Skip to content
Snippets Groups Projects
Commit 25da773d authored by arose's avatar arose
Browse files

fixes

parent c19474cd
No related branches found
No related tags found
No related merge requests found
......@@ -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)
......
......@@ -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)) {
......
......@@ -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;
......
......@@ -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) {
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment