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molstar

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A comprehensive macromolecular library.

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"use strict"; /** * Copyright (c) 2019-2024 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.StructureEllipsoidMeshParams = exports.EllipsoidMeshParams = void 0; exports.createEllipsoidMesh = createEllipsoidMesh; exports.EllipsoidMeshVisual = EllipsoidMeshVisual; exports.createStructureEllipsoidMesh = createStructureEllipsoidMesh; exports.StructureEllipsoidMeshVisual = StructureEllipsoidMeshVisual; const param_definition_1 = require("../../../mol-util/param-definition"); const units_visual_1 = require("../../../mol-repr/structure/units-visual"); const element_1 = require("../../../mol-repr/structure/visual/util/element"); const structure_1 = require("../../../mol-model/structure"); const mesh_1 = require("../../../mol-geo/geometry/mesh/mesh"); const sphere_1 = require("../../../mol-geo/primitive/sphere"); const mesh_builder_1 = require("../../../mol-geo/geometry/mesh/mesh-builder"); const linear_algebra_1 = require("../../../mol-math/linear-algebra"); const ellipsoid_1 = require("../../../mol-geo/geometry/mesh/builder/ellipsoid"); const anisotropic_1 = require("../../../mol-model-formats/structure/property/anisotropic"); const common_1 = require("../../../mol-math/linear-algebra/3d/common"); const sphere_2 = require("../../../mol-geo/geometry/mesh/builder/sphere"); const geometry_1 = require("../../../mol-math/geometry"); const base_1 = require("../../../mol-geo/geometry/base"); const complex_visual_1 = require("../complex-visual"); // avoiding namespace lookup improved performance in Chrome (Aug 2020) const v3add = linear_algebra_1.Vec3.add; function createEllipsoidMesh(ctx, unit, structure, theme, props, mesh) { const { child } = structure; const childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id); if (child && !childUnit) return mesh_1.Mesh.createEmpty(mesh); const { detail, sizeFactor } = props; const { elements, model } = unit; const elementCount = elements.length; const vertexCount = elementCount * (0, sphere_1.sphereVertexCount)(detail); const builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 2, mesh); const atomSiteAnisotrop = anisotropic_1.AtomSiteAnisotrop.Provider.get(model); if (!atomSiteAnisotrop) return mesh_1.Mesh.createEmpty(mesh); const v = (0, linear_algebra_1.Vec3)(); const mat = (0, linear_algebra_1.Mat3)(); const eigvals = (0, linear_algebra_1.Vec3)(); const eigvec1 = (0, linear_algebra_1.Vec3)(); const eigvec2 = (0, linear_algebra_1.Vec3)(); const { elementToAnsiotrop, data } = atomSiteAnisotrop; const { U } = data; const space = data._schema.U.space; const c = unit.conformation; const l = structure_1.StructureElement.Location.create(structure); l.unit = unit; const ignore = (0, element_1.makeElementIgnoreTest)(structure, unit, props); const center = (0, linear_algebra_1.Vec3)(); let count = 0; for (let i = 0; i < elementCount; i++) { const ei = elements[i]; const ai = elementToAnsiotrop[ei]; if (ai === -1) continue; if (ignore && ignore(elements[i])) continue; l.element = ei; c.invariantPosition(ei, v); v3add(center, center, v); count += 1; 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 (let 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_1.equalEps)(eigvals[0], eigvals[1], linear_algebra_1.EPSILON) && (0, common_1.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); } } const m = mesh_builder_1.MeshBuilder.getMesh(builderState); if (count === 0) return m; // re-use boundingSphere if it has not changed much let boundingSphere; linear_algebra_1.Vec3.scale(center, center, 1 / count); const oldBoundingSphere = mesh ? geometry_1.Sphere3D.clone(mesh.boundingSphere) : undefined; if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 0.1) { boundingSphere = oldBoundingSphere; } else { boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (childUnit !== null && childUnit !== void 0 ? childUnit : unit).boundary.sphere, 1 * sizeFactor * 2); } m.setBoundingSphere(boundingSphere); return m; } exports.EllipsoidMeshParams = { ...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), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), traceOnly: 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: (state, newProps, currentProps) => { state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor || newProps.detail !== currentProps.detail || newProps.ignoreHydrogens !== currentProps.ignoreHydrogens); } }, materialId); } // function createStructureEllipsoidMesh(ctx, structure, theme, props, mesh) { const { child } = structure; const { detail, sizeFactor } = props; const { getSerialIndex } = structure.serialMapping; const structureElementCount = structure.elementCount; const vertexCount = structureElementCount * (0, sphere_1.sphereVertexCount)(detail); const builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 2, mesh); const v = (0, linear_algebra_1.Vec3)(); const mat = (0, linear_algebra_1.Mat3)(); const eigvals = (0, linear_algebra_1.Vec3)(); const eigvec1 = (0, linear_algebra_1.Vec3)(); const eigvec2 = (0, linear_algebra_1.Vec3)(); const center = (0, linear_algebra_1.Vec3)(); let count = 0; for (const unit of structure.units) { const childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id); if (child && !childUnit) return mesh_1.Mesh.createEmpty(mesh); const { elements, model } = unit; const elementCount = elements.length; const atomSiteAnisotrop = anisotropic_1.AtomSiteAnisotrop.Provider.get(model); if (!atomSiteAnisotrop) return mesh_1.Mesh.createEmpty(mesh); const ignore = (0, element_1.makeElementIgnoreTest)(structure, unit, props); const { elementToAnsiotrop, data } = atomSiteAnisotrop; const { U } = data; const space = data._schema.U.space; const c = unit.conformation; const l = structure_1.StructureElement.Location.create(structure); l.unit = unit; // for (let i = 0 as StructureElement.UnitIndex; i < elementCount; i++) { // if (ignore && ignore(elements[i])) continue; // if (lone && Unit.isAtomic(unit) && hasUnitVisibleBonds(unit, props) && bondCount(structure, unit, i) !== 0) continue; // c.position(elements[i], p); // v3add(center, center, p); // count += 1; // const si = getSerialIndex(unit, elements[i]); // v3scaleAndAdd(s, p, v3unitX, r); // v3scaleAndAdd(e, p, v3unitX, -r); // builder.add(s[0], s[1], s[2], e[0], e[1], e[2], si); // v3scaleAndAdd(s, p, v3unitY, r); // v3scaleAndAdd(e, p, v3unitY, -r); // builder.add(s[0], s[1], s[2], e[0], e[1], e[2], si); // v3scaleAndAdd(s, p, v3unitZ, r); // v3scaleAndAdd(e, p, v3unitZ, -r); // builder.add(s[0], s[1], s[2], e[0], e[1], e[2], si); // } for (let i = 0; i < elementCount; i++) { const ei = elements[i]; const ai = elementToAnsiotrop[ei]; if (ai === -1) continue; if (ignore && ignore(elements[i])) continue; l.element = ei; c.position(ei, v); v3add(center, center, v); count += 1; builderState.currentGroup = getSerialIndex(unit, elements[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 (let 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_1.equalEps)(eigvals[0], eigvals[1], linear_algebra_1.EPSILON) && (0, common_1.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); } } } const m = mesh_builder_1.MeshBuilder.getMesh(builderState); if (count === 0) return m; // re-use boundingSphere if it has not changed much let boundingSphere; linear_algebra_1.Vec3.scale(center, center, 1 / count); const oldBoundingSphere = mesh ? geometry_1.Sphere3D.clone(mesh.boundingSphere) : undefined; if (oldBoundingSphere && linear_algebra_1.Vec3.distance(center, oldBoundingSphere.center) / oldBoundingSphere.radius < 1.0) { boundingSphere = oldBoundingSphere; } else { boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), (child !== null && child !== void 0 ? child : structure).boundary.sphere, 1 * sizeFactor * 2); } m.setBoundingSphere(boundingSphere); return m; } exports.StructureEllipsoidMeshParams = { ...complex_visual_1.ComplexMeshParams, 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), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), traceOnly: param_definition_1.ParamDefinition.Boolean(false), }; function StructureEllipsoidMeshVisual(materialId) { return (0, complex_visual_1.ComplexMeshVisual)({ defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.StructureEllipsoidMeshParams), createGeometry: createStructureEllipsoidMesh, createLocationIterator: element_1.ElementIterator.fromStructure, getLoci: element_1.getSerialElementLoci, eachLocation: element_1.eachSerialElement, setUpdateState: (state, newProps, currentProps) => { state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor || newProps.detail !== currentProps.detail || newProps.ignoreHydrogens !== currentProps.ignoreHydrogens); } }, materialId); }