From ebd3ebe7b2e3531b51cd0beb04d9e259ee762847 Mon Sep 17 00:00:00 2001
From: David Sehnal <dsehnal@users.noreply.github.com>
Date: Tue, 25 Apr 2023 16:25:39 +0200
Subject: [PATCH] fix struct conn for waters (#803)
---
CHANGELOG.md | 1 +
.../structure/structure/structure.ts | 6 ++-
.../structure/unit/bonds/inter-compute.ts | 40 +++++++++++++------
3 files changed, 32 insertions(+), 15 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3b376fdaf..45a70d71a 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
## [Unreleased]
- Add a uniform color theme for NtC tube that still paints residue and segment dividers in a different color
+- Fix bond assignments `struct_conn` records referencing waters
## [v3.34.0] - 2023-04-16
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index e42d697cc..33324a2f7 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -1225,8 +1225,10 @@ namespace Structure {
const closeUnits = lookup.findUnitIndices(imageCenter[0], imageCenter[1], imageCenter[2], bs.radius + maxRadius);
for (let i = 0; i < closeUnits.count; i++) {
const other = structure.units[closeUnits.indices[i]];
+ if (unit.id >= other.id) continue;
+
if (other.elements.length > 3 && !Box3D.overlaps(bbox, other.boundary.box)) continue;
- if (!validUnit(other) || unit.id >= other.id || !validUnitPair(unit, other)) continue;
+ if (!validUnit(other) || !validUnitPair(unit, other)) continue;
if (other.elements.length >= unit.elements.length) callback(unit, other);
else callback(other, unit);
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 69f51afb6..1a8603945 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -243,6 +243,11 @@ function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondCo
...p,
validUnit: (props && props.validUnit) || (u => Unit.isAtomic(u)),
validUnitPair: (props && props.validUnitPair) || ((s, a, b) => {
+ // In case both units have a struct conn record, ignore other criteria
+ if (hasCommonStructConnRecord(a, b)) {
+ return Structure.validUnitPair(s, a, b);
+ }
+
const mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
const mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
const notWater = (
@@ -250,25 +255,34 @@ function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondCo
(!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Water)
);
- 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 notIonA = (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Ion);
+ const notIonB = (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Ion);
const notIon = notIonA && notIonB;
return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
}),
});
}
-function hasStructConnRecord(unit: Unit) {
- if (!Unit.isAtomic(unit)) return false;
+function hasCommonStructConnRecord(unitA: Unit, unitB: Unit) {
+ if (unitA.model !== unitB.model || !Unit.isAtomic(unitA) || !Unit.isAtomic(unitB)) return false;
+ const structConn = StructConn.Provider.get(unitA.model);
+ if (!structConn) return false;
- 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;
- }
+ const smaller = unitA.elements.length < unitB.elements.length ? unitA : unitB;
+ const bigger = unitA.elements.length >= unitB.elements.length ? unitA : unitB;
+
+ const { elements: xs } = smaller;
+ const { elements: ys } = bigger;
+ const { indexOf } = SortedArray;
+
+ for (let i = 0, _i = xs.length; i < _i; i++) {
+ const aI = xs[i];
+ const entries = structConn.byAtomIndex.get(aI);
+ if (!entries?.length) continue;
+
+ for (const e of entries) {
+ const bI = e.partnerA.atomIndex === aI ? e.partnerB.atomIndex : e.partnerA.atomIndex;
+ if (indexOf(ys, bI) >= 0) return true;
}
}
return false;
--
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