polymer fixes

src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts

@@ -33,6 +33,7 @@ const sVec = Vec3.zero()
 async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, props: {}, mesh?: Mesh) {
     if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
 
+    // TODO better vertex count estimate
     const builder = MeshBuilder.create(256, 128, mesh)
 
     const { elements, model } = unit

src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Unit, StructureElement } from 'mol-model/structure';
+import { Unit } from 'mol-model/structure';
 import { UnitsVisual } from '..';
 import { RuntimeContext } from 'mol-task'
 import { Mesh } from '../../../shape/mesh';
@@ -16,6 +16,7 @@ import { StructureElementIterator } from './util/location-iterator';
 import { DefaultUnitsMeshProps, UnitsMeshVisual } from '../units-visual';
 import { SizeThemeProps, SizeTheme } from 'mol-view/theme/size';
 import { CylinderProps } from '../../../primitive/cylinder';
+import { OrderedSet } from 'mol-data/int';
 
 export interface PolymerBackboneCylinderProps {
     sizeTheme: SizeThemeProps
@@ -36,26 +37,21 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
     const pos = unit.conformation.invariantPosition
     const pA = Vec3.zero()
     const pB = Vec3.zero()
-    const l = StructureElement.create(unit)
     const cylinderProps: CylinderProps = { radiusTop: 1, radiusBottom: 1, radialSegments }
 
     let i = 0
     const polymerBackboneIt = PolymerBackboneIterator(unit)
     while (polymerBackboneIt.hasNext) {
         const { centerA, centerB } = polymerBackboneIt.move()
-        const elmA = elements[centerA.element]
-        const elmB = elements[centerB.element]
-        pos(elmA, pA)
-        pos(elmB, pB)
+        pos(centerA.element, pA)
+        pos(centerB.element, pB)
 
-        l.element = elmA
-        cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(l)
-        builder.setId(centerA.element)
+        cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerA)
+        builder.setId(OrderedSet.findPredecessorIndex(elements, centerA.element))
         builder.addCylinder(pA, pB, 0.5, cylinderProps)
 
-        l.element = elmB
-        cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(l)
-        builder.setId(centerB.element)
+        cylinderProps.radiusTop = cylinderProps.radiusBottom = sizeTheme.size(centerB)
+        builder.setId(OrderedSet.findPredecessorIndex(elements, centerB.element))
         builder.addCylinder(pB, pA, 0.5, cylinderProps)
 
         if (i % 10000 === 0 && ctx.shouldUpdate) {

src/mol-geo/representation/structure/visual/util/polymer/backbone-iterator.ts

@@ -5,11 +5,10 @@
  */
 
 import { Unit, StructureElement, ElementIndex, ResidueIndex } from 'mol-model/structure';
-import { Segmentation, SortedArray } from 'mol-data/int';
+import { Segmentation } from 'mol-data/int';
 import Iterator from 'mol-data/iterator';
 import SortedRanges from 'mol-data/int/sorted-ranges';
 import { getElementIndexForAtomRole } from 'mol-model/structure/util';
-import { AtomRole } from 'mol-model/structure/model/types';
 import { getPolymerRanges } from '../polymer';
 
 /** Iterates over consecutive pairs of residues/coarse elements in polymers */
@@ -44,23 +43,13 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
     private residueSegment: Segmentation.Segment<ResidueIndex>
     hasNext: boolean = false;
 
-    private getElementIndex(residueIndex: ResidueIndex, atomRole: AtomRole) {
-        const index = getElementIndexForAtomRole(this.unit.model, residueIndex, atomRole)
-        // TODO handle case when it returns -1
-        const elementIndex = SortedArray.indexOf(this.unit.elements, index) as ElementIndex
-        if (elementIndex === -1) {
-            console.log('-1', residueIndex, atomRole, index)
-        }
-        return elementIndex === -1 ? 0 as ElementIndex : elementIndex
-    }
-
     move() {
         if (this.state === AtomicPolymerBackboneIteratorState.nextPolymer) {
             while (this.polymerIt.hasNext) {
                 this.residueIt.setSegment(this.polymerIt.move());
                 if (this.residueIt.hasNext) {
                     this.residueSegment = this.residueIt.move()
-                    this.value.centerB.element = this.getElementIndex(this.residueSegment.index, 'trace')
+                    this.value.centerB.element = getElementIndexForAtomRole(this.unit.model, this.residueSegment.index, 'trace')
                     this.state = AtomicPolymerBackboneIteratorState.nextResidue
                     break
                 }
@@ -70,7 +59,7 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
         if (this.state === AtomicPolymerBackboneIteratorState.nextResidue) {
             this.residueSegment = this.residueIt.move()
             this.value.centerA.element = this.value.centerB.element
-            this.value.centerB.element = this.getElementIndex(this.residueSegment.index, 'trace')
+            this.value.centerB.element = getElementIndexForAtomRole(this.unit.model, this.residueSegment.index, 'trace')
             if (!this.residueIt.hasNext) {
                 if (this.unit.model.atomicHierarchy.cyclicPolymerMap.has(this.residueSegment.index)) {
                     this.state = AtomicPolymerBackboneIteratorState.cycle
@@ -82,7 +71,7 @@ export class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePa
         } else if (this.state === AtomicPolymerBackboneIteratorState.cycle) {
             const { cyclicPolymerMap } = this.unit.model.atomicHierarchy
             this.value.centerA.element = this.value.centerB.element
-            this.value.centerB.element = this.getElementIndex(cyclicPolymerMap.get(this.residueSegment.index)!, 'trace')
+            this.value.centerB.element = getElementIndexForAtomRole(this.unit.model, cyclicPolymerMap.get(this.residueSegment.index)!, 'trace')
             // TODO need to advance to a polymer that has two or more residues (can't assume it has)
             this.state = AtomicPolymerBackboneIteratorState.nextPolymer
         }

src/mol-view/stage.ts

@@ -21,6 +21,7 @@ import { CarbohydrateProps } from 'mol-geo/representation/structure/representati
 const spacefillProps: Partial<SpacefillProps> = {
     doubleSided: true,
     colorTheme: { name: 'chain-id' },
+    sizeTheme: { name: 'physical', factor: 1.0 },
     quality: 'auto',
     useFog: false
 }
@@ -88,7 +89,7 @@ export class Stage {
         // this.loadPdbid('1hrv') // viral assembly
         // this.loadPdbid('1rb8') // virus
         // this.loadPdbid('1blu') // metal coordination
-        this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
+        // this.loadPdbid('3pqr') // inter unit bonds, two polymer chains, ligands, water, carbohydrates linked to protein
         // this.loadPdbid('4v5a') // ribosome
         // this.loadPdbid('3j3q') // ...
         // this.loadPdbid('2np2') // dna
@@ -123,25 +124,24 @@ export class Stage {
         // this.loadPdbid('5u0q') // mixed dna/rna in same polymer
         // this.loadPdbid('5u0q') // temp
 
-        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`) // ok
+        this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000002.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000003.cif`) // ok
-        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000004.cif`) // TODO issue with cross-link extraction
+        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000004.cif`) // TODO issue with cross-link extraction, not shown
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000005.cif`) // ok
-        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000006.cif`) // TODO only three spacefill atoms rendered
-        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000007.cif`) // TODO only three spacefill atoms rendered
+        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000006.cif`) // ok
+        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000007.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000008.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000010.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000011.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000012.cif`) // ok
         // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000014.cif`) // ok
-        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000016.cif`) // TODO only three spacefill atoms rendered
+        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000016.cif`) // ok
     }
 
     async loadMmcifUrl (url: string) {
         const urlEntity = UrlEntity.ofUrl(this.ctx, url)
         const modelEntity = await MmcifUrlToModel.apply(this.ctx, urlEntity)
-        console.log(modelEntity.value)
         const structureEntity = await ModelToStructure.apply(this.ctx, modelEntity)
 
         StructureToBallAndStick.apply(this.ctx, structureEntity, { ...ballAndStickProps, visible: true })