From 27963b5aedd801195aabafc5f7924fe8092e17f0 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 13 Aug 2019 14:54:38 -0700
Subject: [PATCH] added option to ignore hydrogens in structure representations
---
src/mol-math/geometry/common.ts | 1 +
src/mol-math/geometry/gaussian-density/cpu.ts | 4 +-
src/mol-math/geometry/gaussian-density/gpu.ts | 4 +-
src/mol-math/geometry/molecular-surface.ts | 6 +-
.../visual/carbohydrate-link-cylinder.ts | 3 +-
.../carbohydrate-terminal-link-cylinder.ts | 3 +-
.../visual/cross-link-restraint-cylinder.ts | 3 +-
.../structure/visual/element-point.ts | 1 +
.../structure/visual/element-sphere.ts | 8 ++-
.../visual/gaussian-density-volume.ts | 4 +-
.../structure/visual/gaussian-surface-mesh.ts | 6 +-
.../visual/gaussian-surface-wireframe.ts | 5 +-
.../visual/inter-unit-link-cylinder.ts | 14 ++++-
.../visual/intra-unit-link-cylinder.ts | 12 +++-
.../visual/molecular-surface-mesh.ts | 8 ++-
src/mol-repr/structure/visual/util/common.ts | 62 ++++++++++++++-----
src/mol-repr/structure/visual/util/element.ts | 12 +++-
.../structure/visual/util/gaussian.ts | 12 ++--
src/mol-repr/structure/visual/util/link.ts | 5 +-
.../visual/util/molecular-surface.ts | 13 ++--
20 files changed, 133 insertions(+), 53 deletions(-)
diff --git a/src/mol-math/geometry/common.ts b/src/mol-math/geometry/common.ts
index 60fbd3c44..184034082 100644
--- a/src/mol-math/geometry/common.ts
+++ b/src/mol-math/geometry/common.ts
@@ -14,6 +14,7 @@ export interface PositionData {
x: ArrayLike<number>,
y: ArrayLike<number>,
z: ArrayLike<number>,
+ id: ArrayLike<number>,
/** subset of indices into the x/y/z/radius arrays */
indices: OrderedSet,
/** optional element radius */
diff --git a/src/mol-math/geometry/gaussian-density/cpu.ts b/src/mol-math/geometry/gaussian-density/cpu.ts
index d1a8c2d16..bb74c6d12 100644
--- a/src/mol-math/geometry/gaussian-density/cpu.ts
+++ b/src/mol-math/geometry/gaussian-density/cpu.ts
@@ -15,7 +15,7 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
const { resolution, radiusOffset, smoothness } = props
const scaleFactor = 1 / resolution
- const { indices, x, y, z } = position
+ const { indices, x, y, z, id } = position
const n = OrderedSet.size(indices)
const radii = new Float32Array(n)
@@ -100,7 +100,7 @@ export async function GaussianDensityCPU(ctx: RuntimeContext, position: Position
data[idx] += dens
if (dens > densData[idx]) {
densData[idx] = dens
- idData[idx] = i
+ idData[idx] = id[i]
}
}
}
diff --git a/src/mol-math/geometry/gaussian-density/gpu.ts b/src/mol-math/geometry/gaussian-density/gpu.ts
index 949d5cae7..2128478a6 100644
--- a/src/mol-math/geometry/gaussian-density/gpu.ts
+++ b/src/mol-math/geometry/gaussian-density/gpu.ts
@@ -224,7 +224,7 @@ function prepareGaussianDensityData(position: PositionData, box: Box3D, radius:
const { resolution, radiusOffset } = props
const scaleFactor = 1 / resolution
- const { indices, x, y, z } = position
+ const { indices, x, y, z, id } = position
const n = OrderedSet.size(indices)
const positions = new Float32Array(n * 3)
@@ -242,7 +242,7 @@ function prepareGaussianDensityData(position: PositionData, box: Box3D, radius:
const r = radius(j) + radiusOffset
if (maxRadius < r) maxRadius = r
radii[i] = r
- groups[i] = i
+ groups[i] = id[i]
}
const pad = maxRadius * 2 + resolution * 4
diff --git a/src/mol-math/geometry/molecular-surface.ts b/src/mol-math/geometry/molecular-surface.ts
index a133e6704..be6c60127 100644
--- a/src/mol-math/geometry/molecular-surface.ts
+++ b/src/mol-math/geometry/molecular-surface.ts
@@ -169,7 +169,7 @@ export async function calcMolecularSurface(ctx: RuntimeContext, position: Requir
const dd = rad - d
if (dd < data[idx]) {
data[idx] = dd
- idData[idx] = i
+ idData[idx] = id[i]
}
}
}
@@ -282,7 +282,7 @@ export async function calcMolecularSurface(ctx: RuntimeContext, position: Requir
// Is this grid point closer to a or b?
// Take dot product of atob and gridpoint->p (dx, dy, dz)
const dp = dx * atob[0] + dy * atob[1] + dz * atob[2]
- idData[idx] = OrderedSet.indexOf(position.indices, dp < 0.0 ? b : a)
+ idData[idx] = id[OrderedSet.indexOf(position.indices, dp < 0.0 ? b : a)]
}
}
}
@@ -323,7 +323,7 @@ export async function calcMolecularSurface(ctx: RuntimeContext, position: Requir
const lookup3d = GridLookup3D(position, cellSize)
const neighbours = lookup3d.result
const box = lookup3d.boundary.box
- const { indices, x: px, y: py, z: pz, radius } = position
+ const { indices, x: px, y: py, z: pz, id, radius } = position
const n = OrderedSet.size(indices)
const pad = maxRadius * 2 + resolution
diff --git a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
index 094aef3ee..382adbf8f 100644
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
@@ -42,7 +42,8 @@ function createCarbohydrateLinkCylinderMesh(ctx: VisualContext, structure: Struc
location.unit = elements[l.carbohydrateIndexA].unit
location.element = elements[l.carbohydrateIndexA].anomericCarbon
return theme.size.size(location) * linkSizeFactor
- }
+ },
+ ignore: (edgeIndex: number) => false
}
return createLinkCylinderMesh(ctx, builderProps, props, mesh)
diff --git a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
index 460343df6..b0c92d1f7 100644
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
@@ -52,7 +52,8 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx: VisualContext, structur
location.element = l.elementUnit.elements[l.elementIndex]
}
return theme.size.size(location) * linkSizeFactor
- }
+ },
+ ignore: (edgeIndex: number) => false
}
return createLinkCylinderMesh(ctx, builderProps, props, mesh)
diff --git a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
index 1971a36e4..b215e9e03 100644
--- a/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
+++ b/src/mol-repr/structure/visual/cross-link-restraint-cylinder.ts
@@ -44,7 +44,8 @@ function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Str
location.unit = b.unitA
location.element = b.unitA.elements[b.indexA]
return theme.size.size(location) * sizeFactor
- }
+ },
+ ignore: () => false
}
return createLinkCylinderMesh(ctx, builderProps, props, mesh)
diff --git a/src/mol-repr/structure/visual/element-point.ts b/src/mol-repr/structure/visual/element-point.ts
index 1ee303c06..f234613c3 100644
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -19,6 +19,7 @@ export const ElementPointParams = {
...UnitsPointsParams,
// sizeFactor: PD.Numeric(1.0, { min: 0, max: 10, step: 0.01 }),
pointSizeAttenuation: PD.Boolean(false),
+ showHydrogens: PD.Boolean(true),
}
export type ElementPointParams = typeof ElementPointParams
diff --git a/src/mol-repr/structure/visual/element-sphere.ts b/src/mol-repr/structure/visual/element-sphere.ts
index cffa6ff95..76715a640 100644
--- a/src/mol-repr/structure/visual/element-sphere.ts
+++ b/src/mol-repr/structure/visual/element-sphere.ts
@@ -16,6 +16,7 @@ export const ElementSphereParams = {
...UnitsSpheresParams,
sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
+ ignoreHydrogens: PD.Boolean(false),
}
export type ElementSphereParams = typeof ElementSphereParams
@@ -31,7 +32,9 @@ export function ElementSphereImpostorVisual(materialId: number): UnitsVisual<Ele
getLoci: getElementLoci,
eachLocation: eachElement,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementSphereParams>, currentProps: PD.Values<ElementSphereParams>) => {
-
+ state.createGeometry = (
+ newProps.ignoreHydrogens !== currentProps.ignoreHydrogens
+ )
}
}, materialId)
}
@@ -46,7 +49,8 @@ export function ElementSphereMeshVisual(materialId: number): UnitsVisual<Element
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementSphereParams>, currentProps: PD.Values<ElementSphereParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
- newProps.detail !== currentProps.detail
+ newProps.detail !== currentProps.detail ||
+ newProps.ignoreHydrogens !== currentProps.ignoreHydrogens
)
}
}, materialId)
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index 7c49603af..dd12a7b82 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -30,7 +30,8 @@ async function createGaussianDensityVolume(ctx: VisualContext, structure: Struct
export const GaussianDensityVolumeParams = {
...ComplexDirectVolumeParams,
- ...GaussianDensityTextureParams
+ ...GaussianDensityTextureParams,
+ ignoreHydrogens: PD.Boolean(false),
}
export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
@@ -48,6 +49,7 @@ export function GaussianDensityVolumeVisual(materialId: number): ComplexVisual<G
state.createGeometry = true
newProps.isoValueNorm = Math.exp(-newProps.smoothness)
}
+ if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true
}
}, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index f937cedf0..d77e36c94 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -6,12 +6,11 @@
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsMeshParams, UnitsTextureMeshParams, UnitsVisual, UnitsMeshVisual, UnitsTextureMeshVisual } from '../units-visual';
-import { GaussianDensityParams, computeUnitGaussianDensity, GaussianDensityTextureProps, computeUnitGaussianDensityTexture2d } from './util/gaussian';
+import { GaussianDensityParams, computeUnitGaussianDensity, GaussianDensityTextureProps, computeUnitGaussianDensityTexture2d, GaussianDensityProps } from './util/gaussian';
import { WebGLContext } from '../../../mol-gl/webgl/context';
import { VisualContext } from '../../visual';
import { Unit, Structure } from '../../../mol-model/structure';
import { Theme } from '../../../mol-theme/theme';
-import { GaussianDensityProps } from '../../../mol-math/geometry/gaussian-density';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
import { StructureElementIterator, getElementLoci, eachElement } from './util/element';
@@ -26,6 +25,7 @@ export const GaussianSurfaceMeshParams = {
...UnitsMeshParams,
...UnitsTextureMeshParams,
...GaussianDensityParams,
+ ignoreHydrogens: PD.Boolean(false),
}
export type GaussianSurfaceMeshParams = typeof GaussianSurfaceMeshParams
@@ -64,6 +64,7 @@ export function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<Gauss
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
+ if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true
}
}, materialId)
}
@@ -108,6 +109,7 @@ export function GaussianSurfaceTextureMeshVisual(materialId: number): UnitsVisua
if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
+ if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true
}
}, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index 241f86b8b..bc5b4910f 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -8,9 +8,8 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { VisualContext } from '../../visual';
import { Unit, Structure } from '../../../mol-model/structure';
import { Theme } from '../../../mol-theme/theme';
-import { GaussianDensityProps } from '../../../mol-math/geometry/gaussian-density';
import { Lines } from '../../../mol-geo/geometry/lines/lines';
-import { computeUnitGaussianDensity, GaussianDensityParams } from './util/gaussian';
+import { computeUnitGaussianDensity, GaussianDensityParams, GaussianDensityProps } from './util/gaussian';
import { computeMarchingCubesLines } from '../../../mol-geo/util/marching-cubes/algorithm';
import { UnitsLinesParams, UnitsVisual, UnitsLinesVisual } from '../units-visual';
import { StructureElementIterator, getElementLoci, eachElement } from './util/element';
@@ -36,6 +35,7 @@ export const GaussianWireframeParams = {
...UnitsLinesParams,
...GaussianDensityParams,
lineSizeAttenuation: PD.Boolean(false),
+ ignoreHydrogens: PD.Boolean(false),
}
export type GaussianWireframeParams = typeof GaussianWireframeParams
@@ -51,6 +51,7 @@ export function GaussianWireframeVisual(materialId: number): UnitsVisual<Gaussia
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true
if (newProps.useGpu !== currentProps.useGpu) state.createGeometry = true
+ if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true
}
}, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
index 775534ce9..615f29cb4 100644
--- a/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/inter-unit-link-cylinder.ts
@@ -17,11 +17,12 @@ import { VisualUpdateState } from '../../util';
import { PickingId } from '../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
import { Interval, OrderedSet } from '../../../mol-data/int';
+import { isHydrogen } from './util/common';
function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitLinkParams>, mesh?: Mesh) {
const links = structure.links
const { bondCount, bonds } = links
- const { sizeFactor, sizeAspectRatio } = props
+ const { sizeFactor, sizeAspectRatio, ignoreHydrogens } = props
if (!bondCount) return Mesh.createEmpty(mesh)
@@ -43,7 +44,12 @@ function createInterUnitLinkCylinderMesh(ctx: VisualContext, structure: Structur
location.unit = b.unitA
location.element = b.unitA.elements[b.indexA]
return theme.size.size(location) * sizeFactor * sizeAspectRatio
- }
+ },
+ ignore: ignoreHydrogens ? (edgeIndex: number) => {
+ const b = bonds[edgeIndex]
+ const uA = b.unitA, uB = b.unitB
+ return isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])
+ } : () => false
}
return createLinkCylinderMesh(ctx, builderProps, props, mesh)
@@ -54,6 +60,7 @@ export const InterUnitLinkParams = {
...LinkCylinderParams,
sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(2/3, { min: 0, max: 3, step: 0.01 }),
+ ignoreHydrogens: PD.Boolean(false),
}
export type InterUnitLinkParams = typeof InterUnitLinkParams
@@ -70,7 +77,8 @@ export function InterUnitLinkVisual(materialId: number): ComplexVisual<InterUnit
newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.linkScale !== currentProps.linkScale ||
- newProps.linkSpacing !== currentProps.linkSpacing
+ newProps.linkSpacing !== currentProps.linkSpacing ||
+ newProps.ignoreHydrogens !== currentProps.ignoreHydrogens
)
}
}, materialId)
diff --git a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
index a881695b1..4ead21c95 100644
--- a/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/intra-unit-link-cylinder.ts
@@ -18,6 +18,7 @@ import { VisualUpdateState } from '../../util';
import { PickingId } from '../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
import { Interval, OrderedSet } from '../../../mol-data/int';
+import { isHydrogen } from './util/common';
function createIntraUnitLinkCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<IntraUnitLinkParams>, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -28,7 +29,7 @@ function createIntraUnitLinkCylinderMesh(ctx: VisualContext, unit: Unit, structu
const links = unit.links
const { edgeCount, a, b, edgeProps, offset } = links
const { order: _order, flags: _flags } = edgeProps
- const { sizeFactor, sizeAspectRatio } = props
+ const { sizeFactor, sizeAspectRatio, ignoreHydrogens } = props
if (!edgeCount) return Mesh.createEmpty(mesh)
@@ -63,7 +64,10 @@ function createIntraUnitLinkCylinderMesh(ctx: VisualContext, unit: Unit, structu
radius: (edgeIndex: number) => {
location.element = elements[a[edgeIndex]]
return theme.size.size(location) * sizeFactor * sizeAspectRatio
- }
+ },
+ ignore: ignoreHydrogens ? (edgeIndex: number) => {
+ return isHydrogen(unit, elements[a[edgeIndex]]) || isHydrogen(unit, elements[b[edgeIndex]])
+ } : () => false
}
return createLinkCylinderMesh(ctx, builderProps, props, mesh)
@@ -74,6 +78,7 @@ export const IntraUnitLinkParams = {
...LinkCylinderParams,
sizeFactor: PD.Numeric(0.3, { min: 0, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(2/3, { min: 0, max: 3, step: 0.01 }),
+ ignoreHydrogens: PD.Boolean(false),
}
export type IntraUnitLinkParams = typeof IntraUnitLinkParams
@@ -90,7 +95,8 @@ export function IntraUnitLinkVisual(materialId: number): UnitsVisual<IntraUnitLi
newProps.sizeAspectRatio !== currentProps.sizeAspectRatio ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.linkScale !== currentProps.linkScale ||
- newProps.linkSpacing !== currentProps.linkSpacing
+ newProps.linkSpacing !== currentProps.linkSpacing ||
+ newProps.ignoreHydrogens !== currentProps.ignoreHydrogens
)
}
}, materialId)
diff --git a/src/mol-repr/structure/visual/molecular-surface-mesh.ts b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
index 2aa8c863e..cba0730ac 100644
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -6,12 +6,12 @@
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsMeshParams, UnitsTextureMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
-import { MolecularSurfaceCalculationParams, MolecularSurfaceCalculationProps } from '../../../mol-math/geometry/molecular-surface';
+import { MolecularSurfaceCalculationParams } from '../../../mol-math/geometry/molecular-surface';
import { VisualContext } from '../../visual';
import { Unit, Structure } from '../../../mol-model/structure';
import { Theme } from '../../../mol-theme/theme';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-import { computeUnitMolecularSurface } from './util/molecular-surface';
+import { computeUnitMolecularSurface, MolecularSurfaceProps } from './util/molecular-surface';
import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
import { StructureElementIterator, getElementLoci, eachElement } from './util/element';
import { VisualUpdateState } from '../../util';
@@ -20,12 +20,13 @@ export const MolecularSurfaceMeshParams = {
...UnitsMeshParams,
...UnitsTextureMeshParams,
...MolecularSurfaceCalculationParams,
+ ignoreHydrogens: PD.Boolean(false),
}
export type MolecularSurfaceMeshParams = typeof MolecularSurfaceMeshParams
//
-async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: MolecularSurfaceCalculationProps, mesh?: Mesh): Promise<Mesh> {
+async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: MolecularSurfaceProps, mesh?: Mesh): Promise<Mesh> {
const { transform, field, idField } = await computeUnitMolecularSurface(unit, props).runInContext(ctx.runtime)
const params = {
@@ -52,6 +53,7 @@ export function MolecularSurfaceMeshVisual(materialId: number): UnitsVisual<Mole
if (newProps.resolution !== currentProps.resolution) state.createGeometry = true
if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true
if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true
+ if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true
}
}, materialId)
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index de52db7f5..33d909faf 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -10,6 +10,8 @@ import { TransformData, createTransform } from '../../../../mol-geo/geometry/tra
import { OrderedSet, SortedArray } from '../../../../mol-data/int';
import { EmptyLoci, Loci } from '../../../../mol-model/loci';
import { PhysicalSizeTheme } from '../../../../mol-theme/size/physical';
+import { AtomicNumbers, AtomNumber } from '../../../../mol-model/structure/model/properties/atomic';
+import { fillSerial } from '../../../../mol-util/array';
/** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
@@ -95,14 +97,34 @@ export function getConformation(unit: Unit) {
}
}
-export function getUnitConformationAndRadius(unit: Unit) {
+export function getUnitConformationAndRadius(unit: Unit, ignoreHydrogens = false) {
const conformation = getConformation(unit)
const { elements } = unit
+
+ let indices: SortedArray<ElementIndex>
+ let id: ArrayLike<number>
+
+ if (ignoreHydrogens) {
+ const _indices = []
+ const _id = []
+ for (let i = 0, il = elements.length; i < il; ++i) {
+ if (isHydrogen(unit, elements[i])) continue
+ _indices.push(elements[i])
+ _id.push(i)
+ }
+ indices = SortedArray.ofSortedArray(_indices)
+ id = _id
+ } else {
+ indices = elements
+ id = fillSerial(new Uint32Array(indices.length))
+ }
+
const position = {
- indices: elements,
+ indices,
x: conformation.x,
y: conformation.y,
- z: conformation.z
+ z: conformation.z,
+ id
}
const l = StructureElement.create(unit)
@@ -115,13 +137,12 @@ export function getUnitConformationAndRadius(unit: Unit) {
return { position, radius }
}
-export function getStructureConformationAndRadius(structure: Structure) {
- const n = structure.elementCount
-
- const xs = new Float32Array(n)
- const ys = new Float32Array(n)
- const zs = new Float32Array(n)
- const rs = new Float32Array(n)
+export function getStructureConformationAndRadius(structure: Structure, ignoreHydrogens = false) {
+ const xs: number[] = []
+ const ys: number[] = []
+ const zs: number[] = []
+ const rs: number[] = []
+ const id: number[] = []
const l = StructureElement.create()
const sizeTheme = PhysicalSizeTheme({}, {})
@@ -134,17 +155,28 @@ export function getStructureConformationAndRadius(structure: Structure) {
l.unit = unit
for (let j = 0, jl = elements.length; j < jl; ++j) {
const eI = elements[j]
- xs[m + j] = x(eI)
- ys[m + j] = y(eI)
- zs[m + j] = z(eI)
+ if (ignoreHydrogens && isHydrogen(unit, eI)) continue
+
+ const mj = m + j
+ xs[mj] = x(eI)
+ ys[mj] = y(eI)
+ zs[mj] = z(eI)
l.element = eI
- rs[m + j] = sizeTheme.size(l)
+ rs[mj] = sizeTheme.size(l)
+ id[mj] = mj
}
m += elements.length
}
- const position = { indices: OrderedSet.ofRange(0, n), x: xs, y: ys, z: zs }
+ const position = { indices: OrderedSet.ofRange(0, m), x: xs, y: ys, z: zs, id }
const radius = (index: number) => rs[index]
return { position, radius }
+}
+
+const _H = AtomicNumbers['H']
+export function isHydrogen(unit: Unit, element: ElementIndex) {
+ if (Unit.isCoarse(unit)) return false
+ if (AtomNumber(unit.model.atomicHierarchy.atoms.type_symbol.value(element)) === _H) return true
+ return false
}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index d70dc06a3..25f536c9a 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -19,10 +19,12 @@ import { Theme } from '../../../../mol-theme/theme';
import { StructureGroup } from '../../../../mol-repr/structure/units-visual';
import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-builder';
+import { isHydrogen } from './common';
export interface ElementSphereMeshProps {
detail: number,
- sizeFactor: number
+ sizeFactor: number,
+ ignoreHydrogens: boolean,
}
export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereMeshProps, mesh?: Mesh): Mesh {
@@ -39,6 +41,8 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
l.unit = unit
for (let i = 0; i < elementCount; i++) {
+ if (props.ignoreHydrogens && isHydrogen(unit, elements[i])) continue
+
l.element = elements[i]
pos(elements[i], v)
@@ -49,7 +53,9 @@ export function createElementSphereMesh(ctx: VisualContext, unit: Unit, structur
return MeshBuilder.getMesh(builderState)
}
-export interface ElementSphereImpostorProps { }
+export interface ElementSphereImpostorProps {
+ ignoreHydrogens: boolean,
+}
export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereImpostorProps, spheres?: Spheres): Spheres {
@@ -61,6 +67,8 @@ export function createElementSphereImpostor(ctx: VisualContext, unit: Unit, stru
const pos = unit.conformation.invariantPosition
for (let i = 0; i < elementCount; i++) {
+ if (props.ignoreHydrogens && isHydrogen(unit, elements[i])) continue
+
pos(elements[i], v)
builder.add(v[0], v[1], v[2], i)
}
diff --git a/src/mol-repr/structure/visual/util/gaussian.ts b/src/mol-repr/structure/visual/util/gaussian.ts
index 401e68a60..fb8509759 100644
--- a/src/mol-repr/structure/visual/util/gaussian.ts
+++ b/src/mol-repr/structure/visual/util/gaussian.ts
@@ -18,6 +18,7 @@ export const GaussianDensityParams = {
radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
useGpu: PD.Boolean(false),
+ ignoreHydrogens: PD.Boolean(false),
}
export const DefaultGaussianDensityProps = PD.getDefaultValues(GaussianDensityParams)
export type GaussianDensityProps = typeof DefaultGaussianDensityProps
@@ -26,6 +27,7 @@ export const GaussianDensityTextureParams = {
resolution: PD.Numeric(1, { min: 0.1, max: 20, step: 0.1 }),
radiusOffset: PD.Numeric(0, { min: 0, max: 10, step: 0.1 }),
smoothness: PD.Numeric(1.5, { min: 0.5, max: 2.5, step: 0.1 }),
+ ignoreHydrogens: PD.Boolean(false),
}
export const DefaultGaussianDensityTextureProps = PD.getDefaultValues(GaussianDensityTextureParams)
export type GaussianDensityTextureProps = typeof DefaultGaussianDensityTextureProps
@@ -33,21 +35,21 @@ export type GaussianDensityTextureProps = typeof DefaultGaussianDensityTexturePr
//
export function computeUnitGaussianDensity(unit: Unit, props: GaussianDensityProps, webgl?: WebGLContext) {
- const { position, radius } = getUnitConformationAndRadius(unit)
+ const { position, radius } = getUnitConformationAndRadius(unit, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return await GaussianDensity(ctx, position, unit.lookup3d.boundary.box, radius, props, webgl);
});
}
export function computeUnitGaussianDensityTexture(unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getUnitConformationAndRadius(unit)
+ const { position, radius } = getUnitConformationAndRadius(unit, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return GaussianDensityTexture(webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
});
}
export function computeUnitGaussianDensityTexture2d(unit: Unit, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getUnitConformationAndRadius(unit)
+ const { position, radius } = getUnitConformationAndRadius(unit, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return GaussianDensityTexture2d(webgl, position, unit.lookup3d.boundary.box, radius, props, texture);
});
@@ -56,14 +58,14 @@ export function computeUnitGaussianDensityTexture2d(unit: Unit, props: GaussianD
//
export function computeStructureGaussianDensity(structure: Structure, props: GaussianDensityProps, webgl?: WebGLContext) {
- const { position, radius } = getStructureConformationAndRadius(structure)
+ const { position, radius } = getStructureConformationAndRadius(structure, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return await GaussianDensity(ctx, position, structure.lookup3d.boundary.box, radius, props, webgl);
});
}
export function computeStructureGaussianDensityTexture(structure: Structure, props: GaussianDensityTextureProps, webgl: WebGLContext, texture?: Texture) {
- const { position, radius } = getStructureConformationAndRadius(structure)
+ const { position, radius } = getStructureConformationAndRadius(structure, props.ignoreHydrogens)
return Task.create('Gaussian Density', async ctx => {
return GaussianDensityTexture(webgl, position, structure.lookup3d.boundary.box, radius, props, texture);
});
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index 0952cd022..69079b62e 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/src/mol-repr/structure/visual/util/link.ts
@@ -59,6 +59,7 @@ export interface LinkCylinderMeshBuilderProps {
order(edgeIndex: number): number
flags(edgeIndex: number): LinkType
radius(edgeIndex: number): number
+ ignore(edgeIndex: number): boolean
}
/**
@@ -66,7 +67,7 @@ export interface LinkCylinderMeshBuilderProps {
* the half closer to the first vertex, i.e. vertex a.
*/
export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkCylinderMeshBuilderProps, props: LinkCylinderProps, mesh?: Mesh) {
- const { linkCount, referencePosition, position, order, flags, radius } = linkBuilder
+ const { linkCount, referencePosition, position, order, flags, radius, ignore } = linkBuilder
if (!linkCount) return Mesh.createEmpty(mesh)
@@ -87,6 +88,8 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkCyli
}
for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
+ if (ignore(edgeIndex)) continue
+
position(va, vb, edgeIndex)
const linkRadius = radius(edgeIndex)
diff --git a/src/mol-repr/structure/visual/util/molecular-surface.ts b/src/mol-repr/structure/visual/util/molecular-surface.ts
index 4444ec061..5d3fd7491 100644
--- a/src/mol-repr/structure/visual/util/molecular-surface.ts
+++ b/src/mol-repr/structure/visual/util/molecular-surface.ts
@@ -11,8 +11,13 @@ import { PositionData, DensityData } from '../../../../mol-math/geometry';
import { MolecularSurfaceCalculationProps, calcMolecularSurface } from '../../../../mol-math/geometry/molecular-surface';
import { OrderedSet } from '../../../../mol-data/int';
-function getPositionDataAndMaxRadius(unit: Unit, props: MolecularSurfaceCalculationProps) {
- const { position, radius } = getUnitConformationAndRadius(unit)
+export type MolecularSurfaceProps = MolecularSurfaceCalculationProps & {
+ ignoreHydrogens: boolean
+}
+
+function getPositionDataAndMaxRadius(unit: Unit, props: MolecularSurfaceProps) {
+ const { probeRadius, ignoreHydrogens } = props
+ const { position, radius } = getUnitConformationAndRadius(unit, ignoreHydrogens)
const { indices } = position
const n = OrderedSet.size(indices)
const radii = new Float32Array(OrderedSet.end(indices))
@@ -22,13 +27,13 @@ function getPositionDataAndMaxRadius(unit: Unit, props: MolecularSurfaceCalculat
const j = OrderedSet.getAt(indices, i)
const r = radius(j)
if (maxRadius < r) maxRadius = r
- radii[j] = r + props.probeRadius
+ radii[j] = r + probeRadius
}
return { position: { ...position, radius: radii }, maxRadius }
}
-export function computeUnitMolecularSurface(unit: Unit, props: MolecularSurfaceCalculationProps) {
+export function computeUnitMolecularSurface(unit: Unit, props: MolecularSurfaceProps) {
const { position, maxRadius } = getPositionDataAndMaxRadius(unit, props)
return Task.create('Molecular Surface', async ctx => {
return await MolecularSurface(ctx, position, maxRadius, props);
--
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