From 7686b617285f88854a1d643b33498a36aeaf5445 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sat, 24 Jul 2021 16:24:27 -0700
Subject: [PATCH] fix includeParent for multi instance bond visuals
---
CHANGELOG.md | 3 ++-
.../dnatco/confal-pyramids/representation.ts | 4 ++--
.../rcsb/validation-report/representation.ts | 3 ++-
src/mol-geo/geometry/spheres/spheres.ts | 3 ---
src/mol-geo/geometry/text/text.ts | 3 ---
.../interactions-intra-unit-cylinder.ts | 3 ++-
src/mol-repr/structure/params.ts | 1 +
.../structure/representation/ball-and-stick.ts | 1 +
src/mol-repr/structure/representation/line.ts | 1 +
src/mol-repr/structure/units-representation.ts | 2 +-
src/mol-repr/structure/units-visual.ts | 12 +++++-------
.../structure/visual/bond-intra-unit-cylinder.ts | 3 ++-
.../structure/visual/bond-intra-unit-line.ts | 3 ++-
src/mol-repr/structure/visual/element-sphere.ts | 3 ++-
.../structure/visual/gaussian-surface-mesh.ts | 4 ++--
.../structure/visual/orientation-ellipsoid-mesh.ts | 3 ++-
.../structure/visual/polymer-backbone-cylinder.ts | 3 ++-
.../structure/visual/polymer-backbone-sphere.ts | 3 ++-
src/mol-repr/structure/visual/polymer-trace-mesh.ts | 3 ++-
src/mol-repr/structure/visual/util/bond.ts | 3 +--
src/mol-repr/structure/visual/util/common.ts | 8 +++++++-
src/mol-repr/structure/visual/util/element.ts | 3 +--
src/mol-repr/structure/visual/util/nucleotide.ts | 3 +--
src/mol-repr/structure/visual/util/polymer.ts | 3 +--
24 files changed, 44 insertions(+), 37 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b4db17981..769a34302 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,9 +10,10 @@ Note that since we don't clearly distinguish between a public and private interf
- Add `SdfFormat` and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
- Fix mononucleotides detected as polymer components (#229)
- Set default outline scale back to 1
-- Improved DCD reader cell angle handling (intepret near 0 angles as 90 deg)
+- Improved DCD reader cell angle handling (interpret near 0 angles as 90 deg)
- Handle more residue/atom names commonly used in force-fields
- Add USDZ support to ``geo-export`` extension.
+- Fix `includeParent` support for multi-instance bond visuals.
## [v2.1.0] - 2021-07-05
diff --git a/src/extensions/dnatco/confal-pyramids/representation.ts b/src/extensions/dnatco/confal-pyramids/representation.ts
index ebb936e62..b0ce90b53 100644
--- a/src/extensions/dnatco/confal-pyramids/representation.ts
+++ b/src/extensions/dnatco/confal-pyramids/representation.ts
@@ -20,10 +20,10 @@ import { Structure, StructureProperties, Unit } from '../../../mol-model/structu
import { CustomProperty } from '../../../mol-model-props/common/custom-property';
import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder, UnitsRepresentation } from '../../../mol-repr/structure/representation';
-import { StructureGroup, UnitsMeshParams, UnitsMeshVisual, UnitsVisual } from '../../../mol-repr/structure/units-visual';
+import { UnitsMeshParams, UnitsMeshVisual, UnitsVisual } from '../../../mol-repr/structure/units-visual';
import { VisualUpdateState } from '../../../mol-repr/util';
import { VisualContext } from '../../../mol-repr/visual';
-import { getAltResidueLociFromId } from '../../../mol-repr/structure/visual/util/common';
+import { getAltResidueLociFromId, StructureGroup } from '../../../mol-repr/structure/visual/util/common';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
import { NullLocation } from '../../../mol-model/location';
diff --git a/src/extensions/rcsb/validation-report/representation.ts b/src/extensions/rcsb/validation-report/representation.ts
index 3e2c4406a..b65f771b5 100644
--- a/src/extensions/rcsb/validation-report/representation.ts
+++ b/src/extensions/rcsb/validation-report/representation.ts
@@ -16,7 +16,7 @@ import { RepresentationContext, RepresentationParamsGetter, Representation } fro
import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
import { VisualContext } from '../../../mol-repr/visual';
import { createLinkCylinderMesh, LinkCylinderParams, LinkStyle } from '../../../mol-repr/structure/visual/util/link';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../../../mol-repr/structure/units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../../../mol-repr/structure/units-visual';
import { VisualUpdateState } from '../../../mol-repr/util';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { ClashesProvider, IntraUnitClashes, InterUnitClashes, ValidationReport } from './prop';
@@ -28,6 +28,7 @@ import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
import { Sphere3D } from '../../../mol-math/geometry';
import { bondLabel } from '../../../mol-theme/label';
import { getUnitKindsParam } from '../../../mol-repr/structure/params';
+import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
//
diff --git a/src/mol-geo/geometry/spheres/spheres.ts b/src/mol-geo/geometry/spheres/spheres.ts
index 14b52ca7a..3163a0961 100644
--- a/src/mol-geo/geometry/spheres/spheres.ts
+++ b/src/mol-geo/geometry/spheres/spheres.ts
@@ -163,9 +163,6 @@ export namespace Spheres {
function createValues(spheres: Spheres, transform: TransformData, locationIt: LocationIterator, theme: Theme, props: PD.Values<Params>): SpheresValues {
const { instanceCount, groupCount } = locationIt;
- if (instanceCount !== transform.instanceCount.ref.value) {
- throw new Error('instanceCount values in TransformData and LocationIterator differ');
- }
const positionIt = createPositionIterator(spheres, transform);
const color = createColors(locationIt, positionIt, theme.color);
diff --git a/src/mol-geo/geometry/text/text.ts b/src/mol-geo/geometry/text/text.ts
index b0f3f51fa..cd4e20719 100644
--- a/src/mol-geo/geometry/text/text.ts
+++ b/src/mol-geo/geometry/text/text.ts
@@ -206,9 +206,6 @@ export namespace Text {
function createValues(text: Text, transform: TransformData, locationIt: LocationIterator, theme: Theme, props: PD.Values<Params>): TextValues {
const { instanceCount, groupCount } = locationIt;
- if (instanceCount !== transform.instanceCount.ref.value) {
- throw new Error('instanceCount values in TransformData and LocationIterator differ');
- }
const positionIt = createPositionIterator(text, transform);
const color = createColors(locationIt, positionIt, theme.color);
diff --git a/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts b/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
index d67a85279..ed89ee955 100644
--- a/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
+++ b/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
@@ -15,12 +15,13 @@ import { VisualContext } from '../../../mol-repr/visual';
import { Theme } from '../../../mol-theme/theme';
import { InteractionsProvider } from '../interactions';
import { createLinkCylinderMesh, LinkCylinderParams, LinkStyle } from '../../../mol-repr/structure/visual/util/link';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../../../mol-repr/structure/units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../../../mol-repr/structure/units-visual';
import { VisualUpdateState } from '../../../mol-repr/util';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { Interactions } from '../interactions/interactions';
import { InteractionFlag } from '../interactions/common';
import { Sphere3D } from '../../../mol-math/geometry';
+import { StructureGroup } from '../../../mol-repr/structure/visual/util/common';
async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<InteractionsIntraUnitParams>, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
diff --git a/src/mol-repr/structure/params.ts b/src/mol-repr/structure/params.ts
index 162e75dff..a838ccb24 100644
--- a/src/mol-repr/structure/params.ts
+++ b/src/mol-repr/structure/params.ts
@@ -22,6 +22,7 @@ export function getUnitKindsParam(defaultValue: UnitKind[]) {
export const StructureParams = {
unitKinds: getUnitKindsParam(['atomic', 'spheres']),
+ includeParent: PD.Boolean(false, { isHidden: true }),
};
export type StructureParams = typeof StructureParams
diff --git a/src/mol-repr/structure/representation/ball-and-stick.ts b/src/mol-repr/structure/representation/ball-and-stick.ts
index 70eb3ab04..ee043e08d 100644
--- a/src/mol-repr/structure/representation/ball-and-stick.ts
+++ b/src/mol-repr/structure/representation/ball-and-stick.ts
@@ -27,6 +27,7 @@ export const BallAndStickParams = {
traceOnly: PD.Boolean(false, { isHidden: true }), // not useful here
...IntraUnitBondCylinderParams,
...InterUnitBondCylinderParams,
+ includeParent: PD.Boolean(false),
unitKinds: getUnitKindsParam(['atomic']),
sizeFactor: PD.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }),
diff --git a/src/mol-repr/structure/representation/line.ts b/src/mol-repr/structure/representation/line.ts
index 013677e00..2f9c5c5d6 100644
--- a/src/mol-repr/structure/representation/line.ts
+++ b/src/mol-repr/structure/representation/line.ts
@@ -23,6 +23,7 @@ const LineVisuals = {
export const LineParams = {
...IntraUnitBondLineParams,
...InterUnitBondLineParams,
+ includeParent: PD.Boolean(false),
sizeFactor: PD.Numeric(1.5, { min: 0.01, max: 10, step: 0.01 }),
unitKinds: getUnitKindsParam(['atomic']),
visuals: PD.MultiSelect(['intra-bond', 'inter-bond'], PD.objectToOptions(LineVisuals))
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 3c9b3305c..d784e37af 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -8,7 +8,6 @@
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationState } from './representation';
import { Visual } from '../visual';
-import { StructureGroup } from './units-visual';
import { RepresentationContext, RepresentationParamsGetter } from '../representation';
import { Structure, Unit, StructureElement, Bond } from '../../mol-model/structure';
import { Subject } from 'rxjs';
@@ -25,6 +24,7 @@ import { Interval } from '../../mol-data/int';
import { StructureParams } from './params';
import { Clipping } from '../../mol-theme/clipping';
import { WebGLContext } from '../../mol-gl/webgl/context';
+import { StructureGroup } from './visual/util/common';
export interface UnitsVisual<P extends StructureParams> extends Visual<StructureGroup, P> { }
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 92ccd37e0..fd28a68df 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -11,7 +11,7 @@ import { Visual, VisualContext } from '../visual';
import { Geometry, GeometryUtils } from '../../mol-geo/geometry/geometry';
import { LocationIterator } from '../../mol-geo/util/location-iterator';
import { Theme } from '../../mol-theme/theme';
-import { createUnitsTransform, includesUnitKind } from './visual/util/common';
+import { createUnitsTransform, includesUnitKind, StructureGroup } from './visual/util/common';
import { createRenderObject, GraphicsRenderObject, RenderObjectValues } from '../../mol-gl/render-object';
import { PickingId } from '../../mol-geo/geometry/picking';
import { Loci, isEveryLoci, EmptyLoci } from '../../mol-model/loci';
@@ -41,13 +41,11 @@ import { Clipping } from '../../mol-theme/clipping';
import { WebGLContext } from '../../mol-gl/webgl/context';
import { isPromiseLike } from '../../mol-util/type-helpers';
-export type StructureGroup = { structure: Structure, group: Unit.SymmetryGroup }
-
export interface UnitsVisual<P extends RepresentationProps = {}> extends Visual<StructureGroup, P> { }
-function createUnitsRenderObject<G extends Geometry>(group: Unit.SymmetryGroup, geometry: G, locationIt: LocationIterator, theme: Theme, props: PD.Values<Geometry.Params<G>>, materialId: number) {
+function createUnitsRenderObject<G extends Geometry>(structureGroup: StructureGroup, geometry: G, locationIt: LocationIterator, theme: Theme, props: PD.Values<StructureParams & Geometry.Params<G>>, materialId: number) {
const { createValues, createRenderableState } = Geometry.getUtils(geometry);
- const transform = createUnitsTransform(group);
+ const transform = createUnitsTransform(structureGroup, props.includeParent);
const values = createValues(geometry, transform, locationIt, theme, props);
const state = createRenderableState(props);
return createRenderObject(geometry.kind, values, state, materialId);
@@ -179,7 +177,7 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
if (updateState.createNew) {
locationIt = createLocationIterator(newStructureGroup);
if (newGeometry) {
- renderObject = createUnitsRenderObject(newStructureGroup.group, newGeometry, locationIt, newTheme, newProps, materialId);
+ renderObject = createUnitsRenderObject(newStructureGroup, newGeometry, locationIt, newTheme, newProps, materialId);
positionIt = createPositionIterator(newGeometry, renderObject.values);
} else {
throw new Error('expected geometry to be given');
@@ -198,7 +196,7 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
if (updateState.updateMatrix) {
// console.log('update matrix');
- createUnitsTransform(newStructureGroup.group, renderObject.values);
+ createUnitsTransform(newStructureGroup, newProps.includeParent, renderObject.values);
}
if (updateState.createGeometry) {
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index cd10168f0..7aae65c38 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -13,7 +13,7 @@ import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { arrayEqual } from '../../../mol-util';
import { createLinkCylinderImpostors, createLinkCylinderMesh, LinkBuilderProps, LinkStyle } from './util/link';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup, UnitsCylindersParams, UnitsCylindersVisual } from '../units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsCylindersParams, UnitsCylindersVisual } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { BondType } from '../../../mol-model/structure/model/types';
import { BondCylinderParams, BondIterator, eachIntraBond, getIntraBondLoci, makeIntraBondIgnoreTest } from './util/bond';
@@ -23,6 +23,7 @@ import { WebGLContext } from '../../../mol-gl/webgl/context';
import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
import { SortedArray } from '../../../mol-data/int';
import { arrayIntersectionSize } from '../../../mol-util/array';
+import { StructureGroup } from './util/common';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const isBondType = BondType.is;
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-line.ts b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
index 8cc4cbeee..f55e7eb0d 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -11,7 +11,7 @@ import { Theme } from '../../../mol-theme/theme';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { arrayEqual } from '../../../mol-util';
import { LinkStyle, createLinkLines, LinkBuilderProps } from './util/link';
-import { UnitsVisual, UnitsLinesParams, UnitsLinesVisual, StructureGroup } from '../units-visual';
+import { UnitsVisual, UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { BondType } from '../../../mol-model/structure/model/types';
import { BondIterator, BondLineParams, getIntraBondLoci, eachIntraBond, makeIntraBondIgnoreTest } from './util/bond';
@@ -19,6 +19,7 @@ import { Sphere3D } from '../../../mol-math/geometry';
import { Lines } from '../../../mol-geo/geometry/lines/lines';
import { IntAdjacencyGraph } from '../../../mol-math/graph';
import { arrayIntersectionSize } from '../../../mol-util/array';
+import { StructureGroup } from './util/common';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const isBondType = BondType.is;
diff --git a/src/mol-repr/structure/visual/element-sphere.ts b/src/mol-repr/structure/visual/element-sphere.ts
index def4843cb..e7fc70aa0 100644
--- a/src/mol-repr/structure/visual/element-sphere.ts
+++ b/src/mol-repr/structure/visual/element-sphere.ts
@@ -6,12 +6,13 @@
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsMeshParams, UnitsSpheresParams, UnitsVisual, UnitsSpheresVisual, UnitsMeshVisual, StructureGroup } from '../units-visual';
+import { UnitsMeshParams, UnitsSpheresParams, UnitsVisual, UnitsSpheresVisual, UnitsMeshVisual } from '../units-visual';
import { WebGLContext } from '../../../mol-gl/webgl/context';
import { createElementSphereImpostor, ElementIterator, getElementLoci, eachElement, createElementSphereMesh } from './util/element';
import { VisualUpdateState } from '../../util';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Structure } from '../../../mol-model/structure';
+import { StructureGroup } from './util/common';
export const ElementSphereParams = {
...UnitsMeshParams,
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index 51ab5372e..a63788c9b 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -5,7 +5,7 @@
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsMeshParams, UnitsTextureMeshParams, UnitsVisual, UnitsMeshVisual, UnitsTextureMeshVisual, StructureGroup } from '../units-visual';
+import { UnitsMeshParams, UnitsTextureMeshParams, UnitsVisual, UnitsMeshVisual, UnitsTextureMeshVisual } from '../units-visual';
import { GaussianDensityParams, computeUnitGaussianDensity, computeUnitGaussianDensityTexture2d, GaussianDensityProps, computeStructureGaussianDensity, computeStructureGaussianDensityTexture2d } from './util/gaussian';
import { VisualContext } from '../../visual';
import { Unit, Structure } from '../../../mol-model/structure';
@@ -18,7 +18,7 @@ import { TextureMesh } from '../../../mol-geo/geometry/texture-mesh/texture-mesh
import { extractIsosurface } from '../../../mol-gl/compute/marching-cubes/isosurface';
import { Sphere3D } from '../../../mol-math/geometry';
import { ComplexVisual, ComplexMeshParams, ComplexMeshVisual, ComplexTextureMeshVisual, ComplexTextureMeshParams } from '../complex-visual';
-import { getUnitExtraRadius, getStructureExtraRadius, getVolumeSliceInfo } from './util/common';
+import { getUnitExtraRadius, getStructureExtraRadius, getVolumeSliceInfo, StructureGroup } from './util/common';
import { WebGLContext } from '../../../mol-gl/webgl/context';
import { MeshValues } from '../../../mol-gl/renderable/mesh';
import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
diff --git a/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts b/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts
index 717efa5bc..76e355547 100644
--- a/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts
+++ b/src/mol-repr/structure/visual/orientation-ellipsoid-mesh.ts
@@ -5,7 +5,7 @@
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../../../mol-repr/structure/units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../../../mol-repr/structure/units-visual';
import { VisualUpdateState } from '../../../mol-repr/util';
import { VisualContext } from '../../../mol-repr/visual';
import { Unit, Structure, StructureElement } from '../../../mol-model/structure';
@@ -22,6 +22,7 @@ import { UnitIndex } from '../../../mol-model/structure/structure/element/elemen
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { MoleculeType } from '../../../mol-model/structure/model/types';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { StructureGroup } from './util/common';
export const OrientationEllipsoidMeshParams = {
...UnitsMeshParams,
diff --git a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
index accf0d45e..249f55348 100644
--- a/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
+++ b/src/mol-repr/structure/visual/polymer-backbone-cylinder.ts
@@ -14,7 +14,7 @@ import { Vec3 } from '../../../mol-math/linear-algebra';
import { CylinderProps } from '../../../mol-geo/primitive/cylinder';
import { eachPolymerElement, getPolymerElementLoci, NucleicShift, PolymerLocationIterator, StandardShift } from './util/polymer';
import { addCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsCylindersVisual, UnitsCylindersParams, StructureGroup } from '../units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsCylindersVisual, UnitsCylindersParams } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
@@ -23,6 +23,7 @@ import { WebGLContext } from '../../../mol-gl/webgl/context';
import { Cylinders } from '../../../mol-geo/geometry/cylinders/cylinders';
import { CylindersBuilder } from '../../../mol-geo/geometry/cylinders/cylinders-builder';
import { eachPolymerBackboneLink } from './util/polymer/backbone';
+import { StructureGroup } from './util/common';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3scale = Vec3.scale;
diff --git a/src/mol-repr/structure/visual/polymer-backbone-sphere.ts b/src/mol-repr/structure/visual/polymer-backbone-sphere.ts
index 9557e22b9..d09dbe1f9 100644
--- a/src/mol-repr/structure/visual/polymer-backbone-sphere.ts
+++ b/src/mol-repr/structure/visual/polymer-backbone-sphere.ts
@@ -12,7 +12,7 @@ import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { eachPolymerElement, getPolymerElementLoci, PolymerLocationIterator } from './util/polymer';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsSpheresVisual, UnitsSpheresParams, StructureGroup } from '../units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, UnitsSpheresVisual, UnitsSpheresParams } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
@@ -22,6 +22,7 @@ import { WebGLContext } from '../../../mol-gl/webgl/context';
import { Spheres } from '../../../mol-geo/geometry/spheres/spheres';
import { SpheresBuilder } from '../../../mol-geo/geometry/spheres/spheres-builder';
import { eachPolymerBackboneElement } from './util/polymer/backbone';
+import { StructureGroup } from './util/common';
export const PolymerBackboneSphereParams = {
...UnitsMeshParams,
diff --git a/src/mol-repr/structure/visual/polymer-trace-mesh.ts b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
index 52804b344..416c3f4be 100644
--- a/src/mol-repr/structure/visual/polymer-trace-mesh.ts
+++ b/src/mol-repr/structure/visual/polymer-trace-mesh.ts
@@ -14,7 +14,7 @@ import { createCurveSegmentState, PolymerTraceIterator, interpolateCurveSegment,
import { isNucleic, SecondaryStructureType } from '../../../mol-model/structure/model/types';
import { addSheet } from '../../../mol-geo/geometry/mesh/builder/sheet';
import { addTube } from '../../../mol-geo/geometry/mesh/builder/tube';
-import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../units-visual';
+import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual } from '../units-visual';
import { VisualUpdateState } from '../../util';
import { SecondaryStructureProvider } from '../../../mol-model-props/computed/secondary-structure';
import { addRibbon } from '../../../mol-geo/geometry/mesh/builder/ribbon';
@@ -22,6 +22,7 @@ import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
+import { StructureGroup } from './util/common';
export const PolymerTraceMeshParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index bd30f7428..983a7612a 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -8,13 +8,12 @@ import { BondType } from '../../../../mol-model/structure/model/types';
import { Unit, StructureElement, Structure, Bond } from '../../../../mol-model/structure';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { LocationIterator } from '../../../../mol-geo/util/location-iterator';
-import { StructureGroup } from '../../units-visual';
import { LinkCylinderParams, LinkLineParams } from './link';
import { ObjectKeys } from '../../../../mol-util/type-helpers';
import { PickingId } from '../../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../../mol-model/loci';
import { Interval, OrderedSet, SortedArray } from '../../../../mol-data/int';
-import { isH, isHydrogen } from './common';
+import { isH, isHydrogen, StructureGroup } from './common';
export const BondParams = {
includeTypes: PD.MultiSelect(ObjectKeys(BondType.Names), PD.objectToOptions(BondType.Names)),
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index ac7a53dc6..89a6f52b8 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -71,7 +71,13 @@ export function getAltResidueLociFromId(structure: Structure, unit: Unit.Atomic,
//
-export function createUnitsTransform({ units }: Unit.SymmetryGroup, transformData?: TransformData) {
+export type StructureGroup = { structure: Structure, group: Unit.SymmetryGroup }
+
+export function createUnitsTransform(structureGroup: StructureGroup, includeParent: boolean, transformData?: TransformData) {
+ const { child } = structureGroup.structure;
+ const units: ReadonlyArray<Unit> = includeParent && child
+ ? structureGroup.group.units.filter(u => child.unitMap.has(u.id))
+ : structureGroup.group.units;
const unitCount = units.length;
const n = unitCount * 16;
const array = transformData && transformData.aTransform.ref.value.length >= n ? transformData.aTransform.ref.value : new Float32Array(n);
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index 1c80d73fb..b9a8ea919 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -17,10 +17,9 @@ import { PickingId } from '../../../../mol-geo/geometry/picking';
import { LocationIterator } from '../../../../mol-geo/util/location-iterator';
import { VisualContext } from '../../../../mol-repr/visual';
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 { isTrace, isH } from './common';
+import { isTrace, isH, StructureGroup } from './common';
import { Sphere3D } from '../../../../mol-math/geometry';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
diff --git a/src/mol-repr/structure/visual/util/nucleotide.ts b/src/mol-repr/structure/visual/util/nucleotide.ts
index 60f9d276c..fe97efd55 100644
--- a/src/mol-repr/structure/visual/util/nucleotide.ts
+++ b/src/mol-repr/structure/visual/util/nucleotide.ts
@@ -9,8 +9,7 @@ import { Loci, EmptyLoci } from '../../../../mol-model/loci';
import { Interval } from '../../../../mol-data/int';
import { LocationIterator } from '../../../../mol-geo/util/location-iterator';
import { PickingId } from '../../../../mol-geo/geometry/picking';
-import { StructureGroup } from '../../../../mol-repr/structure/units-visual';
-import { getResidueLoci } from './common';
+import { getResidueLoci, StructureGroup } from './common';
import { eachAtomicUnitTracedElement } from './polymer';
export namespace NucleotideLocationIterator {
diff --git a/src/mol-repr/structure/visual/util/polymer.ts b/src/mol-repr/structure/visual/util/polymer.ts
index 1311e55f3..3ba2da690 100644
--- a/src/mol-repr/structure/visual/util/polymer.ts
+++ b/src/mol-repr/structure/visual/util/polymer.ts
@@ -11,8 +11,7 @@ import { OrderedSet, Interval, SortedArray } from '../../../../mol-data/int';
import { EmptyLoci, Loci } from '../../../../mol-model/loci';
import { LocationIterator } from '../../../../mol-geo/util/location-iterator';
import { PickingId } from '../../../../mol-geo/geometry/picking';
-import { StructureGroup } from '../../../structure/units-visual';
-import { getResidueLoci } from './common';
+import { getResidueLoci, StructureGroup } from './common';
export * from './polymer/backbone';
export * from './polymer/gap-iterator';
--
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