From 25da773da1a36b26aba5389d4c018605f3fbb1ed Mon Sep 17 00:00:00 2001
From: arose <alexander.rose@weirdbyte.de>
Date: Thu, 28 Jun 2018 19:33:17 -0700
Subject: [PATCH] fixes
---
.../structure/visual/polymer-backbone-cylinder.ts | 10 ++++++++--
.../representation/structure/visual/util/polymer.ts | 12 ++++++------
.../structure/model/formats/mmcif/atomic.ts | 4 +---
src/mol-view/stage.ts | 3 ++-
4 files changed, 17 insertions(+), 12 deletions(-)
diff --git a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
index 7c63398f5..9068225e5 100644
--- a/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts
@@ -46,10 +46,12 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
const residuesIt = Segmentation.transientSegments(residueSegments, elements);
let i = 0
+ let first = true
while (polymerIt.hasNext) {
const polymerSegment = polymerIt.move();
residuesIt.setSegment(polymerSegment);
+ first = true
while (residuesIt.hasNext) {
const residueSegment = residuesIt.move();
l.element = elements[residueSegment.start];
@@ -70,8 +72,12 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
}
pos(l.element, curV)
- builder.setId(residueSegment.start)
- builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
+ if (!first) {
+ builder.setId(residueSegment.start)
+ builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
+ } else {
+ first = false
+ }
Vec3.copy(prevV, curV)
diff --git a/src/mol-geo/representation/structure/visual/util/polymer.ts b/src/mol-geo/representation/structure/visual/util/polymer.ts
index e54cf1e01..3f8c7bf3f 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer.ts
@@ -13,14 +13,14 @@ export function getPolymerElementCount(unit: Unit) {
const { elements } = unit
const l = Element.Location(unit)
if (Unit.isAtomic(unit)) {
- const { chainSegments, residueSegments } = unit.model.atomicHierarchy
- const chainsIt = Segmentation.transientSegments(chainSegments, elements);
+ const { polymerSegments, residueSegments } = unit.model.atomicHierarchy
+ const polymerIt = Segmentation.transientSegments(polymerSegments, elements);
const residuesIt = Segmentation.transientSegments(residueSegments, elements);
- while (chainsIt.hasNext) {
- residuesIt.setSegment(chainsIt.move());
+ while (polymerIt.hasNext) {
+ residuesIt.setSegment(polymerIt.move());
while (residuesIt.hasNext) {
- l.element = elements[residuesIt.move().start];
- if (StructureProperties.entity.type(l) === 'polymer') count++
+ residuesIt.move();
+ count++
}
}
} else if (Unit.isSpheres(unit)) {
diff --git a/src/mol-model/structure/model/formats/mmcif/atomic.ts b/src/mol-model/structure/model/formats/mmcif/atomic.ts
index b38b230d4..736c81fe6 100644
--- a/src/mol-model/structure/model/formats/mmcif/atomic.ts
+++ b/src/mol-model/structure/model/formats/mmcif/atomic.ts
@@ -29,14 +29,12 @@ function findHierarchyOffsets(atom_site: AtomSite) {
for (let i = start + 1; i < end; i++) {
const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
- // TODO improve???
- const newPolymer = newChain
- || label_seq_id.value(i - 1) !== label_seq_id.value(i) - 1;
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);
+ const newPolymer = newResidue && label_seq_id.value(i - 1) !== label_seq_id.value(i) - 1;
if (newResidue) residues[residues.length] = i as Element;
if (newPolymer) polymers[polymers.length] = i as Element;
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index 49eef29d6..3809a7271 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -74,9 +74,10 @@ export class Stage {
// this.loadPdbid('3pqr') // inter unit bonds
// this.loadPdbid('4v5a') // ribosome
// this.loadPdbid('3j3q') // ...
+ this.loadPdbid('3sn6') // ...
// this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
- this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
+ // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
}
async loadMmcifUrl (url: string) {
--
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