From 52a8a0e55b205865e0324143de3bb7d269a02204 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Fri, 8 Jun 2018 16:29:08 +0200
Subject: [PATCH] Merge "single residue units" together in Structure.ofModel
---
src/apps/structure-info/model.ts | 11 +++++------
src/mol-app/skin/components/sequence-view.scss | 1 +
src/mol-model/structure/model/formats/mmcif.ts | 5 +++--
src/mol-model/structure/structure/structure.ts | 15 ++++++++++++++-
src/mol-view/stage.ts | 2 +-
5 files changed, 24 insertions(+), 10 deletions(-)
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index ed012d465..c06c66e4e 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -99,10 +99,9 @@ export function printLinks(structure: Structure, showIntra: boolean, showInter:
if (!Unit.isAtomic(unit)) continue;
for (const pairLinks of links.getLinkedUnits(unit)) {
- if (!pairLinks.areUnitsOrdered) continue;
+ if (!pairLinks.areUnitsOrdered || pairLinks.bondCount === 0) continue;
const { unitA, unitB } = pairLinks;
-
console.log(`${pairLinks.unitA.id} - ${pairLinks.unitB.id}: ${pairLinks.bondCount} bond(s)`);
for (const aI of pairLinks.linkedElementIndices) {
@@ -193,12 +192,12 @@ export function printIHMModels(model: Model) {
async function run(mmcif: mmCIF_Database) {
const models = await Model.create({ kind: 'mmCIF', data: mmcif }).run();
const structure = Structure.ofModel(models[0]);
- printSequence(models[0]);
+ //printSequence(models[0]);
//printIHMModels(models[0]);
printUnits(structure);
- printRings(structure);
- printLinks(structure, false, true);
- printModRes(models[0]);
+ //printRings(structure);
+ printLinks(structure, true, true);
+ //printModRes(models[0]);
//printSecStructure(models[0]);
}
diff --git a/src/mol-app/skin/components/sequence-view.scss b/src/mol-app/skin/components/sequence-view.scss
index 2be5ea580..b8bf89167 100644
--- a/src/mol-app/skin/components/sequence-view.scss
+++ b/src/mol-app/skin/components/sequence-view.scss
@@ -5,4 +5,5 @@
left: 0;
bottom: 0;
overflow: hidden;
+ overflow-x: scroll;
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 49bcfc52c..a5c8c5008 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -39,11 +39,12 @@ function findHierarchyOffsets({ data }: mmCIF_Format, bounds: Interval) {
const start = Interval.start(bounds), end = Interval.end(bounds);
const residues = [start], chains = [start];
- const { label_entity_id, auth_asym_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = data.atom_site;
+ const { label_entity_id, label_asym_id, label_seq_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = data.atom_site;
for (let i = start + 1; i < end; i++) {
- const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !auth_asym_id.areValuesEqual(i - 1, i);
+ const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
+ || !label_seq_id.areValuesEqual(i - 1, i)
|| !auth_seq_id.areValuesEqual(i - 1, i)
|| !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
|| !label_comp_id.areValuesEqual(i - 1, i);
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 52239bb46..22666fb13 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -98,8 +98,21 @@ namespace 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 elements = SortedArray.ofBounds(chains.segments[c], chains.segments[c + 1]);
+ 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) {
+ c++;
+ end = chains.segments[c + 1];
+ rStart = rEnd;
+ rEnd = residueIndex[end - 1];
+ }
+
+ const elements = SortedArray.ofBounds(start, end);
builder.addUnit(Unit.Kind.Atomic, model, SymmetryOperator.Default, elements);
}
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index ae1757971..1f46148e8 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -39,7 +39,7 @@ export class Stage {
this.viewer = Viewer.create(canvas, container)
this.viewer.animate()
this.ctx.viewer = this.viewer
- // this.loadPdbid('1crn')
+ //this.loadPdbid('1jj2')
this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
}
--
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