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@@ -1,17 +1,19 @@
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/**
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- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
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*
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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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*/
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import { Unit, Structure, ElementIndex, StructureElement, ResidueIndex } from '../../../../mol-model/structure';
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-import { Mat4 } from '../../../../mol-math/linear-algebra';
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+import { Mat4, Vec3 } from '../../../../mol-math/linear-algebra';
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import { TransformData, createTransform } from '../../../../mol-geo/geometry/transform-data';
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import { OrderedSet, SortedArray } from '../../../../mol-data/int';
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import { EmptyLoci, Loci } from '../../../../mol-model/loci';
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import { PhysicalSizeTheme } from '../../../../mol-theme/size/physical';
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import { AtomicNumbers, AtomNumber } from '../../../../mol-model/structure/model/properties/atomic';
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import { fillSerial } from '../../../../mol-util/array';
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+import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
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+import { AssignableArrayLike } from '../../../../mol-util/type-helpers';
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/** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
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export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
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@@ -105,37 +107,71 @@ export function getConformation(unit: Unit) {
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}
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}
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-export function getUnitConformationAndRadius(structure: Structure, unit: Unit, ignoreHydrogens = false) {
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- const conformation = getConformation(unit)
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- const { elements } = unit
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+export const CommonSurfaceParams = {
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+ ignoreHydrogens: PD.Boolean(false),
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+ includeParent: PD.Boolean(true, { description: 'Include elements of the parent structure in surface calculation to get a surface patch of the current structure.' }),
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+}
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+export const DefaultCommonSurfaceProps = PD.getDefaultValues(CommonSurfaceParams)
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+export type CommonSurfaceProps = typeof DefaultCommonSurfaceProps
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+
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+const v = Vec3()
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+function squaredDistance(x: number, y: number, z: number, center: Vec3) {
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+ return Vec3.squaredDistance(Vec3.set(v, x, y, z), center)
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+}
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+
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+/** marks `indices` for filtering/ignoring in `id` when not in `elements` */
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+function filterId(id: AssignableArrayLike<number>, elements: SortedArray, indices: SortedArray) {
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+ let start = 0
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+ const end = elements.length
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+ for (let i = 0, il = indices.length; i < il; ++i) {
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+ const idx = SortedArray.indexOfInRange(elements, indices[i], start, end)
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+ if (idx === -1) {
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+ id[i] = -2
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+ } else {
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+ id[i] = idx
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+ start = idx
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+ }
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+ }
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+}
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+
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+export function getUnitConformationAndRadius(structure: Structure, unit: Unit, props: CommonSurfaceProps) {
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+ const { ignoreHydrogens, includeParent } = props
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+ const rootUnit = includeParent ? structure.root.unitMap.get(unit.id) : unit
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+
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+ const { x, y, z } = getConformation(rootUnit)
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+ const { elements } = rootUnit
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+ const { center, radius: sphereRadius } = unit.lookup3d.boundary.sphere
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+ const extraRadius = (2 + 1.5) * 2 // TODO should be twice (the max vdW/sphere radius plus the probe radius)
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+ const radiusSq = (sphereRadius + extraRadius) * (sphereRadius + extraRadius)
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let indices: SortedArray<ElementIndex>
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- let id: ArrayLike<number>
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+ let id: AssignableArrayLike<number>
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- if (ignoreHydrogens) {
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+ if (ignoreHydrogens || (includeParent && rootUnit !== unit)) {
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const _indices = []
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const _id = []
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for (let i = 0, il = elements.length; i < il; ++i) {
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- if (isHydrogen(unit, elements[i])) continue
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- _indices.push(elements[i])
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+ const eI = elements[i]
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+ if (ignoreHydrogens && isHydrogen(rootUnit, eI)) continue
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+ if (includeParent && squaredDistance(x[eI], y[eI], z[eI], center) > radiusSq) continue
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+
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+ _indices.push(eI)
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_id.push(i)
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}
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indices = SortedArray.ofSortedArray(_indices)
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id = _id
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} else {
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indices = elements
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- id = fillSerial(new Uint32Array(indices.length))
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+ id = fillSerial(new Int32Array(indices.length))
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}
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- const position = {
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- indices,
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- x: conformation.x,
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- y: conformation.y,
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- z: conformation.z,
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- id
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+ if (includeParent && rootUnit !== unit) {
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+ filterId(id, unit.elements, indices)
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}
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- const l = StructureElement.Location.create(structure, unit)
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+ const position = { indices, x, y, z, id }
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+
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+ const l = StructureElement.Location.create(structure, rootUnit)
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const sizeTheme = PhysicalSizeTheme({}, {})
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const radius = (index: number) => {
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l.element = index as ElementIndex
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@@ -145,7 +181,7 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, i
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return { position, radius }
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}
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-export function getStructureConformationAndRadius(structure: Structure, ignoreHydrogens = false) {
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+export function getStructureConformationAndRadius(structure: Structure, ignoreHydrogens: boolean) {
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const l = StructureElement.Location.create(structure)
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const sizeTheme = PhysicalSizeTheme({}, {})
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@@ -165,10 +201,11 @@ export function getStructureConformationAndRadius(structure: Structure, ignoreHy
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const unit = structure.units[i]
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const { elements } = unit
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const { x, y, z } = unit.conformation
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+
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l.unit = unit
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for (let j = 0, jl = elements.length; j < jl; ++j) {
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const eI = elements[j]
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- if (ignoreHydrogens && isHydrogen(unit, eI)) continue
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+ if (isHydrogen(unit, eI)) continue
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_xs.push(x(eI))
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_ys.push(y(eI))
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Alexander Rose