molstar
Version:
A comprehensive macromolecular library.
117 lines (116 loc) • 5.14 kB
JavaScript
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Structure, StructureElement, Unit } from '../../../mol-model/structure';
import { EmptyLoci } from '../../../mol-model/loci';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { createLinkCylinderMesh, LinkCylinderParams } from './util/link';
import { OrderedSet, Interval } from '../../../mol-data/int';
import { ComplexMeshVisual } from '../complex-visual';
import { UnitsMeshParams } from '../units-visual';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { getAltResidueLociFromId } from './util/common';
import { Sphere3D } from '../../../mol-math/geometry';
function createCarbohydrateLinkCylinderMesh(ctx, structure, theme, props, mesh) {
const { links, elements } = structure.carbohydrates;
const { linkSizeFactor } = props;
const location = StructureElement.Location.create(structure);
const builderProps = {
linkCount: links.length,
position: (posA, posB, edgeIndex) => {
const l = links[edgeIndex];
Vec3.copy(posA, elements[l.carbohydrateIndexA].geometry.center);
Vec3.copy(posB, elements[l.carbohydrateIndexB].geometry.center);
},
radius: (edgeIndex) => {
const l = links[edgeIndex];
const carbA = elements[l.carbohydrateIndexA];
const ringA = carbA.unit.rings.all[carbA.ringIndex];
location.unit = carbA.unit;
location.element = carbA.unit.elements[ringA[0]];
return theme.size.size(location) * linkSizeFactor;
},
};
const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
if (boundingSphere) {
m.setBoundingSphere(boundingSphere);
}
else if (m.triangleCount > 0) {
const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * linkSizeFactor);
m.setBoundingSphere(sphere);
}
return m;
}
export const CarbohydrateLinkParams = {
...UnitsMeshParams,
...LinkCylinderParams,
linkSizeFactor: PD.Numeric(0.3, { min: 0, max: 3, step: 0.01 }),
};
export function CarbohydrateLinkVisual(materialId) {
return ComplexMeshVisual({
defaultProps: PD.getDefaultValues(CarbohydrateLinkParams),
createGeometry: createCarbohydrateLinkCylinderMesh,
createLocationIterator: CarbohydrateLinkIterator,
getLoci: getLinkLoci,
eachLocation: eachCarbohydrateLink,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.linkSizeFactor !== currentProps.linkSizeFactor ||
newProps.radialSegments !== currentProps.radialSegments ||
newProps.linkCap !== currentProps.linkCap);
}
}, materialId);
}
function CarbohydrateLinkIterator(structure) {
const { elements, links } = structure.carbohydrates;
const groupCount = links.length;
const instanceCount = 1;
const location = StructureElement.Location.create(structure);
const getLocation = (groupIndex) => {
const link = links[groupIndex];
const carbA = elements[link.carbohydrateIndexA];
const ringA = carbA.unit.rings.all[carbA.ringIndex];
location.unit = carbA.unit;
location.element = carbA.unit.elements[ringA[0]];
return location;
};
return LocationIterator(groupCount, instanceCount, 1, getLocation, true);
}
function getLinkLoci(pickingId, structure, id) {
const { objectId, groupId } = pickingId;
if (id === objectId) {
const { links, elements } = structure.carbohydrates;
const l = links[groupId];
const carbA = elements[l.carbohydrateIndexA];
const carbB = elements[l.carbohydrateIndexB];
return StructureElement.Loci.union(getAltResidueLociFromId(structure, carbA.unit, carbA.residueIndex, carbA.altId), getAltResidueLociFromId(structure, carbB.unit, carbB.residueIndex, carbB.altId));
}
return EmptyLoci;
}
const __linkIndicesSet = new Set();
function eachCarbohydrateLink(loci, structure, apply) {
let changed = false;
if (!StructureElement.Loci.is(loci))
return false;
if (!Structure.areEquivalent(loci.structure, structure))
return false;
const { getLinkIndices } = structure.carbohydrates;
for (const { unit, indices } of loci.elements) {
if (!Unit.isAtomic(unit))
continue;
__linkIndicesSet.clear();
OrderedSet.forEach(indices, v => {
const linkIndices = getLinkIndices(unit, unit.elements[v]);
for (let i = 0, il = linkIndices.length; i < il; ++i) {
if (!__linkIndicesSet.has(linkIndices[i])) {
__linkIndicesSet.add(linkIndices[i]);
if (apply(Interval.ofSingleton(linkIndices[i])))
changed = true;
}
}
});
}
return changed;
}