From dd6dcddabad88e971b64fadbc6ce9cc9b8a26e2b Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Sat, 9 Jun 2018 12:41:27 +0200
Subject: [PATCH] Update Structure construction from Model
---
src/apps/structure-info/model.ts | 2 +-
.../structure/structure/structure.ts | 20 ++++++++++---------
2 files changed, 12 insertions(+), 10 deletions(-)
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index c06c66e4e..6a8ce6309 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -196,7 +196,7 @@ async function run(mmcif: mmCIF_Database) {
//printIHMModels(models[0]);
printUnits(structure);
//printRings(structure);
- printLinks(structure, true, true);
+ //printLinks(structure, true, true);
//printModRes(models[0]);
//printSecStructure(models[0]);
}
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 22666fb13..78ef1b470 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -94,25 +94,27 @@ namespace Structure {
export function create(units: ReadonlyArray<Unit>): Structure { return new Structure(units); }
+ /**
+ * Construct a Structure from a model.
+ *
+ * Generally, a single unit corresponds to a single chain, with the exception
+ * of consecutive "single atom chains".
+ */
export function ofModel(model: Model): Structure {
const chains = model.atomicHierarchy.chainSegments;
const builder = new StructureBuilder();
- const { residueSegments: { segmentMap: residueIndex } } = model.atomicHierarchy;
-
for (let c = 0; c < chains.count; c++) {
const start = chains.segments[c];
- let end = chains.segments[c + 1];
- let rStart = residueIndex[start], rEnd = residueIndex[end - 1];
- while (rEnd - rStart <= 1 && c + 1 < chains.count) {
+ // merge all consecutive "single atom chains"
+ while (c + 1 < chains.count
+ && chains.segments[c + 1] - chains.segments[c] === 1
+ && chains.segments[c + 2] - chains.segments[c + 1] === 1) {
c++;
- end = chains.segments[c + 1];
- rStart = rEnd;
- rEnd = residueIndex[end - 1];
}
- const elements = SortedArray.ofBounds(start, end);
+ const elements = SortedArray.ofBounds(start, chains.segments[c + 1]);
builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
}
--
GitLab