/** * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose <alexander.rose@weirdbyte.de> */ import { ParamDefinition as PD } from '../../../mol-util/param-definition'; import { RepresentationParamsGetter, RepresentationContext } from '../../../mol-repr/representation'; import { VisualContext } from '../../../mol-repr/visual'; import { ThemeRegistryContext, Theme } from '../../../mol-theme/theme'; import { Structure } from '../../../mol-model/structure'; import { StructureRepresentationProvider, StructureRepresentation, ComplexRepresentation, ComplexVisual } from '../../../mol-repr/structure/representation'; import { AssemblySymmetry } from '../assembly-symmetry'; import { Table } from '../../../mol-data/db'; import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder'; import { Tensor, Vec3 } from '../../../mol-math/linear-algebra'; import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere'; import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder'; import { VisualUpdateState } from '../../../mol-repr/util'; import { ComplexMeshVisual, ComplexMeshParams } from '../../../mol-repr/structure/complex-visual'; import { Mesh } from '../../../mol-geo/geometry/mesh/mesh'; import { EmptyLoci, createDataLoci, Loci, isDataLoci } from '../../../mol-model/loci'; import { LocationIterator } from '../../../mol-geo/util/location-iterator'; import { NullLocation } from '../../../mol-model/location'; import { PickingId } from '../../../mol-geo/geometry/picking'; import { OrderedSet, Interval } from '../../../mol-data/int'; import { getSymmetrySelectParam, getAssemblyIds } from '../util'; export const AssemblySymmetryAxesParams = { symmetryId: getSymmetrySelectParam(), sizeFactor: PD.Numeric(0.4, { min: 0, max: 3, step: 0.01 }), ...ComplexMeshParams, radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }), } export type AssemblySymmetryAxesParams = typeof AssemblySymmetryAxesParams export function getAssemblySymmetryAxesParams(ctx: ThemeRegistryContext, structure: Structure) { const params = PD.clone(AssemblySymmetryAxesParams) params.symmetryId = getSymmetrySelectParam(structure) params.unitKinds.isHidden = true return params } export type AssemblySymmetryAxesRepresentation = StructureRepresentation<AssemblySymmetryAxesParams> export function AssemblySymmetryAxesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AssemblySymmetryAxesParams>): AssemblySymmetryAxesRepresentation { return ComplexRepresentation('RCSB Assembly Symmetry Axes', ctx, getParams, AssemblySymmetryAxesVisual) } export const AssemblySymmetryAxesRepresentationProvider: StructureRepresentationProvider<AssemblySymmetryAxesParams> = { label: 'RCSB Assembly Symmetry Axes', description: 'Displays assembly symmetry axes.', factory: AssemblySymmetryAxesRepresentation, getParams: getAssemblySymmetryAxesParams, defaultValues: PD.getDefaultValues(AssemblySymmetryAxesParams), defaultColorTheme: 'uniform', defaultSizeTheme: 'uniform', isApplicable: (structure: Structure) => AssemblySymmetry.get(structure.models[0]) !== undefined } // export function AssemblySymmetryAxesVisual(materialId: number): ComplexVisual<AssemblySymmetryAxesParams> { return ComplexMeshVisual<AssemblySymmetryAxesParams>({ defaultProps: PD.getDefaultValues(AssemblySymmetryAxesParams), createGeometry: createAssemblySymmetryAxesMesh, createLocationIterator, getLoci, eachLocation: eachAxisLocation, setUpdateState: (state: VisualUpdateState, newProps: PD.Values<AssemblySymmetryAxesParams>, currentProps: PD.Values<AssemblySymmetryAxesParams>) => { state.createGeometry = ( newProps.sizeFactor !== currentProps.sizeFactor || newProps.detail !== currentProps.detail || newProps.symmetryId !== currentProps.symmetryId ) } }, materialId) } function createLocationIterator(structure: Structure) { const assemblySymmetry = AssemblySymmetry.get(structure.models[0]) const groupCount = assemblySymmetry ? assemblySymmetry.db.rcsb_assembly_symmetry_axis._rowCount : 0 return LocationIterator(groupCount, 1, () => NullLocation) } function getLoci(pickingId: PickingId, structure: Structure, id: number) { const { objectId, groupId } = pickingId if (id === objectId) { const assemblySymmetry = AssemblySymmetry.get(structure.models[0]) if (assemblySymmetry) { return createDataLoci(assemblySymmetry, 'axes', OrderedSet.ofSingleton(groupId)) } } return EmptyLoci } function eachAxisLocation(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) { let changed = false if (!isDataLoci(loci) || loci.tag !== 'axes') return false const assemblySymmetry = AssemblySymmetry.get(structure.models[0]) if (!assemblySymmetry || loci.data !== assemblySymmetry) return false OrderedSet.forEach(loci.indices, v => { if (apply(Interval.ofSingleton(v))) changed = true }) return changed } export function createAssemblySymmetryAxesMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<AssemblySymmetryAxesParams>, mesh?: Mesh) { const { symmetryId, sizeFactor } = props const assemblySymmetry = AssemblySymmetry.get(structure.models[0]) if (!assemblySymmetry) return Mesh.createEmpty(mesh) const s = assemblySymmetry.db.rcsb_assembly_symmetry const symmetry = Table.pickRow(s, i => s.id.value(i) === symmetryId) if (!symmetry) return Mesh.createEmpty(mesh) // check if structure.units operators have symmetry.assembly_id if (!getAssemblyIds(structure.units).includes(symmetry.assembly_id)) return Mesh.createEmpty(mesh) const axes = assemblySymmetry.db.rcsb_assembly_symmetry_axis const vectorSpace = AssemblySymmetry.Schema.rcsb_assembly_symmetry_axis.start.space; const radius = 1 * sizeFactor const cylinderProps = { radiusTop: radius, radiusBottom: radius } const builderState = MeshBuilder.createState(256, 128, mesh) for (let i = 0, il = axes._rowCount; i < il; ++i) { if (axes.symmetry_id.value(i) !== symmetryId) continue const start = Tensor.toVec3(Vec3(), vectorSpace, axes.start.value(i)) const end = Tensor.toVec3(Vec3(), vectorSpace, axes.end.value(i)) builderState.currentGroup = i addSphere(builderState, start, radius, 2) addSphere(builderState, end, radius, 2) addCylinder(builderState, start, end, 1, cylinderProps) } return MeshBuilder.getMesh(builderState) }