molstar
Version:
A comprehensive macromolecular library.
102 lines (101 loc) • 5.89 kB
JavaScript
"use strict";
/**
* Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.createEllipsoidMesh = exports.EllipsoidMeshVisual = exports.EllipsoidMeshParams = void 0;
var tslib_1 = require("tslib");
var param_definition_1 = require("../../../mol-util/param-definition");
var units_visual_1 = require("../../../mol-repr/structure/units-visual");
var element_1 = require("../../../mol-repr/structure/visual/util/element");
var structure_1 = require("../../../mol-model/structure");
var mesh_1 = require("../../../mol-geo/geometry/mesh/mesh");
var sphere_1 = require("../../../mol-geo/primitive/sphere");
var mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder");
var linear_algebra_1 = require("../../../mol-math/linear-algebra");
var common_1 = require("../../../mol-repr/structure/visual/util/common");
var ellipsoid_1 = require("../../../mol-geo/geometry/mesh/builder/ellipsoid");
var anisotropic_1 = require("../../../mol-model-formats/structure/property/anisotropic");
var common_2 = require("../../../mol-math/linear-algebra/3d/common");
var sphere_2 = require("../../../mol-geo/geometry/mesh/builder/sphere");
var geometry_1 = require("../../../mol-math/geometry");
var base_1 = require("../../../mol-geo/geometry/base");
var sorted_array_1 = require("../../../mol-data/int/sorted-array");
exports.EllipsoidMeshParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false) });
function EllipsoidMeshVisual(materialId) {
return (0, units_visual_1.UnitsMeshVisual)({
defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.EllipsoidMeshParams),
createGeometry: createEllipsoidMesh,
createLocationIterator: element_1.ElementIterator.fromGroup,
getLoci: element_1.getElementLoci,
eachLocation: element_1.eachElement,
setUpdateState: function (state, newProps, currentProps) {
state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens);
}
}, materialId);
}
exports.EllipsoidMeshVisual = EllipsoidMeshVisual;
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_1.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 * (0, sphere_1.sphereVertexCount)(detail);
var builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
var atomSiteAnisotrop = anisotropic_1.AtomSiteAnisotrop.Provider.get(model);
if (!atomSiteAnisotrop)
return mesh_1.Mesh.createEmpty(mesh);
var v = (0, linear_algebra_1.Vec3)();
var mat = (0, linear_algebra_1.Mat3)();
var eigvals = (0, linear_algebra_1.Vec3)();
var eigvec1 = (0, linear_algebra_1.Vec3)();
var eigvec2 = (0, linear_algebra_1.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 = structure_1.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 && !sorted_array_1.SortedArray.has(childUnit.elements, ei))) ||
(ignoreHydrogens && (0, common_1.isH)(atomicNumber, ei)))
continue;
l.element = ei;
pos(ei, v);
builderState.currentGroup = i;
linear_algebra_1.Tensor.toMat3(mat, space, U.value(ai));
linear_algebra_1.Mat3.symmtricFromLower(mat, mat);
linear_algebra_1.Mat3.symmetricEigenvalues(eigvals, mat);
linear_algebra_1.Mat3.eigenvector(eigvec1, mat, eigvals[1]);
linear_algebra_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 ((0, common_2.equalEps)(eigvals[0], eigvals[1], linear_algebra_1.EPSILON) && (0, common_2.equalEps)(eigvals[1], eigvals[2], linear_algebra_1.EPSILON)) {
(0, sphere_2.addSphere)(builderState, v, eigvals[0], detail);
}
else {
(0, ellipsoid_1.addEllipsoid)(builderState, v, eigvec2, eigvec1, eigvals, detail);
}
}
var m = mesh_builder_1.MeshBuilder.getMesh(builderState);
var sphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit || unit).boundary.sphere, 1 * sizeFactor);
m.setBoundingSphere(sphere);
return m;
}
exports.createEllipsoidMesh = createEllipsoidMesh;