molstar
Version:
A comprehensive macromolecular library.
86 lines (85 loc) • 4.29 kB
JavaScript
/**
* Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Gianluca Tomasello <giagitom@gmail.com>
*/
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
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 { PolymerGapIterator, PolymerGapLocationIterator, getPolymerGapElementLoci, eachPolymerGapElement } from './util/polymer';
import { addFixedCountDashedCylinder } from '../../../mol-geo/geometry/mesh/builder/cylinder';
import { UnitsMeshParams, UnitsMeshVisual } from '../units-visual';
import { BaseGeometry } from '../../../mol-geo/geometry/base';
import { Sphere3D } from '../../../mol-math/geometry';
// import { TriangularPyramid } from '../../../mol-geo/primitive/pyramid';
const segmentCount = 10;
export const PolymerGapCylinderParams = {
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo),
};
export const DefaultPolymerGapCylinderProps = PD.getDefaultValues(PolymerGapCylinderParams);
// const triangularPyramid = TriangularPyramid()
// const t = Mat4.identity()
// const pd = Vec3.zero()
function createPolymerGapCylinderMesh(ctx, unit, structure, theme, props, mesh) {
const polymerGapCount = unit.gapElements.length;
if (!polymerGapCount)
return Mesh.createEmpty(mesh);
const { sizeFactor, radialSegments } = props;
const vertexCountEstimate = segmentCount * radialSegments * 2 * polymerGapCount * 2;
const builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 10, mesh);
const pA = Vec3();
const pB = Vec3();
const cylinderProps = {
radiusTop: 1, radiusBottom: 1, topCap: true, bottomCap: true, radialSegments
};
let i = 0;
const polymerGapIt = PolymerGapIterator(structure, unit);
while (polymerGapIt.hasNext) {
const { centerA, centerB } = polymerGapIt.move();
if (centerA.element === centerB.element) {
// TODO
// builderState.currentGroup = i
// pos(centerA.element, pA)
// Vec3.add(pd, pA, Vec3.create(1, 0, 0))
// Mat4.targetTo(t, pA, pd, Vec3.create(0, 1, 0))
// Mat4.setTranslation(t, pA)
// Mat4.scale(t, t, Vec3.create(0.7, 0.7, 2.5))
// MeshBuilder.addPrimitive(builderState, t, triangularPyramid)
}
else {
unit.conformation.invariantPosition(centerA.element, pA);
unit.conformation.invariantPosition(centerB.element, pB);
cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerA) * sizeFactor;
builderState.currentGroup = i;
addFixedCountDashedCylinder(builderState, pA, pB, 0.5, segmentCount, false, cylinderProps);
cylinderProps.radiusTop = cylinderProps.radiusBottom = theme.size.size(centerB) * sizeFactor;
builderState.currentGroup = i + 1;
addFixedCountDashedCylinder(builderState, pB, pA, 0.5, segmentCount, false, cylinderProps);
}
i += 2;
}
const m = MeshBuilder.getMesh(builderState);
const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
export const PolymerGapParams = {
...UnitsMeshParams,
...PolymerGapCylinderParams
};
export function PolymerGapVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(PolymerGapParams),
createGeometry: createPolymerGapCylinderMesh,
createLocationIterator: (structureGroup) => PolymerGapLocationIterator.fromGroup(structureGroup, { asSecondary: true }),
getLoci: getPolymerGapElementLoci,
eachLocation: eachPolymerGapElement,
setUpdateState: (state, newProps, currentProps) => {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.radialSegments !== currentProps.radialSegments);
}
}, materialId);
}