location-iterator tweaks

- consolidate BondIterator.fromGroup/.fromStructure
- use options argument in PolymerLocationIterator.fromGroup
- remove 'any' type

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

@@ -28,6 +28,7 @@ export const BackboneParams = {
     sizeAspectRatio: PD.Numeric(1, { min: 0.1, max: 3, step: 0.1 }),
     visuals: PD.MultiSelect(['polymer-backbone-cylinder', 'polymer-backbone-sphere', 'polymer-gap'], PD.objectToOptions(BackboneVisuals)),
     bumpFrequency: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
+    colorMode: PD.Select('default', PD.arrayToOptions(['default', 'interpolate'] as const), { ...BaseGeometry.ShadingCategory, isHidden: true }),
 };
 export type BackboneParams = typeof BackboneParams
 export function getBackboneParams(ctx: ThemeRegistryContext, structure: Structure) {

src/mol-repr/structure/units-visual.ts

@@ -56,7 +56,7 @@ function createUnitsRenderObject<G extends Geometry>(structureGroup: StructureGr
 interface UnitsVisualBuilder<P extends StructureParams, G extends Geometry> {
     defaultProps: PD.Values<P>
     createGeometry(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G
-    createLocationIterator(structureGroup: StructureGroup, props: any): LocationIterator
+    createLocationIterator(structureGroup: StructureGroup, props: PD.Values<P>): LocationIterator
     getLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Loci
     eachLocation(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean): boolean
     setUpdateState(state: VisualUpdateState, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup): void

src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts

@@ -214,7 +214,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
     return ComplexCylindersVisual<InterUnitBondCylinderParams>({
         defaultProps: PD.getDefaultValues(InterUnitBondCylinderParams),
         createGeometry: createInterUnitBondCylinderImpostors,
-        createLocationIterator: BondIterator.fromStructureLoc2,
+        createLocationIterator: (structure: Structure, props: PD.Values<InterUnitBondCylinderParams>) => BondIterator.fromStructure(structure, { includeLocation2: props.colorMode === 'interpolate' }),
         getLoci: getInterBondLoci,
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondCylinderParams>, currentProps: PD.Values<InterUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructure: Structure, currentStructure: Structure) => {
@@ -238,6 +238,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
                 newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
                 newProps.multipleBonds !== currentProps.multipleBonds
             );
+
             if (newProps.colorMode !== currentProps.colorMode) {
                 state.createGeometry = true;
                 state.updateTransform = true;
@@ -261,7 +262,7 @@ export function InterUnitBondCylinderMeshVisual(materialId: number): ComplexVisu
     return ComplexMeshVisual<InterUnitBondCylinderParams>({
         defaultProps: PD.getDefaultValues(InterUnitBondCylinderParams),
         createGeometry: createInterUnitBondCylinderMesh,
-        createLocationIterator: BondIterator.fromStructure,
+        createLocationIterator: (structure: Structure) => BondIterator.fromStructure(structure),
         getLoci: getInterBondLoci,
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondCylinderParams>, currentProps: PD.Values<InterUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructure: Structure, currentStructure: Structure) => {

src/mol-repr/structure/visual/bond-inter-unit-line.ts

@@ -127,7 +127,7 @@ export function InterUnitBondLineVisual(materialId: number): ComplexVisual<Inter
     return ComplexLinesVisual<InterUnitBondLineParams>({
         defaultProps: PD.getDefaultValues(InterUnitBondLineParams),
         createGeometry: createInterUnitBondLines,
-        createLocationIterator: BondIterator.fromStructure,
+        createLocationIterator: (structure: Structure) => BondIterator.fromStructure(structure),
         getLoci: getInterBondLoci,
         eachLocation: eachInterBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<InterUnitBondLineParams>, currentProps: PD.Values<InterUnitBondLineParams>, newTheme: Theme, currentTheme: Theme, newStructure: Structure, currentStructure: Structure) => {

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -231,7 +231,7 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
     return UnitsCylindersVisual<IntraUnitBondCylinderParams>({
         defaultProps: PD.getDefaultValues(IntraUnitBondCylinderParams),
         createGeometry: createIntraUnitBondCylinderImpostors,
-        createLocationIterator: BondIterator.fromGroupLoc2,
+        createLocationIterator: (structureGroup: StructureGroup, props) => BondIterator.fromGroup(structureGroup, { includeLocation2: props.colorMode === 'interpolate' }),
         getLoci: getIntraBondLoci,
         eachLocation: eachIntraBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitBondCylinderParams>, currentProps: PD.Values<IntraUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {
@@ -284,7 +284,7 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
     return UnitsMeshVisual<IntraUnitBondCylinderParams>({
         defaultProps: PD.getDefaultValues(IntraUnitBondCylinderParams),
         createGeometry: createIntraUnitBondCylinderMesh,
-        createLocationIterator: BondIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => BondIterator.fromGroup(structureGroup),
         getLoci: getIntraBondLoci,
         eachLocation: eachIntraBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitBondCylinderParams>, currentProps: PD.Values<IntraUnitBondCylinderParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {

src/mol-repr/structure/visual/bond-intra-unit-line.ts

@@ -153,7 +153,7 @@ export function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUn
     return UnitsLinesVisual<IntraUnitBondLineParams>({
         defaultProps: PD.getDefaultValues(IntraUnitBondLineParams),
         createGeometry: createIntraUnitBondLines,
-        createLocationIterator: BondIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => BondIterator.fromGroup(structureGroup),
         getLoci: getIntraBondLoci,
         eachLocation: eachIntraBond,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<IntraUnitBondLineParams>, currentProps: PD.Values<IntraUnitBondLineParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {

src/mol-repr/structure/visual/polymer-backbone-cylinder.ts

@@ -88,7 +88,7 @@ export function PolymerBackboneCylinderImpostorVisual(materialId: number): Units
     return UnitsCylindersVisual<PolymerBackboneCylinderParams>({
         defaultProps: PD.getDefaultValues(PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderImpostor,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneCylinderParams>, currentProps: PD.Values<PolymerBackboneCylinderParams>) => { },
@@ -148,7 +148,7 @@ export function PolymerBackboneCylinderMeshVisual(materialId: number): UnitsVisu
     return UnitsMeshVisual<PolymerBackboneCylinderParams>({
         defaultProps: PD.getDefaultValues(PolymerBackboneCylinderParams),
         createGeometry: createPolymerBackboneCylinderMesh,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneCylinderParams>, currentProps: PD.Values<PolymerBackboneCylinderParams>) => {

src/mol-repr/structure/visual/polymer-backbone-sphere.ts

@@ -72,7 +72,7 @@ export function PolymerBackboneSphereImpostorVisual(materialId: number): UnitsVi
     return UnitsSpheresVisual<PolymerBackboneSphereParams>({
         defaultProps: PD.getDefaultValues(PolymerBackboneSphereParams),
         createGeometry: createPolymerBackboneSphereImpostor,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneSphereParams>, currentProps: PD.Values<PolymerBackboneSphereParams>) => { },
@@ -116,7 +116,7 @@ export function PolymerBackboneSphereMeshVisual(materialId: number): UnitsVisual
     return UnitsMeshVisual<PolymerBackboneSphereParams>({
         defaultProps: PD.getDefaultValues(PolymerBackboneSphereParams),
         createGeometry: createPolymerBackboneSphereMesh,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerBackboneSphereParams>, currentProps: PD.Values<PolymerBackboneSphereParams>) => {

src/mol-repr/structure/visual/polymer-direction-wedge.ts

@@ -17,6 +17,7 @@ import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
 import { VisualUpdateState } from '../../util';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { StructureGroup } from './util/common';
 
 const t = Mat4.identity();
 const sVec = Vec3.zero();
@@ -101,7 +102,7 @@ export function PolymerDirectionVisual(materialId: number): UnitsVisual<PolymerD
     return UnitsMeshVisual<PolymerDirectionParams>({
         defaultProps: PD.getDefaultValues(PolymerDirectionParams),
         createGeometry: createPolymerDirectionWedgeMesh,
-        createLocationIterator: PolymerLocationIterator.fromGroup,
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerDirectionParams>, currentProps: PD.Values<PolymerDirectionParams>) => {

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

@@ -187,7 +187,7 @@ export function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTrace
     return UnitsMeshVisual<PolymerTraceParams>({
         defaultProps: PD.getDefaultValues(PolymerTraceParams),
         createGeometry: createPolymerTraceMesh,
-        createLocationIterator: sg => PolymerLocationIterator.fromGroup(sg, true),
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup, { asSecondary: true }),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTraceParams>, currentProps: PD.Values<PolymerTraceParams>, newTheme: Theme, currentTheme: Theme, newStructureGroup: StructureGroup, currentStructureGroup: StructureGroup) => {

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

@@ -21,6 +21,7 @@ import { Vec3 } from '../../../mol-math/linear-algebra';
 import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
 import { Sphere3D } from '../../../mol-math/geometry';
+import { StructureGroup } from './util/common';
 
 export const PolymerTubeMeshParams = {
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
@@ -117,7 +118,7 @@ export function PolymerTubeVisual(materialId: number): UnitsVisual<PolymerTubePa
     return UnitsMeshVisual<PolymerTubeParams>({
         defaultProps: PD.getDefaultValues(PolymerTubeParams),
         createGeometry: createPolymerTubeMesh,
-        createLocationIterator: sg => PolymerLocationIterator.fromGroup(sg, true),
+        createLocationIterator: (structureGroup: StructureGroup) => PolymerLocationIterator.fromGroup(structureGroup, { asSecondary: true }),
         getLoci: getPolymerElementLoci,
         eachLocation: eachPolymerElement,
         setUpdateState: (state: VisualUpdateState, newProps: PD.Values<PolymerTubeParams>, currentProps: PD.Values<PolymerTubeParams>) => {

src/mol-repr/structure/visual/util/bond.ts

@@ -126,7 +126,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
 }
 
 export namespace BondIterator {
-    export function fromGroup(structureGroup: StructureGroup): LocationIterator {
+    export function fromGroup(structureGroup: StructureGroup, props?: { includeLocation2?: boolean }): LocationIterator {
         const { group, structure } = structureGroup;
         const unit = group.units[0] as Unit.Atomic;
         const groupCount = Unit.isAtomic(unit) ? unit.bonds.edgeCount * 2 : 0;
@@ -140,26 +140,9 @@ export namespace BondIterator {
             location.bIndex = unit.bonds.b[groupIndex];
             return location;
         };
-        return LocationIterator(groupCount, instanceCount, 1, getLocation);
-    }
-
-    export function fromGroupLoc2(structureGroup: StructureGroup, props: PD.Values): LocationIterator {
-        const { group, structure } = structureGroup;
-        const unit = group.units[0] as Unit.Atomic;
-        const groupCount = Unit.isAtomic(unit) ? unit.bonds.edgeCount * 2 : 0;
-        const instanceCount = group.units.length;
-        const location = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
-        const getLocation = (groupIndex: number, instanceIndex: number) => {
-            const unit = group.units[instanceIndex] as Unit.Atomic;
-            location.aUnit = unit;
-            location.bUnit = unit;
-            location.aIndex = unit.bonds.a[groupIndex];
-            location.bIndex = unit.bonds.b[groupIndex];
-            return location;
-        };
-        if (props.colorMode === 'interpolate') {
+        if (props?.includeLocation2) {
             const location2 = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
-            const getLocation2 = (groupIndex: number, instanceIndex: number) => { // inverting A with B
+            const getLocation2 = (groupIndex: number, instanceIndex: number) => { // swapping A and B
                 const unit = group.units[instanceIndex] as Unit.Atomic;
                 location2.aUnit = unit;
                 location2.bUnit = unit;
@@ -172,22 +155,7 @@ export namespace BondIterator {
         return LocationIterator(groupCount, instanceCount, 1, getLocation);
     }
 
-    export function fromStructure(structure: Structure): LocationIterator {
-        const groupCount = structure.interUnitBonds.edgeCount;
-        const instanceCount = 1;
-        const location = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
-        const getLocation = (groupIndex: number) => {
-            const bond = structure.interUnitBonds.edges[groupIndex];
-            location.aUnit = structure.unitMap.get(bond.unitA);
-            location.aIndex = bond.indexA;
-            location.bUnit = structure.unitMap.get(bond.unitB);
-            location.bIndex = bond.indexB;
-            return location;
-        };
-        return LocationIterator(groupCount, instanceCount, 1, getLocation, true);
-    }
-
-    export function fromStructureLoc2(structure: Structure, props: PD.Values): LocationIterator {
+    export function fromStructure(structure: Structure, props?: { includeLocation2?: boolean }): LocationIterator {
         const groupCount = structure.interUnitBonds.edgeCount;
         const instanceCount = 1;
         const location = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
@@ -199,9 +167,9 @@ export namespace BondIterator {
             location.bIndex = bond.indexB;
             return location;
         };
-        if (props.colorMode === 'interpolate') {
+        if (props?.includeLocation2) {
             const location2 = Bond.Location(structure, undefined, undefined, structure, undefined, undefined);
-            const getLocation2 = (groupIndex: number) => { // inverting A with B
+            const getLocation2 = (groupIndex: number) => { // swapping A and B
                 const bond = structure.interUnitBonds.edges[groupIndex];
                 location2.aUnit = structure.unitMap.get(bond.unitB);
                 location2.aIndex = bond.indexB;

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

@@ -41,7 +41,7 @@ export function getGapRanges(unit: Unit): SortedRanges<ElementIndex> {
 }
 
 export namespace PolymerLocationIterator {
-    export function fromGroup(structureGroup: StructureGroup, asSecondary = false): LocationIterator {
+    export function fromGroup(structureGroup: StructureGroup, options?: { asSecondary?: boolean }): LocationIterator {
         const { group, structure } = structureGroup;
         const polymerElements = group.units[0].polymerElements;
         const groupCount = polymerElements.length;
@@ -53,6 +53,7 @@ export namespace PolymerLocationIterator {
             location.element = polymerElements[groupIndex];
             return location;
         };
+        const asSecondary = !!options?.asSecondary;
         function isSecondary(elementIndex: number, instanceIndex: number) {
             return asSecondary;
         }