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- /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
- import { Structure, Link, StructureElement } from 'mol-model/structure';
- import { Loci, EmptyLoci } from 'mol-model/loci';
- import { Vec3 } from 'mol-math/linear-algebra';
- import { createLinkCylinderMesh, LinkCylinderProps, LinkCylinderParams } from './util/link';
- import { OrderedSet, Interval } from 'mol-data/int';
- import { ComplexMeshVisual, ComplexVisual } from '../complex-visual';
- import { SizeThemeName, SizeThemeOptions } from 'mol-theme/size';
- import { LinkType } from 'mol-model/structure/model/types';
- import { BitFlags } from 'mol-util';
- import { UnitsMeshParams } from '../units-visual';
- import { ParamDefinition as PD } from 'mol-util/param-definition';
- import { Mesh } from 'mol-geo/geometry/mesh/mesh';
- import { LocationIterator } from 'mol-geo/util/location-iterator';
- import { PickingId } from 'mol-geo/geometry/picking';
- import { VisualUpdateState } from '../../util';
- import { VisualContext } from 'mol-repr';
- import { Theme } from 'mol-geo/geometry/geometry';
- // TODO create seperate visual
- // for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {
- // const tl = carbohydrates.terminalLinks[i]
- // const center = carbohydrates.elements[tl.carbohydrateIndex].geometry.center
- // tl.elementUnit.conformation.position(tl.elementUnit.elements[tl.elementIndex], p)
- // if (tl.fromCarbohydrate) {
- // builder.addCylinder(center, p, 0.5, linkParams)
- // } else {
- // builder.addCylinder(p, center, 0.5, linkParams)
- // }
- // }
- const radiusFactor = 0.3
- async function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: LinkCylinderProps, mesh?: Mesh) {
- const { links, elements } = structure.carbohydrates
- const location = StructureElement.create()
- const builderProps = {
- linkCount: links.length,
- referencePosition: (edgeIndex: number) => null,
- position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
- const l = links[edgeIndex]
- Vec3.copy(posA, elements[l.carbohydrateIndexA].geometry.center)
- Vec3.copy(posB, elements[l.carbohydrateIndexB].geometry.center)
- },
- order: (edgeIndex: number) => 1,
- flags: (edgeIndex: number) => BitFlags.create(LinkType.Flag.None),
- radius: (edgeIndex: number) => {
- const l = links[edgeIndex]
- location.unit = elements[l.carbohydrateIndexA].unit
- location.element = elements[l.carbohydrateIndexA].anomericCarbon
- return theme.size.size(location) * radiusFactor
- }
- }
- return createLinkCylinderMesh(ctx, builderProps, props, mesh)
- }
- export const CarbohydrateLinkParams = {
- ...UnitsMeshParams,
- ...LinkCylinderParams,
- sizeTheme: PD.Select<SizeThemeName>('Size Theme', '', 'physical', SizeThemeOptions),
- sizeValue: PD.Numeric('Size Value', '', 1, 0, 20, 0.1),
- detail: PD.Numeric('Sphere Detail', '', 0, 0, 3, 1),
- }
- export const DefaultCarbohydrateLinkProps = PD.getDefaultValues(CarbohydrateLinkParams)
- export type CarbohydrateLinkProps = typeof DefaultCarbohydrateLinkProps
- export function CarbohydrateLinkVisual(): ComplexVisual<CarbohydrateLinkProps> {
- return ComplexMeshVisual<CarbohydrateLinkProps>({
- defaultProps: DefaultCarbohydrateLinkProps,
- createGeometry: createCarbohydrateLinkCylinderMesh,
- createLocationIterator: CarbohydrateLinkIterator,
- getLoci: getLinkLoci,
- mark: markLink,
- setUpdateState: (state: VisualUpdateState, newProps: CarbohydrateLinkProps, currentProps: CarbohydrateLinkProps) => {
- state.createGeometry = newProps.radialSegments !== currentProps.radialSegments
- }
- })
- }
- function CarbohydrateLinkIterator(structure: Structure): LocationIterator {
- const { elements, links } = structure.carbohydrates
- const groupCount = links.length
- const instanceCount = 1
- const location = Link.Location()
- const getLocation = (groupIndex: number) => {
- const link = links[groupIndex]
- const carbA = elements[link.carbohydrateIndexA]
- const carbB = elements[link.carbohydrateIndexB]
- const indexA = OrderedSet.indexOf(carbA.unit.elements, carbA.anomericCarbon)
- const indexB = OrderedSet.indexOf(carbB.unit.elements, carbB.anomericCarbon)
- location.aUnit = carbA.unit
- location.aIndex = indexA as StructureElement.UnitIndex
- location.bUnit = carbB.unit
- location.bIndex = indexB as StructureElement.UnitIndex
- return location
- }
- return LocationIterator(groupCount, instanceCount, getLocation, true)
- }
- function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
- const { objectId, groupId } = pickingId
- if (id === objectId) {
- const { links, elements } = structure.carbohydrates
- const l = links[groupId]
- const carbA = elements[l.carbohydrateIndexA]
- const carbB = elements[l.carbohydrateIndexB]
- const indexA = OrderedSet.indexOf(carbA.unit.elements, carbA.anomericCarbon)
- const indexB = OrderedSet.indexOf(carbB.unit.elements, carbB.anomericCarbon)
- if (indexA !== -1 && indexB !== -1) {
- return Link.Loci([
- Link.Location(
- carbA.unit, indexA as StructureElement.UnitIndex,
- carbB.unit, indexB as StructureElement.UnitIndex
- )
- ])
- }
- }
- return EmptyLoci
- }
- function markLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
- const { getLinkIndex } = structure.carbohydrates
- let changed = false
- if (Link.isLoci(loci)) {
- for (const l of loci.links) {
- const idx = getLinkIndex(l.aUnit, l.aUnit.elements[l.aIndex], l.bUnit, l.bUnit.elements[l.bIndex])
- if (idx !== undefined) {
- if (apply(Interval.ofSingleton(idx))) changed = true
- }
- }
- }
- return changed
- }
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