per-unit dssp as structure property

src/mol-model-formats/structure/mmcif/secondary-structure.ts

@@ -19,14 +19,17 @@ export function getSecondaryStructure(data: mmCIF_Database, hierarchy: AtomicHie
     // must add Helices 1st because of 'key' value assignment.
     addSheets(data.struct_sheet_range, map, data.struct_conf._rowCount, elements);
 
+    const n = hierarchy.residues._rowCount
+    const getIndex = (rI: ResidueIndex) => rI
+
     const secStruct: SecondaryStructureData = {
-        type: new Int32Array(hierarchy.residues._rowCount) as any,
-        key: new Int32Array(hierarchy.residues._rowCount) as any,
+        type: new Int32Array(n) as any,
+        key: new Int32Array(n) as any,
         elements
     };
 
     if (map.size > 0) assignSecondaryStructureRanges(hierarchy, map, secStruct);
-    return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements);
+    return SecondaryStructure(secStruct.type, secStruct.key, secStruct.elements, getIndex);
 }
 
 type SecondaryStructureEntry = {

src/mol-model-props/computed/secondary-structure.ts

@@ -59,7 +59,8 @@ export type SecondaryStructureComputationProps = PD.Values<SecondaryStructureCom
 
 async function computeSecondaryStructure(structure: Structure, params: Partial<SecondaryStructureComputationProps>): Promise<ComputedSecondaryStructure.Property> {
     const p = { ...PD.getDefaultValues(SecondaryStructureComputationParams), params }
-    // TODO take inter-unit hbonds into account
+    // TODO take inter-unit hbonds into account for bridge, ladder, sheet assignment
+    // TODO store unit-only secStruc as custom unit property???
     // TODO use Zhang-Skolnik for CA alpha only parts or for coarse parts with per-residue elements
     const map = new Map<number, SecondaryStructure>()
     for (let i = 0, il = structure.unitSymmetryGroups.length; i < il; ++i) {

src/mol-model-props/computed/secondary-structure/dssp.ts

@@ -20,6 +20,8 @@ import { calculateUnitDihedralAngles } from './dssp/dihedral-angles';
 import { calcUnitProteinTraceLookup3D } from './dssp/trace-lookup';
 import { Unit } from 'mol-model/structure';
 import { getUnitProteinInfo } from './dssp/protein-info';
+import { ResidueIndex } from 'mol-model/structure/model';
+import { SortedArray } from 'mol-data/int';
 
 /**
  * TODO bugs to fix:
@@ -37,7 +39,6 @@ export type DSSPComputationParams = typeof DSSPComputationParams
 export type DSSPComputationProps = PD.Values<DSSPComputationParams>
 
 export async function computeUnitDSSP(unit: Unit.Atomic, params: DSSPComputationProps): Promise<SecondaryStructure> {
-
     const proteinInfo = getUnitProteinInfo(unit)
     const { residueIndices } = proteinInfo
     const lookup3d = calcUnitProteinTraceLookup3D(unit, residueIndices)
@@ -83,20 +84,20 @@ export async function computeUnitDSSP(unit: Unit.Atomic, params: DSSPComputation
     const type = new Uint32Array(residueCount) as unknown as SecondaryStructureType[]
     const keys: number[] = []
     const elements: SecondaryStructure.Element[] = []
+    const getIndex = (rI: ResidueIndex) => SortedArray.indexOf(residueIndices, rI)
 
     for (let i = 0, il = residueIndices.length; i < il; ++i) {
         const assign = assignment[i]
-        type[residueIndices[i]] = assign
+        type[i] = assign
         const flag = getResidueFlag(flags[i])
+        // console.log(i, SortedArray.indexOf(residueIndices, i), getFlagName(flags[i]))
         // TODO is this expected behavior? elements will be strictly split depending on 'winning' flag
         if (elements.length === 0 /* would fail at very start */ || flag !== (elements[elements.length - 1] as SecondaryStructure.Helix | SecondaryStructure.Sheet | SecondaryStructure.Turn).flags /* flag changed */) {
             elements[elements.length] = createElement(mapToKind(assign), flags[i], getResidueFlag)
         }
         keys[i] = elements.length - 1
     }
-    // TODO expose model to unit residueIndex mapping
-
-    return SecondaryStructure(type, keys, elements)
+    return SecondaryStructure(type, keys, elements, getIndex)
 }
 
 function createElement(kind: string, flag: DSSPType.Flag, getResidueFlag: (f: DSSPType) => SecondaryStructureType): SecondaryStructure.Element {

src/mol-model-props/computed/secondary-structure/dssp/trace-lookup.ts

@@ -14,7 +14,7 @@ export function calcUnitProteinTraceLookup3D(unit: Unit.Atomic, unitProteinResid
     const { traceElementIndex } = unit.model.atomicHierarchy.derived.residue
     const indices = new Uint32Array(unitProteinResidues.length)
     for (let i = 0, il = unitProteinResidues.length; i < il; ++i) {
-        indices[indices.length] = traceElementIndex[unitProteinResidues[i]]
+        indices[i] = traceElementIndex[unitProteinResidues[i]]
     }
     return GridLookup3D({ x, y, z, indices: SortedArray.ofSortedArray(indices) });
 }

src/mol-model/structure/model/properties/seconday-structure.ts

@@ -5,6 +5,7 @@
  */
 
 import { SecondaryStructureType } from '../types';
+import { ResidueIndex } from '../indexing';
 
 /** Secondary structure "indexed" by residues. */
 interface SecondaryStructure {
@@ -13,10 +14,12 @@ interface SecondaryStructure {
     readonly key: ArrayLike<number>,
     /** indexed by key */
     readonly elements: ReadonlyArray<SecondaryStructure.Element>
+    /** mapping from residue index */
+    readonly getIndex: (rI: ResidueIndex) => number,
 }
 
-function SecondaryStructure(type: SecondaryStructure['type'], key: SecondaryStructure['key'], elements: SecondaryStructure['elements']) {
-    return { type, key, elements }
+function SecondaryStructure(type: SecondaryStructure['type'], key: SecondaryStructure['key'], elements: SecondaryStructure['elements'], getIndex: SecondaryStructure['getIndex']) {
+    return { type, key, elements, getIndex }
 }
 
 namespace SecondaryStructure {

src/mol-repr/structure/visual/util/polymer/trace-iterator.ts

@@ -14,6 +14,7 @@ import { CoarseSphereConformation, CoarseGaussianConformation } from 'mol-model/
 import { getPolymerRanges } from '../polymer';
 import { AtomicConformation } from 'mol-model/structure/model/properties/atomic';
 import { ComputedSecondaryStructure } from 'mol-model-props/computed/secondary-structure';
+import { SecondaryStructure } from 'mol-model/structure/model/properties/seconday-structure';
 
 /**
  * Iterates over individual residues/coarse elements in polymers of a unit while
@@ -69,7 +70,8 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
     private residueIt: Segmentation.SegmentIterator<ResidueIndex>
     private polymerSegment: Segmentation.Segment<ResidueIndex>
     private cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
-    private secondaryStructureType: ArrayLike<SecondaryStructureType>
+    private secondaryStructureType: SecondaryStructure['type']
+    private secondaryStructureGetIndex: SecondaryStructure['getIndex']
     private residueSegmentMin: ResidueIndex
     private residueSegmentMax: ResidueIndex
     private prevSecStrucType: SecondaryStructureType
@@ -133,8 +135,12 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         return residueIndex as ResidueIndex
     }
 
+    private getSecStruc(residueIndex: number) {
+        return this.secondaryStructureType[this.secondaryStructureGetIndex(residueIndex as ResidueIndex)]
+    }
+
     private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
-        const ss =  this.secondaryStructureType[residueIndex]
+        const ss =  this.getSecStruc(residueIndex)
         if (SecondaryStructureType.is(ss, SecondaryStructureType.Flag.Beta)) {
             Vec3.scale(out, Vec3.add(out, p1, Vec3.add(out, p3, Vec3.add(out, p2, p2))), 1/4)
         } else {
@@ -153,7 +159,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
                 if (residueIt.hasNext) {
                     this.state = AtomicPolymerTraceIteratorState.nextResidue
                     this.currSecStrucType = SecStrucTypeNA
-                    this.nextSecStrucType = this.secondaryStructureType[this.residueSegmentMin]
+                    this.nextSecStrucType = this.getSecStruc(this.residueSegmentMin)
                     this.currCoarseBackbone = false
                     this.nextCoarseBackbone = this.directionElementIndex[this.residueSegmentMin] === -1
                     break
@@ -165,7 +171,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
             const { index: residueIndex } = residueIt.move();
             this.prevSecStrucType = this.currSecStrucType
             this.currSecStrucType = this.nextSecStrucType
-            this.nextSecStrucType = residueIt.hasNext ? this.secondaryStructureType[residueIndex + 1] : SecStrucTypeNA
+            this.nextSecStrucType = residueIt.hasNext ? this.getSecStruc(residueIndex + 1) : SecStrucTypeNA
 
             this.prevCoarseBackbone = this.currCoarseBackbone
             this.currCoarseBackbone = this.nextCoarseBackbone
@@ -250,10 +256,14 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext
 
         this.secondaryStructureType = unit.model.properties.secondaryStructure.type
+        this.secondaryStructureGetIndex = unit.model.properties.secondaryStructure.getIndex
         const computedSecondaryStructure = ComputedSecondaryStructure.get(structure)
         if (computedSecondaryStructure) {
             const secondaryStructure = computedSecondaryStructure.map.get(unit.invariantId)
-            if (secondaryStructure) this.secondaryStructureType = secondaryStructure.type
+            if (secondaryStructure) {
+                this.secondaryStructureType = secondaryStructure.type
+                this.secondaryStructureGetIndex = secondaryStructure.getIndex
+            }
         }
     }
 }

src/mol-theme/color/secondary-structure.ts

@@ -47,7 +47,7 @@ export function secondaryStructureColor(unit: Unit, element: ElementIndex, compu
         secStrucType = unit.model.properties.secondaryStructure.type[unit.residueIndex[element]]
         if (computedSecondaryStructure) {
             const secondaryStructure = computedSecondaryStructure.map.get(unit.invariantId)
-            if (secondaryStructure) secStrucType = secondaryStructure.type[unit.residueIndex[element]]
+            if (secondaryStructure) secStrucType = secondaryStructure.type[secondaryStructure.getIndex(unit.residueIndex[element])]
         }
     }