From 4455bab6ac1ae7b21c01f194c597ef8b4edef24b Mon Sep 17 00:00:00 2001
From: dsehnal <david.sehnal@gmail.com>
Date: Tue, 13 Dec 2022 16:06:19 +0100
Subject: [PATCH] Fix struct_conn bond assignment for ions
---
CHANGELOG.md | 1 +
.../structure/unit/bonds/inter-compute.ts | 23 +++++++++++++++----
2 files changed, 20 insertions(+), 4 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae05abb51..0e022d7ac 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Add per-pixel object clipping
- Fix `QualityAssessment` assignment bug for structures with different auth vs label sequence numbering
- Refresh `ApplyActionControl`'s param definition when toggling expanded state
+- Fix `struct_conn` bond assignment for ions
## [v3.26.0] - 2022-12-04
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 ab11f3f7b..1b803d401 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -20,6 +20,7 @@ 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';
+import { StructureProperties } from '../../properties';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3distance = Vec3.distance;
@@ -249,13 +250,27 @@ function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondCo
(!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Water) &&
(!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Water)
);
- const notIon = (
- (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Ion) &&
- (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Ion)
- );
+
+ const sameModel = a.model === b.model;
+ const notIonA = (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Ion) || (sameModel && hasStructConnRecord(a));
+ const notIonB = (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Ion) || (sameModel && hasStructConnRecord(b));
+ const notIon = notIonA && notIonB;
return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
}),
});
}
+function hasStructConnRecord(unit: Unit) {
+ const elements = unit.elements;
+ const structConn = StructConn.Provider.get(unit.model);
+ if (structConn) {
+ for (let i = 0, _i = elements.length; i < _i; i++) {
+ if (structConn.byAtomIndex.get(elements[i])) {
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
export { computeInterUnitBonds };
--
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