molstar
Version:
A comprehensive macromolecular library.
97 lines (96 loc) • 5.07 kB
JavaScript
/**
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { __assign } from "tslib";
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { UnitsMeshParams, UnitsMeshVisual } from '../../../mol-repr/structure/units-visual';
import { ElementIterator, getElementLoci, eachElement } from '../../../mol-repr/structure/visual/util/element';
import { StructureElement } from '../../../mol-model/structure';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { sphereVertexCount } from '../../../mol-geo/primitive/sphere';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
import { Vec3, Mat3, Tensor, EPSILON } from '../../../mol-math/linear-algebra';
import { isH } from '../../../mol-repr/structure/visual/util/common';
import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
import { AtomSiteAnisotrop } from '../../../mol-model-formats/structure/property/anisotropic';
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 var EllipsoidMeshParams = __assign(__assign({}, UnitsMeshParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: PD.Boolean(false) });
export function EllipsoidMeshVisual(materialId) {
return UnitsMeshVisual({
defaultProps: PD.getDefaultValues(EllipsoidMeshParams),
createGeometry: createEllipsoidMesh,
createLocationIterator: ElementIterator.fromGroup,
getLoci: getElementLoci,
eachLocation: eachElement,
setUpdateState: function (state, newProps, currentProps) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens);
}
}, materialId);
}
export function createEllipsoidMesh(ctx, unit, structure, theme, props, mesh) {
var child = structure.child;
var childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
if (child && !childUnit)
return Mesh.createEmpty(mesh);
var detail = props.detail, sizeFactor = props.sizeFactor, ignoreHydrogens = props.ignoreHydrogens;
var elements = unit.elements, model = unit.model;
var atomicNumber = unit.model.atomicHierarchy.derived.atom.atomicNumber;
var elementCount = elements.length;
var vertexCount = elementCount * sphereVertexCount(detail);
var builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
var atomSiteAnisotrop = AtomSiteAnisotrop.Provider.get(model);
if (!atomSiteAnisotrop)
return Mesh.createEmpty(mesh);
var v = Vec3();
var mat = Mat3();
var eigvals = Vec3();
var eigvec1 = Vec3();
var eigvec2 = Vec3();
var elementToAnsiotrop = atomSiteAnisotrop.elementToAnsiotrop, data = atomSiteAnisotrop.data;
var U = data.U;
var space = data._schema.U.space;
var pos = unit.conformation.invariantPosition;
var l = StructureElement.Location.create(structure);
l.unit = unit;
for (var i = 0; i < elementCount; i++) {
var ei = elements[i];
var ai = elementToAnsiotrop[ei];
if (ai === -1)
continue;
if (((!!childUnit && !SortedArray.has(childUnit.elements, ei))) ||
(ignoreHydrogens && isH(atomicNumber, ei)))
continue;
l.element = ei;
pos(ei, v);
builderState.currentGroup = i;
Tensor.toMat3(mat, space, U.value(ai));
Mat3.symmtricFromLower(mat, mat);
Mat3.symmetricEigenvalues(eigvals, mat);
Mat3.eigenvector(eigvec1, mat, eigvals[1]);
Mat3.eigenvector(eigvec2, mat, eigvals[2]);
for (var j = 0; j < 3; ++j) {
// show 50% probability surface, needs sqrt as U matrix is in angstrom-squared
// take abs of eigenvalue to avoid reflection
// multiply by given size-factor
eigvals[j] = sizeFactor * 1.5958 * Math.sqrt(Math.abs(eigvals[j]));
}
if (equalEps(eigvals[0], eigvals[1], EPSILON) && equalEps(eigvals[1], eigvals[2], EPSILON)) {
addSphere(builderState, v, eigvals[0], detail);
}
else {
addEllipsoid(builderState, v, eigvec2, eigvec1, eigvals, detail);
}
}
var m = MeshBuilder.getMesh(builderState);
var sphere = Sphere3D.expand(Sphere3D(), (childUnit || unit).boundary.sphere, 1 * sizeFactor);
m.setBoundingSphere(sphere);
return m;
}