From 36eae744af13cd22fa756fa54d7d124e699fda0a Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 30 Jul 2019 16:24:54 -0700
Subject: [PATCH] ensure that "single atom chains" units have same entity id
---
src/mol-model/structure/structure/structure.ts | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index ef5283561..11069dda8 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -373,7 +373,7 @@ namespace Structure {
* Construct a Structure from a model.
*
* Generally, a single unit corresponds to a single chain, with the exception
- * of consecutive "single atom chains".
+ * of consecutive "single atom chains" with same entity id.
*/
export function ofModel(model: Model): Structure {
const chains = model.atomicHierarchy.chainAtomSegments;
@@ -382,16 +382,20 @@ namespace Structure {
for (let c = 0; c < chains.count; c++) {
const start = chains.offsets[c];
- // merge all consecutive "single atom chains"
+ // merge all consecutive "single atom chains" with same entity id
while (c + 1 < chains.count
&& chains.offsets[c + 1] - chains.offsets[c] === 1
- && chains.offsets[c + 2] - chains.offsets[c + 1] === 1) {
+ && chains.offsets[c + 2] - chains.offsets[c + 1] === 1
+ ) {
c++;
+ const e1 = model.atomicHierarchy.index.getEntityFromChain(c as ChainIndex);
+ const e2 = model.atomicHierarchy.index.getEntityFromChain(c + 1 as ChainIndex);
+ if (e1 !== e2) break
}
const elements = SortedArray.ofBounds(start as ElementIndex, chains.offsets[c + 1] as ElementIndex);
- if (isWaterChain(model, c as ChainIndex, elements)) {
+ if (isWaterChain(model, c as ChainIndex)) {
partitionAtomicUnit(model, elements, builder);
} else {
builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
@@ -411,7 +415,7 @@ namespace Structure {
return builder.getStructure();
}
- function isWaterChain(model: Model, chainIndex: ChainIndex, indices: SortedArray) {
+ function isWaterChain(model: Model, chainIndex: ChainIndex) {
const e = model.atomicHierarchy.index.getEntityFromChain(chainIndex);
return model.entities.data.type.value(e) === 'water';
}
--
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