI = SortedArray.indexOf(unit.elements, bI) as StructureElement.UnitIndex;