diff --git a/CHANGELOG.md b/CHANGELOG.md
index c5667a79c9f84710336247e681f434786a578286..40b0426843bf46aaa4db84f662c14388229f14c6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,8 +6,35 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+
+## [v3.11.0] - 2022-07-04
+
+- Add ``instanceGranularity`` option for marker, transparency, clipping, overpaint, substance data to save memory
- CellPack extension tweaks
- Use instancing to create DNA/RNA curves to save memory
+ - Enable ``instanceGranularity`` by default
+ - Add ``adjustStyle`` option to LoadCellPackModel action (stylized, no multi-sample, no far clipping, chain picking)
+- Structure Superposition now respects pivot's coordinate system
+
+## [v3.10.2] - 2022-06-26
+
+- Fix superfluous shader varying
+- Improve use of gl_VertexID when possible
+
+## [v3.10.1] - 2022-06-26
+
+- Fix groupCount when updating TextureMesh-based visuals
+
+## [v3.10.0] - 2022-06-24
+
+- Add support for Glycam saccharide names
+- Add ``PluginConfig.Viewport.ShowTrajectoryControls`` config option
+
+## [v3.9.1] - 2022-06-19
+
+- Fix missing ``super.componentWillUnmount()`` calls (@simeonborko)
+- Fix missing ``uGroupCount`` update for visuals
+- Fix missing aromatic bond display
## [v3.9.0] - 2022-05-30
diff --git a/package-lock.json b/package-lock.json
index 5e96935695f45d9e876484d5b3939a0e7cfb23b1..5acf9fba0766a64a8b2c37ec7bf200c239bf765c 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index acb6108265e2486282fabc6c1025a1f96367ddbb..ece9b6560bf7eecac8db21e68935222dcd031c0d 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "3.10.2",
+ "version": "3.11.0",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 3bab461ff5be6c4db129491d5663a7ff3396ce50..a9babdc05b52181522f83db0b3569ed3a19a3b6a 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -415,6 +415,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
.apply(StructureFromAssemblies, undefined, { state: { isGhost: true } })
.commit({ revertOnError: true });
const membraneParams = {
+ ignoreLight: params.preset.adjustStyle,
representation: params.preset.representation,
};
await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
@@ -431,6 +432,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
.apply(StateTransforms.Model.StructureFromModel, props, { state: { isGhost: true } })
.commit({ revertOnError: true });
const membraneParams = {
+ ignoreLight: params.preset.adjustStyle,
representation: params.preset.representation,
};
await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
@@ -514,6 +516,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
const packingParams = {
traceOnly: params.preset.traceOnly,
+ ignoreLight: params.preset.adjustStyle,
representation: params.preset.representation,
};
await CellpackPackingPreset.apply(packing, packingParams, plugin);
@@ -565,6 +568,7 @@ const LoadCellPackModelParams = {
ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredient files' }),
preset: PD.Group({
traceOnly: PD.Boolean(false),
+ adjustStyle: PD.Boolean(true),
representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation'] as const))
}, { isExpanded: true })
};
@@ -575,5 +579,32 @@ export const LoadCellPackModel = StateAction.build({
params: LoadCellPackModelParams,
from: PSO.Root
})(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
+ if (params.preset.adjustStyle) {
+ ctx.managers.interactivity.setProps({ granularity: 'chain' });
+ ctx.canvas3d?.setProps({
+ multiSample: { mode: 'off' },
+ cameraClipping: { far: false },
+ postprocessing: {
+ occlusion: {
+ name: 'on',
+ params: {
+ samples: 32,
+ radius: 8,
+ bias: 1,
+ blurKernelSize: 15,
+ resolutionScale: 1,
+ }
+ },
+ outline: {
+ name: 'on',
+ params: {
+ scale: 1,
+ threshold: 0.33,
+ color: ColorNames.black,
+ }
+ }
+ }
+ });
+ }
await loadPackings(ctx, taskCtx, state, params);
}));
diff --git a/src/extensions/cellpack/preset.ts b/src/extensions/cellpack/preset.ts
index 6fbfe6ca8c271a0ec3a2728e511c23d3dd2165db..12a0c256e976d5460817badc41e5a8089d90ecab 100644
--- a/src/extensions/cellpack/preset.ts
+++ b/src/extensions/cellpack/preset.ts
@@ -13,6 +13,7 @@ import { CellPackGenerateColorThemeProvider } from './color/generate';
export const CellpackPackingPresetParams = {
traceOnly: PD.Boolean(true),
+ ignoreLight: PD.Boolean(false),
representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'] as const)),
};
export type CellpackPackingPresetParams = PD.ValuesFor<typeof CellpackPackingPresetParams>
@@ -27,7 +28,9 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
const reprProps = {
ignoreHydrogens: true,
- traceOnly: params.traceOnly
+ traceOnly: params.traceOnly,
+ instanceGranularity: true,
+ ignoreLight: params.ignoreLight,
};
const components = {
polymer: await presetStaticComponent(plugin, structureCell, 'polymer')
@@ -57,6 +60,7 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
//
export const CellpackMembranePresetParams = {
+ ignoreLight: PD.Boolean(false),
representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'] as const)),
};
export type CellpackMembranePresetParams = PD.ValuesFor<typeof CellpackMembranePresetParams>
@@ -71,6 +75,8 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({
const reprProps = {
ignoreHydrogens: true,
+ instanceGranularity: true,
+ ignoreLight: params.ignoreLight,
};
const components = {
membrane: await presetStaticComponent(plugin, structureCell, 'all', { label: 'Membrane' })
diff --git a/src/mol-geo/geometry/base.ts b/src/mol-geo/geometry/base.ts
index 953ebdf1a797c03ecf4a8942ebcc085c0d9fc7c0..ca2ba47d8f0a1a50b974cc56fffd31543e4568bd 100644
--- a/src/mol-geo/geometry/base.ts
+++ b/src/mol-geo/geometry/base.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -83,6 +83,7 @@ export namespace BaseGeometry {
quality: PD.Select<VisualQuality>('auto', VisualQualityOptions, { isEssential: true, description: 'Visual/rendering quality of the representation.' }),
material: Material.getParam(),
clip: PD.Group(Clip.Params),
+ instanceGranularity: PD.Boolean(false, { description: 'Use instance granularity for marker, transparency, clipping, overpaint, substance data to save memory.' }),
};
export type Params = typeof Params
@@ -118,6 +119,8 @@ export namespace BaseGeometry {
uClipObjectPosition: ValueCell.create(clip.objects.position),
uClipObjectRotation: ValueCell.create(clip.objects.rotation),
uClipObjectScale: ValueCell.create(clip.objects.scale),
+
+ instanceGranularity: ValueCell.create(props.instanceGranularity),
};
}
@@ -135,6 +138,8 @@ export namespace BaseGeometry {
ValueCell.update(values.uClipObjectPosition, clip.objects.position);
ValueCell.update(values.uClipObjectRotation, clip.objects.rotation);
ValueCell.update(values.uClipObjectScale, clip.objects.scale);
+
+ ValueCell.updateIfChanged(values.instanceGranularity, props.instanceGranularity);
}
export function createRenderableState(props: Partial<PD.Values<Params>> = {}): RenderableState {
diff --git a/src/mol-geo/geometry/clipping-data.ts b/src/mol-geo/geometry/clipping-data.ts
index 8c7b36336020266af3e11815c0edbe5338e2d491..e2c7720694d84eb954421feb1e06dd8043ac786b 100644
--- a/src/mol-geo/geometry/clipping-data.ts
+++ b/src/mol-geo/geometry/clipping-data.ts
@@ -9,10 +9,13 @@ import { Vec2 } from '../../mol-math/linear-algebra';
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { Clipping } from '../../mol-theme/clipping';
+export type ClippingType = 'instance' | 'groupInstance';
+
export type ClippingData = {
tClipping: ValueCell<TextureImage<Uint8Array>>
uClippingTexDim: ValueCell<Vec2>
- dClipping: ValueCell<boolean>,
+ dClipping: ValueCell<boolean>
+ dClippingType: ValueCell<string>
}
export function applyClippingGroups(array: Uint8Array, start: number, end: number, groups: Clipping.Groups) {
@@ -24,18 +27,20 @@ export function clearClipping(array: Uint8Array, start: number, end: number) {
array.fill(0, start, end);
}
-export function createClipping(count: number, clippingData?: ClippingData): ClippingData {
+export function createClipping(count: number, type: ClippingType, clippingData?: ClippingData): ClippingData {
const clipping = createTextureImage(Math.max(1, count), 1, Uint8Array, clippingData && clippingData.tClipping.ref.value.array);
if (clippingData) {
ValueCell.update(clippingData.tClipping, clipping);
ValueCell.update(clippingData.uClippingTexDim, Vec2.create(clipping.width, clipping.height));
ValueCell.updateIfChanged(clippingData.dClipping, count > 0);
+ ValueCell.updateIfChanged(clippingData.dClippingType, type);
return clippingData;
} else {
return {
tClipping: ValueCell.create(clipping),
uClippingTexDim: ValueCell.create(Vec2.create(clipping.width, clipping.height)),
dClipping: ValueCell.create(count > 0),
+ dClippingType: ValueCell.create(type),
};
}
}
@@ -52,6 +57,7 @@ export function createEmptyClipping(clippingData?: ClippingData): ClippingData {
tClipping: ValueCell.create(emptyClippingTexture),
uClippingTexDim: ValueCell.create(Vec2.create(1, 1)),
dClipping: ValueCell.create(false),
+ dClippingType: ValueCell.create('groupInstance'),
};
}
}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/cylinders/cylinders.ts b/src/mol-geo/geometry/cylinders/cylinders.ts
index 341bc72fcec7344096c4bed5d31f318089315557..99929acd159c5d62398dd813a2892a28d5a7037f 100644
--- a/src/mol-geo/geometry/cylinders/cylinders.ts
+++ b/src/mol-geo/geometry/cylinders/cylinders.ts
@@ -201,7 +201,9 @@ export namespace Cylinders {
const color = createColors(locationIt, positionIt, theme.color);
const size = createSizes(locationIt, theme.size);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/direct-volume/direct-volume.ts b/src/mol-geo/geometry/direct-volume/direct-volume.ts
index f0cf9cf16321f9919797eba8b5bdee27bf5f7c37..a298d597e4bf3bae58a710702756399d563d98a4 100644
--- a/src/mol-geo/geometry/direct-volume/direct-volume.ts
+++ b/src/mol-geo/geometry/direct-volume/direct-volume.ts
@@ -211,7 +211,9 @@ export namespace DirectVolume {
const positionIt = Utils.createPositionIterator(directVolume, transform);
const color = createColors(locationIt, positionIt, theme.color);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/image/image.ts b/src/mol-geo/geometry/image/image.ts
index e479434faca3396a1c7064512f3638628da93277..cd4e1992272a9324bae51ebe851d94c6569df819 100644
--- a/src/mol-geo/geometry/image/image.ts
+++ b/src/mol-geo/geometry/image/image.ts
@@ -143,7 +143,9 @@ namespace Image {
const positionIt = Utils.createPositionIterator(image, transform);
const color = createColors(locationIt, positionIt, theme.color);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/lines/lines.ts b/src/mol-geo/geometry/lines/lines.ts
index 5452ac7611d4698522c1cf08c31ccddd1272f2c3..ecf1aa21b50583167562dd3c4feac7f8e2badf04 100644
--- a/src/mol-geo/geometry/lines/lines.ts
+++ b/src/mol-geo/geometry/lines/lines.ts
@@ -208,7 +208,9 @@ export namespace Lines {
const color = createColors(locationIt, positionIt, theme.color);
const size = createSizes(locationIt, theme.size);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/marker-data.ts b/src/mol-geo/geometry/marker-data.ts
index a159eb3a4cbe54a7b0454a1191c50321df0bab55..58356b0b298c1295be1037a180d1753a678306fc 100644
--- a/src/mol-geo/geometry/marker-data.ts
+++ b/src/mol-geo/geometry/marker-data.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -8,12 +8,15 @@ import { ValueCell } from '../../mol-util/value-cell';
import { Vec2 } from '../../mol-math/linear-algebra';
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
+export type MarkerType = 'instance' | 'groupInstance';
+
export type MarkerData = {
- uMarker: ValueCell<number>,
+ uMarker: ValueCell<number>
tMarker: ValueCell<TextureImage<Uint8Array>>
uMarkerTexDim: ValueCell<Vec2>
markerAverage: ValueCell<number>
markerStatus: ValueCell<number>
+ dMarkerType: ValueCell<string>
}
const MarkerCountLut = new Uint8Array(0x0303 + 1);
@@ -64,7 +67,7 @@ export function getMarkersAverage(array: Uint8Array, count: number): number {
return sum / count;
}
-export function createMarkers(count: number, markerData?: MarkerData): MarkerData {
+export function createMarkers(count: number, type: MarkerType, markerData?: MarkerData): MarkerData {
const markers = createTextureImage(Math.max(1, count), 1, Uint8Array, markerData && markerData.tMarker.ref.value.array);
const average = getMarkersAverage(markers.array, count);
const status = average === 0 ? 0 : -1;
@@ -74,6 +77,7 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
ValueCell.update(markerData.uMarkerTexDim, Vec2.create(markers.width, markers.height));
ValueCell.updateIfChanged(markerData.markerAverage, average);
ValueCell.updateIfChanged(markerData.markerStatus, status);
+ ValueCell.updateIfChanged(markerData.dMarkerType, type);
return markerData;
} else {
return {
@@ -82,6 +86,7 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
uMarkerTexDim: ValueCell.create(Vec2.create(markers.width, markers.height)),
markerAverage: ValueCell.create(average),
markerStatus: ValueCell.create(status),
+ dMarkerType: ValueCell.create(type),
};
}
}
@@ -102,6 +107,7 @@ export function createEmptyMarkers(markerData?: MarkerData): MarkerData {
uMarkerTexDim: ValueCell.create(Vec2.create(1, 1)),
markerAverage: ValueCell.create(0),
markerStatus: ValueCell.create(0),
+ dMarkerType: ValueCell.create('groupInstance'),
};
}
}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/mesh/mesh.ts b/src/mol-geo/geometry/mesh/mesh.ts
index 20daa221d1d228c6c79cd757de1948fffc6041de..29b08ba3a935cac0f9a95f70da6e7bcef23f1ad5 100644
--- a/src/mol-geo/geometry/mesh/mesh.ts
+++ b/src/mol-geo/geometry/mesh/mesh.ts
@@ -666,7 +666,9 @@ export namespace Mesh {
const positionIt = createPositionIterator(mesh, transform);
const color = createColors(locationIt, positionIt, theme.color);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/overpaint-data.ts b/src/mol-geo/geometry/overpaint-data.ts
index 70ab4e67a41adcaad028f264b8ff98ee1ce52d9f..3c90b2bf0d46319461118aa639b47d0fd03a71ad 100644
--- a/src/mol-geo/geometry/overpaint-data.ts
+++ b/src/mol-geo/geometry/overpaint-data.ts
@@ -10,6 +10,8 @@ import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { Color } from '../../mol-util/color';
import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
+export type OverpaintType = 'instance' | 'groupInstance' | 'volumeInstance';
+
export type OverpaintData = {
tOverpaint: ValueCell<TextureImage<Uint8Array>>
uOverpaintTexDim: ValueCell<Vec2>
@@ -34,12 +36,13 @@ export function clearOverpaint(array: Uint8Array, start: number, end: number) {
return true;
}
-export function createOverpaint(count: number, overpaintData?: OverpaintData): OverpaintData {
+export function createOverpaint(count: number, type: OverpaintType, overpaintData?: OverpaintData): OverpaintData {
const overpaint = createTextureImage(Math.max(1, count), 4, Uint8Array, overpaintData && overpaintData.tOverpaint.ref.value.array);
if (overpaintData) {
ValueCell.update(overpaintData.tOverpaint, overpaint);
ValueCell.update(overpaintData.uOverpaintTexDim, Vec2.create(overpaint.width, overpaint.height));
ValueCell.updateIfChanged(overpaintData.dOverpaint, count > 0);
+ ValueCell.updateIfChanged(overpaintData.dOverpaintType, type);
return overpaintData;
} else {
return {
@@ -50,7 +53,7 @@ export function createOverpaint(count: number, overpaintData?: OverpaintData): O
tOverpaintGrid: ValueCell.create(createNullTexture()),
uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
- dOverpaintType: ValueCell.create('groupInstance'),
+ dOverpaintType: ValueCell.create(type),
};
}
}
diff --git a/src/mol-geo/geometry/points/points.ts b/src/mol-geo/geometry/points/points.ts
index 6ff2e72b39eb3e9117046939bfe46b5b7aa90f28..e6c2fbd2defb792b0c6e58b3124c024085677de4 100644
--- a/src/mol-geo/geometry/points/points.ts
+++ b/src/mol-geo/geometry/points/points.ts
@@ -170,7 +170,9 @@ export namespace Points {
const color = createColors(locationIt, positionIt, theme.color);
const size = createSizes(locationIt, theme.size);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/spheres/spheres.ts b/src/mol-geo/geometry/spheres/spheres.ts
index 7b442ca910a94e760bf470321fb404d4a65573f0..b7be6f095ad44f85ee525fc7bd7af1c3f82c6a77 100644
--- a/src/mol-geo/geometry/spheres/spheres.ts
+++ b/src/mol-geo/geometry/spheres/spheres.ts
@@ -171,7 +171,9 @@ export namespace Spheres {
const color = createColors(locationIt, positionIt, theme.color);
const size = createSizes(locationIt, theme.size);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const material = createEmptySubstance();
diff --git a/src/mol-geo/geometry/substance-data.ts b/src/mol-geo/geometry/substance-data.ts
index dfd74ad95332a3b941d1ccd9439fb0891325d393..554d7e9f40fdcedc413249f5566decb70ad3e56c 100644
--- a/src/mol-geo/geometry/substance-data.ts
+++ b/src/mol-geo/geometry/substance-data.ts
@@ -10,6 +10,8 @@ import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
import { Material } from '../../mol-util/material';
+export type SubstanceType = 'instance' | 'groupInstance' | 'volumeInstance';
+
export type SubstanceData = {
tSubstance: ValueCell<TextureImage<Uint8Array>>
uSubstanceTexDim: ValueCell<Vec2>
@@ -34,12 +36,13 @@ export function clearSubstance(array: Uint8Array, start: number, end: number) {
return true;
}
-export function createSubstance(count: number, substanceData?: SubstanceData): SubstanceData {
+export function createSubstance(count: number, type: SubstanceType, substanceData?: SubstanceData): SubstanceData {
const substance = createTextureImage(Math.max(1, count), 4, Uint8Array, substanceData && substanceData.tSubstance.ref.value.array);
if (substanceData) {
ValueCell.update(substanceData.tSubstance, substance);
ValueCell.update(substanceData.uSubstanceTexDim, Vec2.create(substance.width, substance.height));
ValueCell.updateIfChanged(substanceData.dSubstance, count > 0);
+ ValueCell.updateIfChanged(substanceData.dSubstanceType, type);
return substanceData;
} else {
return {
@@ -50,7 +53,7 @@ export function createSubstance(count: number, substanceData?: SubstanceData): S
tSubstanceGrid: ValueCell.create(createNullTexture()),
uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
- dSubstanceType: ValueCell.create('groupInstance'),
+ dSubstanceType: ValueCell.create(type),
};
}
}
diff --git a/src/mol-geo/geometry/text/text.ts b/src/mol-geo/geometry/text/text.ts
index 85a11f973e7aa51b15f666e788a29ddadc102847..c68cae99e1fb883dadc2828317a265461c6158fa 100644
--- a/src/mol-geo/geometry/text/text.ts
+++ b/src/mol-geo/geometry/text/text.ts
@@ -211,7 +211,9 @@ export namespace Text {
const color = createColors(locationIt, positionIt, theme.color);
const size = createSizes(locationIt, theme.size);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const substance = createEmptySubstance();
diff --git a/src/mol-geo/geometry/texture-mesh/texture-mesh.ts b/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
index ff2d989b517b6846e1c0f760d266a8d8c17c545d..8c941543972963b7e949c500ee4c0d5c41ab347e 100644
--- a/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
+++ b/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
@@ -137,7 +137,9 @@ export namespace TextureMesh {
const positionIt = Utils.createPositionIterator(textureMesh, transform);
const color = createColors(locationIt, positionIt, theme.color);
- const marker = createMarkers(instanceCount * groupCount);
+ const marker = props.instanceGranularity
+ ? createMarkers(instanceCount, 'instance')
+ : createMarkers(instanceCount * groupCount, 'groupInstance');
const overpaint = createEmptyOverpaint();
const transparency = createEmptyTransparency();
const substance = createEmptySubstance();
diff --git a/src/mol-geo/geometry/transparency-data.ts b/src/mol-geo/geometry/transparency-data.ts
index fb9df06819e17d041d0a45298d6ba15a0f836822..a619443a7b99c42efc6db9e6e43f6e6abf6e4f36 100644
--- a/src/mol-geo/geometry/transparency-data.ts
+++ b/src/mol-geo/geometry/transparency-data.ts
@@ -9,6 +9,8 @@ import { Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';
import { createNullTexture, Texture } from '../../mol-gl/webgl/texture';
+export type TransparencyType = 'instance' | 'groupInstance' | 'volumeInstance';
+
export type TransparencyData = {
tTransparency: ValueCell<TextureImage<Uint8Array>>
uTransparencyTexDim: ValueCell<Vec2>
@@ -41,13 +43,14 @@ export function clearTransparency(array: Uint8Array, start: number, end: number)
array.fill(0, start, end);
}
-export function createTransparency(count: number, transparencyData?: TransparencyData): TransparencyData {
+export function createTransparency(count: number, type: TransparencyType, transparencyData?: TransparencyData): TransparencyData {
const transparency = createTextureImage(Math.max(1, count), 1, Uint8Array, transparencyData && transparencyData.tTransparency.ref.value.array);
if (transparencyData) {
ValueCell.update(transparencyData.tTransparency, transparency);
ValueCell.update(transparencyData.uTransparencyTexDim, Vec2.create(transparency.width, transparency.height));
ValueCell.updateIfChanged(transparencyData.dTransparency, count > 0);
ValueCell.updateIfChanged(transparencyData.transparencyAverage, getTransparencyAverage(transparency.array, count));
+ ValueCell.updateIfChanged(transparencyData.dTransparencyType, type);
return transparencyData;
} else {
return {
@@ -59,7 +62,7 @@ export function createTransparency(count: number, transparencyData?: Transparenc
tTransparencyGrid: ValueCell.create(createNullTexture()),
uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
- dTransparencyType: ValueCell.create('groupInstance'),
+ dTransparencyType: ValueCell.create(type),
};
}
}
diff --git a/src/mol-gl/renderable/schema.ts b/src/mol-gl/renderable/schema.ts
index 9881dc80730278dcfc5ec501df26c77362135e99..6880287cbf44de7927555000c09b8a04b38487cf 100644
--- a/src/mol-gl/renderable/schema.ts
+++ b/src/mol-gl/renderable/schema.ts
@@ -205,6 +205,7 @@ export const MarkerSchema = {
tMarker: TextureSpec('image-uint8', 'alpha', 'ubyte', 'nearest'),
markerAverage: ValueSpec('number'),
markerStatus: ValueSpec('number'),
+ dMarkerType: DefineSpec('string', ['instance', 'groupInstance']),
} as const;
export type MarkerSchema = typeof MarkerSchema
export type MarkerValues = Values<MarkerSchema>
@@ -217,7 +218,7 @@ export const OverpaintSchema = {
uOverpaintGridDim: UniformSpec('v3'),
uOverpaintGridTransform: UniformSpec('v4'),
tOverpaintGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
- dOverpaintType: DefineSpec('string', ['groupInstance', 'volumeInstance']),
+ dOverpaintType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
} as const;
export type OverpaintSchema = typeof OverpaintSchema
export type OverpaintValues = Values<OverpaintSchema>
@@ -231,7 +232,7 @@ export const TransparencySchema = {
uTransparencyGridDim: UniformSpec('v3'),
uTransparencyGridTransform: UniformSpec('v4'),
tTransparencyGrid: TextureSpec('texture', 'alpha', 'ubyte', 'linear'),
- dTransparencyType: DefineSpec('string', ['groupInstance', 'volumeInstance']),
+ dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
} as const;
export type TransparencySchema = typeof TransparencySchema
export type TransparencyValues = Values<TransparencySchema>
@@ -244,7 +245,7 @@ export const SubstanceSchema = {
uSubstanceGridDim: UniformSpec('v3'),
uSubstanceGridTransform: UniformSpec('v4'),
tSubstanceGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
- dSubstanceType: DefineSpec('string', ['groupInstance', 'volumeInstance']),
+ dSubstanceType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
} as const;
export type SubstanceSchema = typeof SubstanceSchema
export type SubstanceValues = Values<SubstanceSchema>
@@ -253,6 +254,7 @@ export const ClippingSchema = {
uClippingTexDim: UniformSpec('v2'),
tClipping: TextureSpec('image-uint8', 'alpha', 'ubyte', 'nearest'),
dClipping: DefineSpec('boolean'),
+ dClippingType: DefineSpec('string', ['instance', 'groupInstance']),
} as const;
export type ClippingSchema = typeof ClippingSchema
export type ClippingValues = Values<ClippingSchema>
@@ -311,6 +313,8 @@ export const BaseSchema = {
extraTransform: ValueSpec('float32'),
/** denotes reflection in transform */
hasReflection: ValueSpec('boolean'),
+ /** use instance granularity for marker, transparency, clipping, overpaint, substance */
+ instanceGranularity: ValueSpec('boolean'),
/** bounding sphere taking aTransform into account and encompases all instances */
boundingSphere: ValueSpec('sphere'),
diff --git a/src/mol-gl/shader/chunks/assign-clipping-varying.glsl.ts b/src/mol-gl/shader/chunks/assign-clipping-varying.glsl.ts
index 3d48b7ecb777bcd7e833d64399ea09edf0f700ee..88ed1b431092d192cddba25d62a90f3fb9de8857 100644
--- a/src/mol-gl/shader/chunks/assign-clipping-varying.glsl.ts
+++ b/src/mol-gl/shader/chunks/assign-clipping-varying.glsl.ts
@@ -1,5 +1,9 @@
export const assign_clipping_varying = `
#if dClipObjectCount != 0 && defined(dClipping)
- vClipping = readFromTexture(tClipping, aInstance * float(uGroupCount) + group, uClippingTexDim).a;
+ #if defined(dClippingType_instance)
+ vClipping = readFromTexture(tClipping, aInstance, uClippingTexDim).a;
+ #elif defined(dMarkerType_groupInstance)
+ vClipping = readFromTexture(tClipping, aInstance * float(uGroupCount) + group, uClippingTexDim).a;
+ #endif
#endif
`;
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts b/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
index fa8ea04fb29668125a0ba59fb1a6fef5214bcec7..7be1d4ff06dad0026c22c578131295e7ea8f37b7 100644
--- a/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
+++ b/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
@@ -25,7 +25,9 @@ export const assign_color_varying = `
#endif
#ifdef dOverpaint
- #if defined(dOverpaintType_groupInstance)
+ #if defined(dOverpaintType_instance)
+ vOverpaint = readFromTexture(tOverpaint, aInstance, uOverpaintTexDim);
+ #elif defined(dOverpaintType_groupInstance)
vOverpaint = readFromTexture(tOverpaint, aInstance * float(uGroupCount) + group, uOverpaintTexDim);
#elif defined(dOverpaintType_vertexInstance)
vOverpaint = readFromTexture(tOverpaint, int(aInstance) * uVertexCount + VertexID, uOverpaintTexDim);
@@ -43,7 +45,9 @@ export const assign_color_varying = `
#endif
#ifdef dSubstance
- #if defined(dSubstanceType_groupInstance)
+ #if defined(dSubstanceType_instance)
+ vSubstance = readFromTexture(tSubstance, aInstance, uSubstanceTexDim);
+ #elif defined(dSubstanceType_groupInstance)
vSubstance = readFromTexture(tSubstance, aInstance * float(uGroupCount) + group, uSubstanceTexDim);
#elif defined(dSubstanceType_vertexInstance)
vSubstance = readFromTexture(tSubstance, int(aInstance) * uVertexCount + VertexID, uSubstanceTexDim);
@@ -72,7 +76,9 @@ export const assign_color_varying = `
#endif
#ifdef dTransparency
- #if defined(dTransparencyType_groupInstance)
+ #if defined(dTransparencyType_instance)
+ vTransparency = readFromTexture(tTransparency, aInstance, uTransparencyTexDim).a;
+ #elif defined(dTransparencyType_groupInstance)
vTransparency = readFromTexture(tTransparency, aInstance * float(uGroupCount) + group, uTransparencyTexDim).a;
#elif defined(dTransparencyType_vertexInstance)
vTransparency = readFromTexture(tTransparency, int(aInstance) * uVertexCount + VertexID, uTransparencyTexDim).a;
diff --git a/src/mol-gl/shader/chunks/assign-marker-varying.glsl.ts b/src/mol-gl/shader/chunks/assign-marker-varying.glsl.ts
index 9509ee52e63cc7fe1ab6f7d14ddcffcb279ad8dc..361ff36decaa432001944ba7a796b11c99203e02 100644
--- a/src/mol-gl/shader/chunks/assign-marker-varying.glsl.ts
+++ b/src/mol-gl/shader/chunks/assign-marker-varying.glsl.ts
@@ -1,5 +1,9 @@
export const assign_marker_varying = `
#if defined(dRenderVariant_color) || defined(dRenderVariant_marking)
- vMarker = readFromTexture(tMarker, aInstance * float(uGroupCount) + group, uMarkerTexDim).a;
+ #if defined(dMarkerType_instance)
+ vMarker = readFromTexture(tMarker, aInstance, uMarkerTexDim).a;
+ #elif defined(dMarkerType_groupInstance)
+ vMarker = readFromTexture(tMarker, aInstance * float(uGroupCount) + group, uMarkerTexDim).a;
+ #endif
#endif
`;
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts b/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
index b57c66a9ea54abae608edb81059e0db31a88eeb3..5459d2fc31658b1eb257bb67852009c2692bea8d 100644
--- a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
+++ b/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
@@ -28,7 +28,7 @@ uniform float uBumpiness;
#endif
#ifdef dOverpaint
- #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)
+ #if defined(dOverpaintType_instance) || defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)
varying vec4 vOverpaint;
uniform vec2 uOverpaintTexDim;
uniform sampler2D tOverpaint;
@@ -42,7 +42,7 @@ uniform float uBumpiness;
#endif
#ifdef dSubstance
- #if defined(dSubstanceType_groupInstance) || defined(dSubstanceType_vertexInstance)
+ #if defined(dSubstanceType_instance) || defined(dSubstanceType_groupInstance) || defined(dSubstanceType_vertexInstance)
varying vec4 vSubstance;
uniform vec2 uSubstanceTexDim;
uniform sampler2D tSubstance;
@@ -75,7 +75,7 @@ uniform float uBumpiness;
#endif
#ifdef dTransparency
- #if defined(dTransparencyType_groupInstance) || defined(dTransparencyType_vertexInstance)
+ #if defined(dTransparencyType_instance) || defined(dTransparencyType_groupInstance) || defined(dTransparencyType_vertexInstance)
varying float vTransparency;
uniform vec2 uTransparencyTexDim;
uniform sampler2D tTransparency;
diff --git a/src/mol-plugin-state/manager/structure/hierarchy.ts b/src/mol-plugin-state/manager/structure/hierarchy.ts
index e9cc03ec62c2a52764b14914e7c5e01b5941adc1..b94db5381cad3fb877e1e12a33af4484d065a405 100644
--- a/src/mol-plugin-state/manager/structure/hierarchy.ts
+++ b/src/mol-plugin-state/manager/structure/hierarchy.ts
@@ -5,6 +5,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
+import { Structure } from '../../../mol-model/structure';
import { setSubtreeVisibility } from '../../../mol-plugin/behavior/static/state';
import { PluginCommands } from '../../../mol-plugin/commands';
import { PluginContext } from '../../../mol-plugin/context';
@@ -12,6 +13,7 @@ import { StateTransform, StateTree } from '../../../mol-state';
import { SetUtils } from '../../../mol-util/set';
import { TrajectoryHierarchyPresetProvider } from '../../builder/structure/hierarchy-preset';
import { PluginComponent } from '../../component';
+import { PluginStateObject } from '../../objects';
import { buildStructureHierarchy, StructureHierarchyRef, ModelRef, StructureComponentRef, StructureHierarchy, StructureRef, TrajectoryRef } from './hierarchy-state';
export class StructureHierarchyManager extends PluginComponent {
@@ -79,6 +81,18 @@ export class StructureHierarchyManager extends PluginComponent {
return ret;
}
+ findStructure(structure: Structure | undefined): StructureRef | undefined {
+ if (!structure) return undefined;
+
+ const parent = this.plugin.helpers.substructureParent.get(structure);
+ if (!parent) return undefined;
+
+ const root = this.plugin.state.data.selectQ(q => q.byValue(parent).rootOfType(PluginStateObject.Molecule.Structure))[0];
+ if (!root) return undefined;
+
+ return this.behaviors.selection.value.structures.find(s => s.cell === root);
+ }
+
private syncCurrent<T extends StructureHierarchyRef>(all: ReadonlyArray<T>, added: Set<StateTransform.Ref>): T[] {
const current = this.seletionSet;
const newCurrent: T[] = [];
diff --git a/src/mol-plugin-ui/structure/superposition.tsx b/src/mol-plugin-ui/structure/superposition.tsx
index 97216a7af2b81f29880ff3172716e2f7bbbc4e87..dc59353b887950753d040b96683d054dc247790d 100644
--- a/src/mol-plugin-ui/structure/superposition.tsx
+++ b/src/mol-plugin-ui/structure/superposition.tsx
@@ -5,25 +5,26 @@
* @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
*/
-import { CollapsableControls, PurePluginUIComponent } from '../base';
-import { Icon, ArrowUpwardSvg, ArrowDownwardSvg, DeleteOutlinedSvg, HelpOutlineSvg, TuneSvg, SuperposeAtomsSvg, SuperposeChainsSvg, SuperpositionSvg } from '../controls/icons';
-import { Button, ToggleButton, IconButton } from '../controls/common';
-import { StructureElement, StructureSelection, QueryContext, Structure, StructureProperties } from '../../mol-model/structure';
+import { SymmetryOperator } from '../../mol-math/geometry';
import { Mat4 } from '../../mol-math/linear-algebra';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { StateObjectRef, StateObjectCell, StateSelection } from '../../mol-state';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { SIFTSMapping } from '../../mol-model-props/sequence/sifts-mapping';
+import { QueryContext, Structure, StructureElement, StructureProperties, StructureSelection } from '../../mol-model/structure';
import { alignAndSuperpose, superpose } from '../../mol-model/structure/structure/util/superposition';
+import { alignAndSuperposeWithSIFTSMapping } from '../../mol-model/structure/structure/util/superposition-sifts-mapping';
import { StructureSelectionQueries } from '../../mol-plugin-state/helpers/structure-selection-query';
-import { structureElementStatsLabel, elementLabel } from '../../mol-theme/label';
-import { ParameterControls } from '../controls/parameters';
-import { stripTags } from '../../mol-util/string';
import { StructureSelectionHistoryEntry } from '../../mol-plugin-state/manager/structure/selection';
-import { ToggleSelectionModeButton } from './selection';
-import { alignAndSuperposeWithSIFTSMapping } from '../../mol-model/structure/structure/util/superposition-sifts-mapping';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
import { PluginCommands } from '../../mol-plugin/commands';
-import { SIFTSMapping } from '../../mol-model-props/sequence/sifts-mapping';
+import { StateObjectCell, StateObjectRef } from '../../mol-state';
+import { elementLabel, structureElementStatsLabel } from '../../mol-theme/label';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { stripTags } from '../../mol-util/string';
+import { CollapsableControls, PurePluginUIComponent } from '../base';
+import { Button, IconButton, ToggleButton } from '../controls/common';
+import { ArrowDownwardSvg, ArrowUpwardSvg, DeleteOutlinedSvg, HelpOutlineSvg, Icon, SuperposeAtomsSvg, SuperposeChainsSvg, SuperpositionSvg, TuneSvg } from '../controls/icons';
+import { ParameterControls } from '../controls/parameters';
+import { ToggleSelectionModeButton } from './selection';
export class StructureSuperpositionControls extends CollapsableControls {
defaultState() {
@@ -104,19 +105,21 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
return this.plugin.managers.structure.selection;
}
- async transform(s: StateObjectRef<PluginStateObject.Molecule.Structure>, matrix: Mat4) {
+ async transform(s: StateObjectRef<PluginStateObject.Molecule.Structure>, matrix: Mat4, coordinateSystem?: SymmetryOperator) {
const r = StateObjectRef.resolveAndCheck(this.plugin.state.data, s);
if (!r) return;
- // TODO should find any TransformStructureConformation decorator instance
- const o = StateSelection.findTagInSubtree(this.plugin.state.data.tree, r.transform.ref, SuperpositionTag);
+ const o = this.plugin.state.data.selectQ(q => q.byRef(r.transform.ref).subtree().withTransformer(StateTransforms.Model.TransformStructureConformation))[0];
+
+ const transform = coordinateSystem && !Mat4.isIdentity(coordinateSystem.matrix)
+ ? Mat4.mul(Mat4(), coordinateSystem.matrix, matrix)
+ : matrix;
const params = {
transform: {
name: 'matrix' as const,
- params: { data: matrix, transpose: false }
+ params: { data: transform, transpose: false }
}
};
- // TODO add .insertOrUpdate to StateBuilder?
const b = o
? this.plugin.state.data.build().to(o).update(params)
: this.plugin.state.data.build().to(s)
@@ -124,19 +127,24 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
await this.plugin.runTask(this.plugin.state.data.updateTree(b));
}
+ private getRootStructure(s: Structure) {
+ const parent = this.plugin.helpers.substructureParent.get(s)!;
+ return this.plugin.state.data.selectQ(q => q.byValue(parent).rootOfType(PluginStateObject.Molecule.Structure))[0].obj?.data!;
+ }
+
superposeChains = async () => {
const { query } = this.state.options.traceOnly ? StructureSelectionQueries.trace : StructureSelectionQueries.polymer;
const entries = this.chainEntries;
- const locis = entries.map((e, i) => {
+ const locis = entries.map(e => {
const s = StructureElement.Loci.toStructure(e.loci);
const loci = StructureSelection.toLociWithSourceUnits(query(new QueryContext(s)));
- return StructureElement.Loci.remap(loci, i === 0
- ? this.plugin.helpers.substructureParent.get(e.loci.structure.root)!.obj!.data
- : loci.structure.root
- );
+ return StructureElement.Loci.remap(loci, this.getRootStructure(e.loci.structure));
});
+ const pivot = this.plugin.managers.structure.hierarchy.findStructure(locis[0]?.structure);
+ const coordinateSystem = pivot?.transform?.cell.obj?.data.coordinateSystem;
+
const transforms = this.state.options.alignSequences
? alignAndSuperpose(locis)
: superpose(locis);
@@ -145,7 +153,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
for (let i = 1, il = locis.length; i < il; ++i) {
const eB = entries[i];
const { bTransform, rmsd } = transforms[i - 1];
- await this.transform(eB.cell, bTransform);
+ await this.transform(eB.cell, bTransform, coordinateSystem);
const labelA = stripTags(eA.label);
const labelB = stripTags(eB.label);
this.plugin.log.info(`Superposed [${labelA}] and [${labelB}] with RMSD ${rmsd.toFixed(2)}.`);
@@ -156,19 +164,19 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
superposeAtoms = async () => {
const entries = this.atomEntries;
- const atomLocis = entries.map((e, i) => {
- return StructureElement.Loci.remap(e.loci, i === 0
- ? this.plugin.helpers.substructureParent.get(e.loci.structure.root)!.obj!.data
- : e.loci.structure.root
- );
+ const atomLocis = entries.map(e => {
+ return StructureElement.Loci.remap(e.loci, this.getRootStructure(e.loci.structure));
});
const transforms = superpose(atomLocis);
+ const pivot = this.plugin.managers.structure.hierarchy.findStructure(atomLocis[0]?.structure);
+ const coordinateSystem = pivot?.transform?.cell.obj?.data.coordinateSystem;
+
const eA = entries[0];
for (let i = 1, il = atomLocis.length; i < il; ++i) {
const eB = entries[i];
const { bTransform, rmsd } = transforms[i - 1];
- await this.transform(eB.cell, bTransform);
+ await this.transform(eB.cell, bTransform, coordinateSystem);
const labelA = stripTags(eA.label);
const labelB = stripTags(eB.label);
const count = entries[i].atoms.length;
@@ -184,10 +192,12 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
const structures = input.map(s => s.cell.obj?.data!);
const { entries, failedPairs, zeroOverlapPairs } = alignAndSuperposeWithSIFTSMapping(structures, { traceOnly });
+ const coordinateSystem = input[0]?.transform?.cell.obj?.data.coordinateSystem;
+
let rmsd = 0;
for (const xform of entries) {
- await this.transform(input[xform.other].cell, xform.transform.bTransform);
+ await this.transform(input[xform.other].cell, xform.transform.bTransform, coordinateSystem);
rmsd += xform.transform.rmsd;
}
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index 8571dc7353e2c74e326c338c708548133a2d3278..803199b180ff825601d3c1c88b2d5c69eef1f6c7 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/src/mol-repr/shape/representation.ts
@@ -78,6 +78,10 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
console.warn('unexpected state');
}
+ if (props.instanceGranularity !== currentProps.instanceGranularity) {
+ updateState.updateTransform = true;
+ }
+
if (updateState.updateTransform) {
updateState.updateColor = true;
updateState.updateSize = true;
@@ -125,7 +129,11 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
Shape.createTransform(_shape.transforms, _renderObject.values);
locationIt = Shape.groupIterator(_shape);
const { instanceCount, groupCount } = locationIt;
- createMarkers(instanceCount * groupCount, _renderObject.values);
+ if (props.instanceGranularity) {
+ createMarkers(instanceCount, 'instance', _renderObject.values);
+ } else {
+ createMarkers(instanceCount * groupCount, 'groupInstance', _renderObject.values);
+ }
}
if (updateState.createGeometry) {
@@ -167,11 +175,30 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
});
}
+ function eachInstance(loci: Loci, shape: Shape, apply: (interval: Interval) => boolean) {
+ let changed = false;
+ if (!ShapeGroup.isLoci(loci)) return false;
+ if (ShapeGroup.isLociEmpty(loci)) return false;
+ if (loci.shape !== shape) return false;
+ for (const g of loci.groups) {
+ if (apply(Interval.ofSingleton(g.instance))) changed = true;
+ }
+ return changed;
+ }
+
function lociApply(loci: Loci, apply: (interval: Interval) => boolean) {
if (isEveryLoci(loci) || (Shape.isLoci(loci) && loci.shape === _shape)) {
- return apply(Interval.ofBounds(0, _shape.groupCount * _shape.transforms.length));
+ if (currentProps.instanceGranularity) {
+ return apply(Interval.ofBounds(0, _shape.transforms.length));
+ } else {
+ return apply(Interval.ofBounds(0, _shape.groupCount * _shape.transforms.length));
+ }
} else {
- return eachShapeGroup(loci, _shape, apply);
+ if (currentProps.instanceGranularity) {
+ return eachInstance(loci, _shape, apply);
+ } else {
+ return eachShapeGroup(loci, _shape, apply);
+ }
}
}
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index e1b13148d48555b8d5bf670e40839783d80952d4..71f5314e921092800bf3a916e11bf2f480776687 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -6,7 +6,7 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Visual, VisualContext } from '../visual';
-import { Structure, StructureElement } from '../../mol-model/structure';
+import { Bond, Structure, StructureElement } from '../../mol-model/structure';
import { Geometry, GeometryUtils } from '../../mol-geo/geometry/geometry';
import { LocationIterator } from '../../mol-geo/util/location-iterator';
import { Theme } from '../../mol-theme/theme';
@@ -126,6 +126,10 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
updateState.createGeometry = true;
}
+ if (newProps.instanceGranularity !== currentProps.instanceGranularity) {
+ updateState.updateTransform = true;
+ }
+
if (updateState.updateSize && !('uSize' in renderObject.values)) {
updateState.createGeometry = true;
}
@@ -154,7 +158,11 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
// console.log('update transform')
locationIt = createLocationIterator(newStructure);
const { instanceCount, groupCount } = locationIt;
- createMarkers(instanceCount * groupCount, renderObject.values);
+ if (newProps.instanceGranularity) {
+ createMarkers(instanceCount, 'instance', renderObject.values);
+ } else {
+ createMarkers(instanceCount * groupCount, 'groupInstance', renderObject.values);
+ }
}
if (updateState.createGeometry) {
@@ -205,11 +213,27 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
return false;
}
+ function eachInstance(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
+ let changed = false;
+ if (!StructureElement.Loci.is(loci) && !Bond.isLoci(loci)) return false;
+ if (!Structure.areEquivalent(loci.structure, structure)) return false;
+ if (apply(Interval.ofSingleton(0))) changed = true;
+ return changed;
+ }
+
function lociApply(loci: Loci, apply: (interval: Interval) => boolean, isMarking: boolean) {
if (lociIsSuperset(loci)) {
- return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
+ if (currentProps.instanceGranularity) {
+ return apply(Interval.ofBounds(0, locationIt.instanceCount));
+ } else {
+ return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
+ }
} else {
- return eachLocation(loci, currentStructure, apply, isMarking);
+ if (currentProps.instanceGranularity) {
+ return eachInstance(loci, currentStructure, apply);
+ } else {
+ return eachLocation(loci, currentStructure, apply, isMarking);
+ }
}
}
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 2325d08b91d80ce263548634d5a19b31b1fcaafd..8c0e3a1d8b7e25488410100f02594b508ed4367a 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -5,7 +5,7 @@
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Structure, Unit, StructureElement } from '../../mol-model/structure';
+import { Structure, Unit, StructureElement, Bond } from '../../mol-model/structure';
import { RepresentationProps } from '../representation';
import { Visual, VisualContext } from '../visual';
import { Geometry, GeometryUtils } from '../../mol-geo/geometry/geometry';
@@ -126,6 +126,10 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
updateState.createGeometry = true;
}
+ if (newProps.instanceGranularity !== currentProps.instanceGranularity) {
+ updateState.updateTransform = true;
+ }
+
if (!deepEqual(newProps.unitKinds, currentProps.unitKinds)) {
// console.log('new unitKinds');
updateState.createGeometry = true;
@@ -194,7 +198,11 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
// console.log('update transform');
locationIt = createLocationIterator(newStructureGroup);
const { instanceCount, groupCount } = locationIt;
- createMarkers(instanceCount * groupCount, renderObject.values);
+ if (newProps.instanceGranularity) {
+ createMarkers(instanceCount, 'instance', renderObject.values);
+ } else {
+ createMarkers(instanceCount * groupCount, 'groupInstance', renderObject.values);
+ }
}
if (updateState.updateMatrix) {
@@ -259,11 +267,44 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
return false;
}
+ function eachInstance(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+ let changed = false;
+ if (Bond.isLoci(loci)) {
+ const { structure, group } = structureGroup;
+ if (!Structure.areEquivalent(loci.structure, structure)) return false;
+ for (const b of loci.bonds) {
+ if (b.aUnit !== b.bUnit) continue;
+ const unitIdx = group.unitIndexMap.get(b.aUnit.id);
+ if (unitIdx !== undefined) {
+ if (apply(Interval.ofSingleton(unitIdx))) changed = true;
+ }
+ }
+ } else if (StructureElement.Loci.is(loci)) {
+ const { structure, group } = structureGroup;
+ if (!Structure.areEquivalent(loci.structure, structure)) return false;
+ for (const e of loci.elements) {
+ const unitIdx = group.unitIndexMap.get(e.unit.id);
+ if (unitIdx !== undefined) {
+ if (apply(Interval.ofSingleton(unitIdx))) changed = true;
+ }
+ }
+ }
+ return changed;
+ }
+
function lociApply(loci: Loci, apply: (interval: Interval) => boolean, isMarking: boolean) {
if (lociIsSuperset(loci)) {
- return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
+ if (currentProps.instanceGranularity) {
+ return apply(Interval.ofBounds(0, locationIt.instanceCount));
+ } else {
+ return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
+ }
} else {
- return eachLocation(loci, currentStructureGroup, apply, isMarking);
+ if (currentProps.instanceGranularity) {
+ return eachInstance(loci, currentStructureGroup, apply);
+ } else {
+ return eachLocation(loci, currentStructureGroup, apply, isMarking);
+ }
}
}
diff --git a/src/mol-repr/visual.ts b/src/mol-repr/visual.ts
index 90e272b4cb925e35626927f7e9e40b40bc475eb3..924e0fb81fa141c54b0b3e001f4b4fafeb02a3c2 100644
--- a/src/mol-repr/visual.ts
+++ b/src/mol-repr/visual.ts
@@ -82,8 +82,10 @@ namespace Visual {
export function mark(renderObject: GraphicsRenderObject | undefined, loci: Loci, action: MarkerAction, lociApply: LociApply, previous?: PreviousMark) {
if (!renderObject || isEmptyLoci(loci)) return false;
- const { tMarker, uMarker, markerAverage, markerStatus, uGroupCount, instanceCount } = renderObject.values;
- const count = uGroupCount.ref.value * instanceCount.ref.value;
+ const { tMarker, uMarker, markerAverage, markerStatus, uGroupCount, instanceCount, instanceGranularity: instanceGranularity } = renderObject.values;
+ const count = instanceGranularity.ref.value
+ ? instanceCount.ref.value
+ : uGroupCount.ref.value * instanceCount.ref.value;
const { array } = tMarker.ref.value;
const currentStatus = markerStatus.ref.value as MarkerInfo['status'];
@@ -158,11 +160,14 @@ namespace Visual {
export function setOverpaint(renderObject: GraphicsRenderObject | undefined, overpaint: Overpaint, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext) {
if (!renderObject) return;
- const { tOverpaint, dOverpaintType, dOverpaint, uGroupCount, instanceCount } = renderObject.values;
- const count = uGroupCount.ref.value * instanceCount.ref.value;
+ const { tOverpaint, dOverpaintType, dOverpaint, uGroupCount, instanceCount, instanceGranularity: instanceGranularity } = renderObject.values;
+ const count = instanceGranularity.ref.value
+ ? instanceCount.ref.value
+ : uGroupCount.ref.value * instanceCount.ref.value;
- // ensure texture has right size
- createOverpaint(overpaint.layers.length ? count : 0, renderObject.values);
+ // ensure texture has right size and type
+ const type = instanceGranularity.ref.value ? 'instance' : 'groupInstance';
+ createOverpaint(overpaint.layers.length ? count : 0, type, renderObject.values);
const { array } = tOverpaint.ref.value;
// clear all if requested
@@ -180,10 +185,11 @@ namespace Visual {
lociApply(loci, apply, false);
}
ValueCell.update(tOverpaint, tOverpaint.ref.value);
- ValueCell.updateIfChanged(dOverpaintType, 'groupInstance');
+ ValueCell.updateIfChanged(dOverpaintType, type);
ValueCell.updateIfChanged(dOverpaint, overpaint.layers.length > 0);
if (overpaint.layers.length === 0) return;
+ if (type === 'instance') return;
if (smoothing && hasColorSmoothingProp(smoothing.props)) {
const { geometry, props, webgl } = smoothing;
@@ -208,11 +214,14 @@ namespace Visual {
export function setTransparency(renderObject: GraphicsRenderObject | undefined, transparency: Transparency, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext) {
if (!renderObject) return;
- const { tTransparency, dTransparencyType, transparencyAverage, dTransparency, uGroupCount, instanceCount } = renderObject.values;
- const count = uGroupCount.ref.value * instanceCount.ref.value;
+ const { tTransparency, dTransparencyType, transparencyAverage, dTransparency, uGroupCount, instanceCount, instanceGranularity: instanceGranularity } = renderObject.values;
+ const count = instanceGranularity.ref.value
+ ? instanceCount.ref.value
+ : uGroupCount.ref.value * instanceCount.ref.value;
- // ensure texture has right size and variant
- createTransparency(transparency.layers.length ? count : 0, renderObject.values);
+ // ensure texture has right size and type
+ const type = instanceGranularity.ref.value ? 'instance' : 'groupInstance';
+ createTransparency(transparency.layers.length ? count : 0, type, renderObject.values);
const { array } = tTransparency.ref.value;
// clear if requested
@@ -229,10 +238,11 @@ namespace Visual {
}
ValueCell.update(tTransparency, tTransparency.ref.value);
ValueCell.updateIfChanged(transparencyAverage, getTransparencyAverage(array, count));
- ValueCell.updateIfChanged(dTransparencyType, 'groupInstance');
+ ValueCell.updateIfChanged(dTransparencyType, type);
ValueCell.updateIfChanged(dTransparency, transparency.layers.length > 0);
if (transparency.layers.length === 0) return;
+ if (type === 'instance') return;
if (smoothing && hasColorSmoothingProp(smoothing.props)) {
const { geometry, props, webgl } = smoothing;
@@ -257,11 +267,14 @@ namespace Visual {
export function setSubstance(renderObject: GraphicsRenderObject | undefined, substance: Substance, lociApply: LociApply, clear: boolean, smoothing?: SmoothingContext) {
if (!renderObject) return;
- const { tSubstance, dSubstanceType, dSubstance, uGroupCount, instanceCount } = renderObject.values;
- const count = uGroupCount.ref.value * instanceCount.ref.value;
+ const { tSubstance, dSubstanceType, dSubstance, uGroupCount, instanceCount, instanceGranularity: instanceGranularity } = renderObject.values;
+ const count = instanceGranularity.ref.value
+ ? instanceCount.ref.value
+ : uGroupCount.ref.value * instanceCount.ref.value;
- // ensure texture has right size
- createSubstance(substance.layers.length ? count : 0, renderObject.values);
+ // ensure texture has right size and type
+ const type = instanceGranularity.ref.value ? 'instance' : 'groupInstance';
+ createSubstance(substance.layers.length ? count : 0, type, renderObject.values);
const { array } = tSubstance.ref.value;
// clear all if requested
@@ -279,10 +292,11 @@ namespace Visual {
lociApply(loci, apply, false);
}
ValueCell.update(tSubstance, tSubstance.ref.value);
- ValueCell.updateIfChanged(dSubstanceType, 'groupInstance');
+ ValueCell.updateIfChanged(dSubstanceType, type);
ValueCell.updateIfChanged(dSubstance, substance.layers.length > 0);
if (substance.layers.length === 0) return;
+ if (type === 'instance') return;
if (smoothing && hasColorSmoothingProp(smoothing.props)) {
const { geometry, props, webgl } = smoothing;
@@ -307,12 +321,15 @@ namespace Visual {
export function setClipping(renderObject: GraphicsRenderObject | undefined, clipping: Clipping, lociApply: LociApply, clear: boolean) {
if (!renderObject) return;
- const { tClipping, dClipping, uGroupCount, instanceCount } = renderObject.values;
- const count = uGroupCount.ref.value * instanceCount.ref.value;
+ const { tClipping, dClippingType, dClipping, uGroupCount, instanceCount, instanceGranularity: instanceGranularity } = renderObject.values;
+ const count = instanceGranularity.ref.value
+ ? instanceCount.ref.value
+ : uGroupCount.ref.value * instanceCount.ref.value;
const { layers } = clipping;
- // ensure texture has right size
- createClipping(layers.length ? count : 0, renderObject.values);
+ // ensure texture has right size and type
+ const type = instanceGranularity.ref.value ? 'instance' : 'groupInstance';
+ createClipping(layers.length ? count : 0, type, renderObject.values);
const { array } = tClipping.ref.value;
// clear if requested
@@ -328,6 +345,7 @@ namespace Visual {
lociApply(loci, apply, false);
}
ValueCell.update(tClipping, tClipping.ref.value);
+ ValueCell.updateIfChanged(dClippingType, type);
ValueCell.updateIfChanged(dClipping, clipping.layers.length > 0);
}
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index bb90f67659a04e2192ad3e5367eac3da97204eb0..fae57da2554529ff0eee4d13a229d8cc6c956271 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -33,6 +33,7 @@ import { Clipping } from '../../mol-theme/clipping';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { isPromiseLike } from '../../mol-util/type-helpers';
import { Substance } from '../../mol-theme/substance';
+import { createMarkers } from '../../mol-geo/geometry/marker-data';
export interface VolumeVisual<P extends VolumeParams> extends Visual<Volume, P> { }
@@ -108,6 +109,10 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
if (updateState.createGeometry) {
updateState.updateColor = true;
}
+
+ if (newProps.instanceGranularity !== currentProps.instanceGranularity) {
+ updateState.updateTransform = true;
+ }
}
function update(newGeometry?: G) {
@@ -124,7 +129,18 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
throw new Error('expected renderObject to be available');
}
- locationIt.reset();
+ if (updateState.updateTransform) {
+ // console.log('update transform');
+ locationIt = createLocationIterator(newVolume);
+ const { instanceCount, groupCount } = locationIt;
+ if (newProps.instanceGranularity) {
+ createMarkers(instanceCount, 'instance', renderObject.values);
+ } else {
+ createMarkers(instanceCount * groupCount, 'groupInstance', renderObject.values);
+ }
+ } else {
+ locationIt.reset();
+ }
if (updateState.createGeometry) {
if (newGeometry) {
@@ -165,11 +181,28 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
}
}
+ function eachInstance(loci: Loci, volume: Volume, apply: (interval: Interval) => boolean) {
+ let changed = false;
+ if (!Volume.Cell.isLoci(loci)) return false;
+ if (Volume.Cell.isLociEmpty(loci)) return false;
+ if (!Volume.areEquivalent(loci.volume, volume)) return false;
+ if (apply(Interval.ofSingleton(0))) changed = true;
+ return changed;
+ }
+
function lociApply(loci: Loci, apply: (interval: Interval) => boolean) {
if (isEveryLoci(loci)) {
- return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
+ if (currentProps.instanceGranularity) {
+ return apply(Interval.ofBounds(0, locationIt.instanceCount));
+ } else {
+ return apply(Interval.ofBounds(0, locationIt.groupCount * locationIt.instanceCount));
+ }
} else {
- return eachLocation(loci, currentVolume, currentProps, apply);
+ if (currentProps.instanceGranularity) {
+ return eachInstance(loci, currentVolume, apply);
+ } else {
+ return eachLocation(loci, currentVolume, currentProps, apply);
+ }
}
}