make putty repr independent of secondary structure

- yields performance when secondary structure would need to be calculated

src/mol-repr/structure/representation/putty.ts

@@ -12,8 +12,6 @@ import { StructureRepresentation, StructureRepresentationProvider, StructureRepr
 import { Representation, RepresentationParamsGetter, RepresentationContext } from '../../../mol-repr/representation';
 import { Structure, Unit } from '../../../mol-model/structure';
 import { ThemeRegistryContext } from '../../../mol-theme/theme';
-import { CustomProperty } from '../../../mol-model-props/common/custom-property';
-import { SecondaryStructureProvider } from '../../../mol-model-props/computed/secondary-structure';
 
 const PuttyVisuals = {
     'polymer-tube': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PolymerTubeParams>) => UnitsRepresentation('Polymer tube mesh', ctx, getParams, PolymerTubeVisual),
@@ -55,8 +53,4 @@ export const PuttyRepresentationProvider = StructureRepresentationProvider({
     defaultColorTheme: { name: 'chain-id' },
     defaultSizeTheme: { name: 'uncertainty' },
     isApplicable: (structure: Structure) => structure.polymerResidueCount > 0,
-    ensureCustomProperties: {
-        attach: (ctx: CustomProperty.Context, structure: Structure) => SecondaryStructureProvider.attach(ctx, structure, void 0, true),
-        detach: (data) => SecondaryStructureProvider.ref(data, false)
-    }
 });

src/mol-repr/structure/visual/polymer-tube-mesh.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,8 +10,8 @@ import { Unit, Structure } from '../../../mol-model/structure';
 import { Theme } from '../../../mol-theme/theme';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, HelixTension, StandardTension, StandardShift, NucleicShift, OverhangFactor } from './util/polymer';
-import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/model/types';
+import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment, interpolateSizes, PolymerLocationIterator, getPolymerElementLoci, eachPolymerElement, StandardTension, StandardShift, NucleicShift, OverhangFactor } from './util/polymer';
+import { isNucleic } from '../../../mol-model/structure/model/types';
 import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
@@ -46,20 +46,18 @@ function createPolymerTubeMesh(ctx: VisualContext, unit: Unit, structure: Struct
     const { curvePoints, normalVectors, binormalVectors, widthValues, heightValues } = state;
 
     let i = 0;
-    const polymerTraceIt = PolymerTraceIterator(unit, structure);
+    const polymerTraceIt = PolymerTraceIterator(unit, structure, true);
     while (polymerTraceIt.hasNext) {
         const v = polymerTraceIt.move();
         builderState.currentGroup = i;
 
         const isNucleicType = isNucleic(v.moleculeType);
-        const isHelix = SecondaryStructureType.is(v.secStrucType, SecondaryStructureType.Flag.Helix);
-        const tension = isHelix ? HelixTension : StandardTension;
         const shift = isNucleicType ? NucleicShift : StandardShift;
 
-        interpolateCurveSegment(state, v, tension, shift);
+        interpolateCurveSegment(state, v, StandardTension, shift);
 
-        const startCap = v.secStrucFirst || v.coarseBackboneFirst || v.first;
-        const endCap = v.secStrucLast || v.coarseBackboneLast || v.last;
+        const startCap = v.coarseBackboneFirst || v.first;
+        const endCap = v.coarseBackboneLast || v.last;
 
         let s0 = theme.size.size(v.centerPrev) * sizeFactor;
         let s1 = theme.size.size(v.center) * sizeFactor;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,15 +14,14 @@ import { CoarseSphereConformation, CoarseGaussianConformation } from '../../../.
 import { getPolymerRanges } from '../polymer';
 import { AtomicConformation } from '../../../../../mol-model/structure/model/properties/atomic';
 import { SecondaryStructureProvider } 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
  * providing information about the neighbourhood in the underlying model for drawing splines
  */
-export function PolymerTraceIterator(unit: Unit, structure: Structure): Iterator<PolymerTraceElement> {
+export function PolymerTraceIterator(unit: Unit, structure: Structure, ignoreSecondaryStructure = false): Iterator<PolymerTraceElement> {
     switch (unit.kind) {
-        case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit, structure);
+        case Unit.Kind.Atomic: return new AtomicPolymerTraceIterator(unit, structure, ignoreSecondaryStructure);
         case Unit.Kind.Spheres:
         case Unit.Kind.Gaussians:
             return new CoarsePolymerTraceIterator(unit, structure);
@@ -76,8 +75,6 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
     private residueIt: Segmentation.SegmentIterator<ResidueIndex>
     private polymerSegment: Segmentation.Segment<number>
     private cyclicPolymerMap: Map<ResidueIndex, ResidueIndex>
-    private secondaryStructureType: SecondaryStructure['type']
-    private secondaryStructureGetIndex: SecondaryStructure['getIndex']
     private residueSegmentMin: ResidueIndex
     private residueSegmentMax: ResidueIndex
     private prevSecStrucType: SecondaryStructureType
@@ -143,9 +140,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         return residueIndex as ResidueIndex;
     }
 
-    private getSecStruc(residueIndex: number) {
-        return this.secondaryStructureType[this.secondaryStructureGetIndex(residueIndex as ResidueIndex)];
-    }
+    private getSecStruc: (residueIndex: ResidueIndex) => SecondaryStructureType.Flag
 
     private setControlPoint(out: Vec3, p1: Vec3, p2: Vec3, p3: Vec3, residueIndex: ResidueIndex) {
         const ss =  this.getSecStruc(residueIndex);
@@ -289,7 +284,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         return this.value;
     }
 
-    constructor(private unit: Unit.Atomic, structure: Structure) {
+    constructor(private unit: Unit.Atomic, structure: Structure, ignoreSecondaryStructure = false) {
         this.atomicConformation = unit.model.atomicConformation;
         this.residueAtomSegments = unit.model.atomicHierarchy.residueAtomSegments;
         this.polymerRanges = unit.model.atomicRanges.polymerRanges;
@@ -303,10 +298,13 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
         this.value = createPolymerTraceElement(structure, unit);
         this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext;
 
-        const secondaryStructure = SecondaryStructureProvider.get(structure).value?.get(unit.invariantId);
-        if (!secondaryStructure) throw new Error('missing secondary structure');
-        this.secondaryStructureType = secondaryStructure.type;
-        this.secondaryStructureGetIndex = secondaryStructure.getIndex;
+        const secondaryStructure = !ignoreSecondaryStructure && SecondaryStructureProvider.get(structure).value?.get(unit.invariantId);
+        if (secondaryStructure) {
+            const { type, getIndex } = secondaryStructure;
+            this.getSecStruc = (residueIndex: ResidueIndex) => type[getIndex(residueIndex as ResidueIndex)];
+        } else {
+            this.getSecStruc = (residueIndex: ResidueIndex) => SecStrucTypeNA;
+        }
     }
 }