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fix ellipsoid repr and support includeParent

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- switch off adjustCylinderLength
- handle structure with child
This commit is contained in:
Alexander Rose
2021-03-20 23:58:48 -07:00
parent eca7da2c72
commit 0bb376706d
3 changed files with 18 additions and 6 deletions
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1
docs/interesting-pdb-entries.md
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@@ -27,3 +27,4 @@
* DNA (5D3G)
* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
* Long linear sugar chain (4HG6)
* Anisotropic B-factors/Ellipsoids (1EJG)

9
src/mol-repr/structure/representation/ellipsoid.ts
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@@ -26,7 +26,6 @@ export const EllipsoidParams = {
...IntraUnitBondCylinderParams,
...InterUnitBondCylinderParams,
adjustCylinderLength: PD.Boolean(false, { isHidden: true }), // not useful here
includeParent: PD.Boolean(false, { isHidden: true }), // not yet supported here
unitKinds: getUnitKindsParam(['atomic']),
sizeFactor: PD.Numeric(1, { min: 0.01, max: 10, step: 0.01 }),
sizeAspectRatio: PD.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }),
@@ -52,5 +51,11 @@ export const EllipsoidRepresentationProvider = StructureRepresentationProvider({
defaultValues: PD.getDefaultValues(EllipsoidParams),
defaultColorTheme: { name: 'element-symbol' },
defaultSizeTheme: { name: 'uniform' },
isApplicable: (structure: Structure) => structure.elementCount > 0 && structure.models.some(m => AtomSiteAnisotrop.Provider.isApplicable(m))
isApplicable: (structure: Structure) => structure.elementCount > 0 && structure.models.some(m => AtomSiteAnisotrop.Provider.isApplicable(m)),
getData: (structure: Structure, props: PD.Values<EllipsoidParams>) => {
return props.includeParent ? Structure.WithChild.fromStructure(structure) : structure;
},
mustRecreate: (oldProps: PD.Values<EllipsoidParams>, newProps: PD.Values<EllipsoidParams>) => {
return oldProps.includeParent !== newProps.includeParent;
}
});

14
src/mol-repr/structure/visual/ellipsoid-mesh.ts
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@@ -1,5 +1,5 @@
/**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -22,6 +22,7 @@ import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
import { addSphere } from '../../../mol-geo/geometry/mesh/builder/sphere';
import { Sphere3D } from '../../../mol-math/geometry';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { SortedArray } from '../../../mol-data/int/sorted-array';
export const EllipsoidMeshParams = {
...UnitsMeshParams,
@@ -57,7 +58,11 @@ export interface EllipsoidMeshProps {
}
export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: EllipsoidMeshProps, mesh?: Mesh): Mesh {
const { detail, sizeFactor } = props;
const child = Structure.WithChild.getChild(structure);
const childUnit = child?.unitMap.get(unit.id);
if (child && !childUnit) return Mesh.createEmpty(mesh);
const { detail, sizeFactor, ignoreHydrogens } = props;
const { elements, model } = unit;
const { atomicNumber } = unit.model.atomicHierarchy.derived.atom;
@@ -84,7 +89,8 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
const ei = elements[i];
const ai = elementToAnsiotrop[ei];
if (ai === -1) continue;
if (props.ignoreHydrogens && isH(atomicNumber, ei)) continue;
if (((!!childUnit && !SortedArray.has(childUnit.elements, ei))) ||
(ignoreHydrogens && isH(atomicNumber, ei))) continue;
l.element = ei;
pos(ei, v);
@@ -111,7 +117,7 @@ export function createEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: S
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * sizeFactor);
const sphere = Sphere3D.expand(Sphere3D(), (childUnit || unit).boundary.sphere, 1 * sizeFactor);
m.setBoundingSphere(sphere);
return m;