@ccp-nc/crystvis-js

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class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="lib_model.module_js-AtomImage.html">AtomImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-BondImage.html">BondImage</a></div><div class="sidebar-section-children"><a href="lib_model.module_js-Model.html">Model</a></div><div class="sidebar-section-children"><a href="lib_modelview.module_js-ModelView.html">ModelView</a></div><div class="sidebar-section-children"><a href="lib_visualizer.module_js-CrystVis.html">CrystVis</a></div></div><div class="sidebar-section-title with-arrow" data-isopen="false" id="sidebar-tutorials"><div>Tutorials</div><svg><use xlink:href="#down-icon"></use></svg></div><div class="sidebar-section-children-container"><div class="sidebar-section-children"><a href="tutorial-Events.html">Events</a></div><div class="sidebar-section-children"><a href="tutorial-Queries.html">Queries</a></div><div class="sidebar-section-children"><a 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class="main-wrapper"><section id="source-page" class="source-page"><header><h1 id="title" class="has-anchor">model.js</h1></header><article><pre class="prettyprint source lang-js"><code>'use strict'; /** * @fileoverview Class holding the atomic models to be plotted * @module */ import _ from 'lodash'; import * as mjs from 'mathjs'; import { PeriodicTable as PeriodicTable } from 'mendeleev'; import { Atoms as Atoms } from '@ccp-nc/crystcif-parse'; import * as utils from './utils.js'; import * as data from './data.js'; import { QueryParser as QueryParser } from './query.js'; import { ModelView as ModelView } from './modelview.js'; const LABEL_HEIGHT = 0.04; // For now fixed, just a value that works /** An 'image' of a single atom from a model. This represents a specific periodic copy of that atom (if applicable). */ class AtomImage { /** * @class * @param {Model} model The model from which the image is from * @param {int} index Index of the atom in the model * @param {Array} ijk Indices of the cell in which the image is located */ constructor(model, index, ijk) { this._model = model; this._index = index; this._ijk = ijk || [0, 0, 0]; // String ID this._id = this._index + '_' + _.join(this._ijk, '_'); // Integer index this._img_index = utils.supercellIndex(index, this._ijk, model.supercell, model.length); this._xyz0 = model._positions[index]; this._bondsFrom = []; // BondImages of bonds for which this is atom1 this._bondsTo = []; // BondImages of bonds for which this is atom2 if (!model.periodic) { this._fxyz0 = null; this._fxyz = null; this._xyz = this._xyz0; } else { this._fxyz0 = model._scaled_positions[index]; this._fxyz = [this._fxyz0[0] + ijk[0], this._fxyz0[1] + ijk[1], this._fxyz0[2] + ijk[2] ]; this._xyz = mjs.multiply(this._fxyz, model._cell); } this._isotope = null; // By default look up the model // Visual properties this._visible = false; this._color = this.cpkColor; this._uses_cpk = true; this._base_radius = this.vdwRadius / 4.0; this._scale = 1.0; this._opacity = 1.0; this._highlighted = false; this._mesh = null; // Will be created when first requested this._aura = null; this._labels = {}; this._ellipsoids = {}; } /** * Model this atom belongs to * @readonly * @type {Model} */ get model() { return this._model; } /** * Renderer used by this atom * @readonly * @type {Renderer} */ get renderer() { var m = this.model; if (m) { return m._renderer; } return null; } /** * Index of the atom * @readonly * @type {int} */ get index() { return this._index; } /** * String ID of the image * @readonly * @type {String} */ get id() { return this._id; } /** * Index of this image * @readonly * @type {int} */ get imgIndex() { return this._img_index; } /** * Index of the species of this atom * @readonly * @type {int} */ get speciesIndex() { return this._model._species_indices[this._index]; } /** * Symbol of this atom's element * @readonly * @type {String} */ get element() { return this._model._elems[this._index]; } /** * Crystal site label of this atom * @readonly * @type {String} */ get crystLabel() { return this._model._labels[this._index]; } /** * Periodic table information for this atom's element * @readonly * @type {Object} */ get elementData() { return data.getElementData(this.element); } /** * Information for this atom's isotope * @readonly * @type {Object} */ get isotopeData() { let idata = this._isotope; if (idata === null) idata = this._model._isotopes[this._index]; return idata; } /** * Atomic mass of this atom's isotope * @type {int} */ get isotope() { return this.isotopeData.A; } set isotope(A) { this._isotope = data.getIsotopeData(this.element, A); if (this._isotope === null) throw Error('Isotope does not exist for this element'); // Reset color if (this._uses_cpk) { this.color = null; } } /** * Atomic mass of the global isotope set as default for this atom's species * @type {int} */ set isotopeGlobal(A) { // Set the isotope for this atom in the model let iso = data.getIsotopeData(this.element, A); if (iso === null) throw Error('Isotope does not exist for this element'); this._model._isotopes[this._index] = iso; // Reset color if (this._uses_cpk) { this.color = null; } } /** * Atomic number of element * @readonly * @type {int} */ get number() { var el = PeriodicTable.getElement(this.element); return (el ? el.number : 0); } /** * Hex integer code of the conventional CPK color used for this element * (altered in case of non-standard isotopes) * @readonly * @type {int} */ get cpkColor() { return data.getCpkColor(this.element, this.isotope); } /** * Van dew Waals radius for this element * @readonly * @type {float} */ get vdwRadius() { return data.getVdwRadius(this.element); } /** * Bonds from this atom * @readonly * @type {BondImage[]} */ get bondsFrom() { return Array.from(this._bondsFrom); } /** * Bonds to this atom * @readonly * @type {BondImage[]} */ get bondsTo() { return Array.from(this._bondsTo); } /** * All bonds connected to this atom * @readonly * @type {BondImage[]} */ get bonds() { return _.concat(this._bondsFrom, this._bondsTo); } /** * All atoms bonded to this atom * @readonly * @type {AtomImage[]} */ get bondedAtoms() { return _.concat(_.map(this._bondsFrom, function(b) { return b.atom2; }), _.map(this._bondsTo, function(b) { return b.atom1; })); } /** * Cell indices of this atom image * @readonly * @type {int[]} */ get ijk() { return Array.from(this._ijk); } /** * Position of this atom's original * @readonly * @type {float[]} */ get xyz0() { return Array.from(this._xyz0); } /** * Position of this atom image * @readonly * @type {float[]} */ get xyz() { return Array.from(this._xyz); } /** * Fractional coordinates of this atom's original * @readonly * @type {float[]} */ get fxyz0() { return Array.from(this._fxyz0); } /** * Fractional coordinates of this atom image * @readonly * @type {float[]} */ get fxyz() { return Array.from(this._fxyz); } /** * Index of the molecule this atom belongs to * @readonly * @type {int} */ get moleculeIndex() { return this._model._molinds[this._index]; } /** * Mesh corresponding to this atom image * @readonly * @type {AtomMesh} */ get mesh() { var r = this.renderer; if (!this._mesh && r) { this._mesh = new r.Primitives.AtomMesh(this._xyz, this.radius, this._color); this._mesh.image = this; } return this._mesh; } /** * Aura used to highlight this atom image * @readonly * @type {AuraMesh} */ get aura() { var r = this.renderer; if (!this._aura && r) { this._aura = new r.Primitives.AuraMesh({ radius: this.radius, scale: 0.02 }); this.mesh.add(this._aura); } return this._aura; } // Get and set graphical properties /** * Whether the atom is visible * @type {bool} */ get visible() { return this._visible; } set visible(v) { this._visible = v; var mesh = this.mesh; if (v) { this.renderer.add(mesh, 'model'); } else { this.renderer.remove(mesh, 'model'); } // Update aura visibility this.highlighted = this._highlighted; // Update connected bonds' visibility for (let i = 0; i < this._bondsFrom.length; ++i) { let b = this._bondsFrom[i]; b.visible = b._visible; } for (let i = 0; i < this._bondsTo.length; ++i) { let b = this._bondsTo[i]; b.visible = b._visible; } } /** * Starting radius of the atom * @type {float} */ get baseRadius() { return this._base_radius; } set baseRadius(r) { if (r == null) { // Default value r = this.vdwRadius / 4.0; } this._base_radius = r; var mesh = this.mesh; mesh.atom_radius = this.radius; } /** * Scale of the atom * @type {float} */ get scale() { return this._scale; } set scale(s) { if (s == null) { s = 1; } this._scale = s; var mesh = this.mesh; mesh.atom_radius = this.radius; } /** * Final radius of the atom (starting radius * scale) * @type {float} */ get radius() { return this._scale * this._base_radius; } set radius(r) { if (r == null) { r == this.baseRadius; } this.scale = r / this._base_radius; } /** * Color of the atom * @type {int} */ get color() { return this._color; } set color(c) { if (c === null) { c = this.cpkColor; this._uses_cpk = true; } else { this._uses_cpk = false; } this._color = c; var mesh = this.mesh; if (mesh) { mesh.atom_color = c; } _.map(this._bondsFrom, function(b) { b.color1 = c; }); _.map(this._bondsTo, function(b) { b.color2 = c; }); } /** * Opacity of the atom * @type {float} */ get opacity() { return this._opacity; } set opacity(o) { if (o == null) { o = 1; } this._opacity = o; var mesh = this.mesh; mesh.atom_opacity = o; _.map(this._bondsFrom, function(b) { b.opacity1 = o; }); _.map(this._bondsTo, function(b) { b.opacity2 = o; }); } /** * Whether the atom is highlighted * @type {bool} */ get highlighted() { return this._highlighted; } set highlighted(h) { if (h == null) { h = false; } this._highlighted = h; var aura = this.aura; if (h && this._visible) { aura.visible = true; } else { aura.visible = false; } } /** * Add a text label to the atom. * * @param {String} text Content of the label * @param {String} name Name to use to refer to the label (necessary to overwrite/erase later) * @param {Object} parameters Dictionary of other options (e.g. font family, text color, etc. See TextSprite) */ addLabel(text, name, parameters = {}) { this.removeLabel(name); // Precautionary var defaults = { faceCamera: true, fixScale: true, shift: [1.0*this.radius, 0, 0], // This just works well height: LABEL_HEIGHT, }; parameters = _.merge(defaults, parameters); parameters.position = [0, 0, 0]; // This is not customizable var r = this.renderer; if (r) { var label = new r.Primitives.TextSprite(text, parameters); this._labels[name] = label; this.mesh.add(label); } } /** * Remove the label of a given name * * @param {String} name Name of the label */ removeLabel(name) { let l = this._labels[name]; if (l) this._mesh.remove(l); delete this._labels[name]; } /** * Retrieve or set a label's properties * * @param {String} name Name of the label * @param {String} property Property to set * @param {?} value Value to set. If omitted, returns the current * value instead. */ labelProperty(name, property, value = null) { if (value) { this._labels[name][property] = value; } else { return this._labels[name][property]; } } /** * Add an ellipsoid to the atom. * * @param {TensorData | Object | Array} data The data to base the * ellipsoid on. Can be: * - a TensorData object; * - an Object with 'eigenvalues' * and 'eigenvectors' members * - an Array of the form * [eigenvalues, eigenvectors] * @param {String} name Name of the ellipsoid * @param {Object} parameters Additional options to * pass (see EllipsoidMesh) */ addEllipsoid(data, name, parameters = {}) { this.removeEllipsoid(name); parameters = _.clone(parameters); // Avoid editing the reference object if (data instanceof Array) { parameters.eigenvalues = data[0]; parameters.eigenvectors = data[1]; } else { parameters.eigenvalues = data.eigenvalues; parameters.eigenvectors = data.eigenvectors; } if (parameters.ditherSeed == null) { // As long as it's consistent for a given atom, the actual value is irrelevant let seed = utils.hashCode(this._fxyz + name); parameters.ditherSeed = seed/4294967295.0; // Reduce to ]0.5,-0.5] } else { } var r = this.renderer; if (r) { var ellips = new r.Primitives.EllipsoidMesh(parameters); this._ellipsoids[name] = ellips; this.mesh.add(ellips); } } /** * Remove the ellipsoid with a given name * * @param {String} name Name of the ellipsoid */ removeEllipsoid(name) { let l = this._ellipsoids[name]; if (l) this._mesh.remove(l); delete this._ellipsoids[name]; } /** * Retrieve or set an ellipsoid's properties * * @param {String} name Name of the ellipsoid * @param {String} property Property to set * @param {?} value Value to set. If omitted, returns the current * value instead. */ ellipsoidProperty(name, property, value = null) { if (value) { this._ellipsoids[name][property] = value; } else { return this._ellipsoids[name][property]; } } /** * Get the value for one array for this image * @param {String} name Name of the array * * @return {*} Value of the array for this atom */ getArrayValue(name) { return this._model.getArray(name)[this._index]; } // Check equality with another image equals(ai) { return (this._model == ai._model && this._index == ai._index && _.isEqual(this._ijk, ai._ijk)); } // Return a copy, possibly shifted to a different cell copy(shift = [0, 0, 0]) { return new AtomImage(this._model, this._index, mjs.add(this._ijk, shift)); } } /** An 'image' of a single bond in the model. This represents the connection between two specific AtomImages */ class BondImage { /** * @class * @param {Model} model The model from which the image is from * @param {AtomImage} im1 AtomImage from which the bond starts * @param {AtomImage} im2 AtomImage to which the bond ends */ constructor(model, im1, im2) { this._model = model; this._im1 = im1; this._im2 = im2; this._im1._bondsFrom.push(this); this._im2._bondsTo.push(this); this._length = mjs.distance(this._im1.xyz, this._im2.xyz); this._key = this._im1.imgIndex + '_' + this._im2.imgIndex; // Visual properties this._visible = true; this._radius = 0.2; this._opacity = 1.0; this._mesh = null; // Created on first request } /** * Model this bond belongs to * @readonly * @type {Model} */ get model() { return this._model; } /** * Renderer used by this bond * @readonly * @type {Renderer} */ get renderer() { var m = this.model; if (m) { return m._renderer; } return null; } /** * First atom connected to this bond * @readonly * @type {AtomImage} */ get atom1() { return this._im1; } /** * Second atom connected to this bond * @readonly * @type {AtomImage} */ get atom2() { return this._im2; } /** * A unique string key used to quickly reference the bond * @readonly * @type {String} */ get key() { // Used in dictionary for quick reference return this._key; } /** * Bond length in Angstroms * @readonly * @type {float} */ get length() { return this._length; } /** * Mesh corresponding to this bond image * @readonly * @type {AtomMesh} */ get mesh() { var r = this.renderer; if (!this._mesh && r) { this._mesh = new r.Primitives.BondMesh(this.atom1.xyz, this.atom2.xyz, this._radius, this.atom1.color, this.atom2.color); } return this._mesh; } /** * Radius of the bond * @type {float} */ get radius() { return this._radius; } set radius(r) { if (r == null) { r = 0.2; } this._radius = r; var mesh = this.mesh; if (mesh) { mesh.bond_radius = r; } } /** * First color of the bond * @type {int} */ set color1(c) { if (c == null) { c = this._im1.color; } var mesh = this.mesh; if (mesh) { mesh.bond_color_1 = c; } } /** * Second color of the bond * @type {int} */ set color2(c) { if (c == null) { c = this._im2.color; } var mesh = this.mesh; if (mesh) { mesh.bond_color_2 = c; } } /** * First opacity of the bond * @type {float} */ set opacity1(o) { if (o == null) { o = this._im1.opacity; } var mesh = this.mesh; if (mesh) { mesh.bond_opacity_1 = o; } } /** * Second opacity of the bond * @type {float} */ set opacity2(o) { if (o == null) { o = this._im2.opacity; } var mesh = this.mesh; if (mesh) { mesh.bond_opacity_2 = o; } } /** * Whether the bond is visible * @type {bool} */ get visible() { return this._visible; } set visible(v) { this._visible = v; v = v && this.atom1.visible && this.atom2.visible; var mesh = this.mesh; if (v) { this.renderer.add(mesh, 'model'); } else { this.renderer.remove(mesh, 'model'); } } } class Model { /** * An object containing an Atomic structure and taking care of its periodic * nature, allowing querying and selection, and so on. * @class * @param {crystcif.Atoms} atoms Atomic structure, in crystcif's Atoms format * @param {Object} parameters Additional options: * * - `supercell` * - `molecularCrystal` (if true, load full molecules in central unit cell) * - `useNMRActiveIsotopes` (if true, all isotopes are set by default to the most common * one with non-zero spin) * - `vdwScaling` (scale van der Waals radii by a constant factor) * - `vdwElementScaling` (table of per-element factors to scale VdW radii by) */ constructor(atoms, parameters = {}) { var defaults = { supercell: [1, 1, 1], molecularCrystal: false, useNMRActiveIsotopes: false, vdwScaling: 1.0, vdwElementScaling: {} }; parameters = _.merge(defaults, parameters); this._vdwScaling = parameters.vdwScaling; this._vdwElementScaling = parameters.vdwElementScaling; const initMolecules = ((atoms, supercell) => { if (!(atoms instanceof Atoms)) { throw new Error('Model must be initialised with a loaded Atoms object'); } this._atoms_base = atoms; this._data = {}; /* Load the positions, cell, and other key data Important: to save memory, we're simply storing references. These are NOT to be changed! */ this._elems = this._atoms_base._arrays['symbols']; this._isotopes = this._elems.map((el) => { const iso = parameters.useNMRActiveIsotopes? 'nmr' : null; let isodata = data.getIsotopeData(el, iso); if (isodata === null) { // No NMR active isotope? isodata = data.getIsotopeData(el); } return isodata; }); this._nums = this._atoms_base._arrays['numbers']; this._positions = this._atoms_base._arrays['positions']; this._cell = this._atoms_base._cell; this._pbc = this._atoms_base._pbc; this._periodic = !this._pbc.includes(false); this._inv_cell = this._atoms_base._inv_cell; this._supercell = [1, 1, 1]; this._supercell_grid = [ [0, 0, 0] ]; // Species indices (used for labels) let sp_count = {}; this._species_indices = []; this._species_indices = this._elems.map((s, i) => { let c = sp_count[s]; c = c? c : 0; sp_count[s] = c+1; return c; }); let has_cif_labels = false; // Crystallographic labels if ('labels' in this._atoms_base._arrays) { // If any of the labels don't match the element, // then we're assuming they're crystallographic (CIF-style) labels if (this._atoms_base._arrays['labels'].some((l, i) => { return l !== this._elems[i]; })) { // then use them has_cif_labels = true; this._labels = this._atoms_base._arrays['labels']; } else { // otherwise, build new ones and // throw a warning to user syaing we're doing this this._labels = []; for (let i = 0; i < this._elems.length; ++i) { this._labels.push(this._elems[i] + '_' + (this._species_indices[i]+1)); } console.warn('No crystallographic labels found in CIF file. Building new ones.'); } } else { // Build them this._labels = []; for (let i = 0; i < this._elems.length; ++i) { this._labels.push(this._elems[i] + '_' + (this._species_indices[i]+1)); } } this._has_cif_labels = has_cif_labels; // defaults to false // Cryst label indices let lab_count = {}; this._label_indices = []; this._label_indices = this._labels.map((s, i) => { let c = lab_count[s]; c = c? c : 0; lab_count[s] = c+1; return c; }); if (this._periodic) { // R matrix: indispensable for calculations of periodic distances this._r_matrix = mjs.multiply(this._cell, mjs.transpose(this._cell)); var ediag = mjs.eigs(this._r_matrix); // Sort by eigenvalue var evecs = ediag.eigenvectors.map(e => e.vector); ediag = _.zip(ediag.values, evecs); ediag = _.sortBy(ediag, function(x) { return x[0]; }); ediag = _.unzip(ediag); this._r_diag = { values: ediag[0], vectors: ediag[1], }; this._supercell = supercell; // Default this._supercell_grid = utils.supercellGrid(supercell); this._scaled_positions = this._atoms_base.get_scaled_positions(); } // Compile all images for this supercell this._atom_images = this._atomImages(); this._computeBonds(); this._computeMolecules(); }).bind(this); initMolecules(atoms, parameters.supercell); // if parameters.molecularCrystal, is null, we need to check if the atoms // contains organic molecules -- i.e. if there is at least one C-H bond if (parameters.molecularCrystal || (parameters.molecularCrystal === null && this._queryCHBond())) { this._molecularCrystal = true; atoms = _.cloneDeep(atoms); var pos = this.positions; for (let i = 0; i < this.length; ++i) { let mol_i = this._molinds[i]; let mol = this._molecules[mol_i]; for (let j = 0; j < mol.length; ++j) { var a = mol[j]; if (a.index == i) { pos[i] = mjs.add(pos[i], this.fracToAbs(a.cell)); } } } atoms.set_array('positions', pos); initMolecules(atoms, parameters.supercell); } this._primitives = {}; // Any additional primitives drawn on this model this._bond_images = this._bondImages(); // A special ModelView for convenience this._all = new ModelView(this, _.range(this._atom_images.length)); // Parser for queries this._qparse = new QueryParser({ 'all': this._queryAll, 'indices': this._queryIndices, 'elements': this._queryElements, 'cell': this._queryCell, 'box': this._queryBox, 'sphere': this._querySphere, 'bonded': this._queryBonded, 'molecule': this._queryMolecule, }, this); // By default no rendering this.renderer = null; } // Using the .get_ methods of _atoms guarantees these are copies, // not pointers to the real thing /** * Number of atoms in this model's original cell * @readonly * @type {int} */ get length() { return this._atoms_base.length(); } /** * Chemical symbols in this model's original cell * @readonly * @type {String[]} */ get symbols() { return this._atoms_base.get_chemical_symbols(); } /** * Atomic numbers in this model's original cell * @readonly * @type {int[]} */ get numbers() { return this._atoms_base.get_atomic_numbers(); } /** * Coordinates of the atoms in this model's original cell * @readonly * @type {Array[]} */ get positions() { return this._atoms_base.get_positions(); } /** * Fractional coordinates of the atoms in this model's original cell * @readonly * @type {Array[]} */ get scaledPositions() { return this._atoms_base.get_scaled_positions(); } /** * Unit cell of the model's original cell * @readonly * @type {Array[]} */ get cell() { return this._atoms_base.get_cell(); } /** * Periodic boundary conditions * @readonly * @type {bool[]} */ get pbc() { return this._atoms_base.get_pbc(); } /** * Additional information from the model's original cell * @readonly * @type {Object} */ get info() { return this._atoms_base.info; } /** * Whether this model is periodic in all three directions of space * @readonly * @type {bool} */ get periodic() { return this._periodic; } /** * Indices of each atom by their species (e.g. C1, C2, H1, C3, H2, etc.) * @readonly * @type {int[]} */ get speciesIndices() { return Array.from(this._species_indices); } /** * Crystallographic labels of each atom * @readonly * @type {String[]} */ get crystalLabels() { return Array.from(this._labels); } /** * Shape of the supercell for this model * @readonly * @type {int[]} */ get supercell() { return Array.from(this._supercell); } /** * Full grid of origin coordinates of the cells making up the supercell * @readonly * @type {Array[]} */ get supercellGrid() { return JSON.parse(JSON.stringify(this._supercell_grid)); } /** * Atom images in this model * @readonly * @type {AtomImage[]} */ get atoms() { return Array.from(this._atom_images); } /** * ModelView containing all the atoms of the image * @readonly * @type {ModelView} */ get all() { return this._all; } /** * Graphical object representing the unit cell's axes * @readonly * @type {AxesMesh} */ get axes() { return this._cartesian_axes; } /** * Graphical object representing the unit cell's box * @readonly * @type {BoxMesh} */ get box() { return this._cartesian_box; } /** * Global scaling factor for Van der Waals radii * @readonly * @type {float} */ get vdwScaling() { return this._vdwScaling; } /** * Table of scaling factors by element for Van der Waals radii * @readonly * @type {Object} */ get vdwElementScaling() { return JSON.parse(JSON.stringify(this._vdwElementScaling)); } /** * Renderer used for this model's graphics * @type {Renderer} */ set renderer(r) { if (r) { this._renderer = r; if (this.periodic) { // Create axes and box if (!this._cartesian_box) { this._cartesian_box = new r.Primitives.BoxMesh(this.cell, {color:r.theme.cell_line_color}); } if (!this._cartesian_axes) { this._cartesian_axes = new r.Primitives.AxesMesh(this.cell, { linewidth: 1.5 }); } r.add(this._cartesian_box); r.add(this._cartesian_axes); } // And the primitives for (var name in this._primitives) { var p = this._primitives[name]; r.add(p); } } else { if (this._renderer) this._renderer.clear(); this._renderer = null; } } // Set and get arrays on the underlying Atoms object /** * Set an array for the underlying Atoms object * @param {String} name Name of the array to use * @param {Array} arr Array to store */ setArray(name, arr) { this._atoms_base.set_array(name, arr); } /** * Retrieve an array from the underlying Atoms object * @param {String} name Name of the array to retrieve * @return {Array} Retrieved array */ getArray(name) { return this._atoms_base.get_array(name); } /** * Check if an array exists in the underlying Atoms object * @param {String} name Name of the array to check * @return {bool} Whether the array exists */ hasArray(name) { return (name in this._atoms_base._arrays); } /** * Delete an array from the underlying Atoms object * @param {String} name Name of the array to delete */ deleteArray(name) { delete this._atoms_base._arrays[name]; } // These functions are for adding and removing graphical representations // that are meant to be drawn on to of the existing 3D model /** * Add link drawn on model * * @param {Atom | Array} from Starting point * @param {Atom | Array} to End point * @param {String} name Name to use for the link object * @param {String} label Text label to add to the link * @param {Object} parameters Additional parameters (see LineMesh) */ addLink(from, to, name = 'link', label = null, parameters = {}) { this.removeGraphics(name); parameters = _.clone(parameters); // Avoid editing the reference object var r = this._renderer; if (r) { var link = new r.Primitives.LineMesh(from, to, parameters); this._primitives[name] = link; r.add(link); if (label) { var text = new r.Primitives.TextSprite(label, { color: parameters.color, fixScale: true, faceCamera: true, height: parameters.height || LABEL_HEIGHT, shift: [LABEL_HEIGHT, 0, 0], onOverlay: parameters.onOverlay }); link.add(text); } } } /** * Add a sphere drawn on model * * @param {Atom | Array} center Center of the sphere * @param {float} radius Radius of the sphere * @param {String} name Name to use for the sphere object * @param {Object} parameters Additional parameters (see EllipsoidMesh) */ addSphere(center, radius, name='sphere', parameters = {}) { this.removeGraphics(name); var r = this._renderer; if (r) { parameters = _.merge({ color: 0xffffff, opacity: 0.5, opacityMode: r.Primitives.EllipsoidMesh.DITHER, showCircles: true, showAxes: true }, parameters); // Avoid editing the reference object var sph = new r.Primitives.EllipsoidMesh({ color: parameters.color, opacity: parameters.opacity, opacityMode: parameters.opacityMode, showCircles: parameters.showCircles, showAxes: parameters.showAxes, scalingFactor: radius, center: center }); this._primitives[name] = sph; r.add(sph); } } /** * Remove the graphical object with a given name * * @param {String} name Name of the graphical object to remove */ removeGraphics(name) { var g = this._primitives[name]; var r = this._renderer; if (g && r) r.remove(g); delete this._primitives[name]; } /** * Remove all graphical objects */ clearGraphics() { var r = this._renderer; if (r) { _.map(this._primitives, function(g) { r.remove(g); }); } this._primitives = {}; } /** * Compute the bonds within the model. For internal use * @private */ _computeBonds() { var N = this.length; this._bondmat = Array(N); // Bond matrix this._bondmat = _.map(this._bondmat, function() { return _.map(Array(N), function() { return []; }); }); // Van der Waals radii by element var vdwf = this._vdwScaling; var vdwf_table = this._vdwElementScaling; var vdwr = _.map(this.symbols, function(s) { var f = vdwf; if (s in vdwf_table) { f = vdwf_table[s]; } return data.getVdwRadius(s)*f; }); var maxr = _.max(vdwr); var cell = this.cell; var sgrid = [ [0, 0, 0] ]; var p = this._positions; if (this._periodic) { var scell = this.minimumSupercell(maxr); sgrid = utils.supercellGrid(scell); } // Now iterate over all atom pairs for (let i = 0; i < this.length; ++i) { var p1 = p[i]; for (let j = i; j < this.length; ++j) { var p2 = p[j]; for (let k = 0; k < sgrid.length; ++k) { var c = sgrid[k]; if ((i == j) && (c[0] == 0 && c[1] == 0 && c[2] == 0)) { // Just the same atom, skip continue; } var r = [0, 0, 0]; // Here we write the algebra explicitly // for efficiency reasons if (this._periodic) { r[0] = c[0] * cell[0][0] + c[1] * cell[1][0] + c[2] * cell[2][0]; r[1] = c[0] * cell[0][1] + c[1] * cell[1][1] + c[2] * cell[2][1]; r[2] = c[0] * cell[0][2] + c[1] * cell[1][2] + c[2] * cell[2][2]; } r = [p2[0] - p1[0] + r[0], p2[1] - p1[1] + r[1], p2[2] - p1[2] + r[2]]; r = Math.sqrt(r[0] * r[0] + r[1] * r[1] + r[2] * r[2]); if (r < (vdwr[i] + vdwr[j]) / 2.0) { // Bond! this._bondmat[i][j].push([c[0], c[1], c[2]]); this._bondmat[j][i].push([-c[0], -c[1], -c[2]]); } } } } } /** * Check if any C-H bonds are present * @return {bool} Whether any C-H bonds are present * @private */ _queryCHBond() { // make sure bondmat is present if (!this._bondmat) { this._computeBonds(); } var symbols = this._atoms_base.get_chemical_symbols(); var bondmat = this._bondmat; var n = symbols.length; for (var i = 0; i < n; i++) { var bonds = bondmat[i]; var a = symbols[i]; if (a == 'C') { // loop over bonds and check if any are H for (var j = 0; j < n; j++) { // if bonds[j] is not an empty array if (bonds[j].length) { if (symbols[j] == 'H') { return true; } } } } } return false; } /** * Compute the molecules within the model. For internal use * @private */ _computeMolecules() { this._molecules = []; this._molinds = []; if (this.length < 2) { // No molecules can be computed this._molecules = null; return; } var mol_sets = []; var unsorted_atoms = _.range(this.length); while (unsorted_atoms.length > 0) { var mol_queue = [ [unsorted_atoms.shift(), [0, 0, 0]] ]; var current_mol = []; var current_mol_cells = []; while (mol_queue.length > 0) { var ac1 = mol_queue.shift(); var a1 = ac1[0]; var c1 = ac1[1]; current_mol.push(a1); current_mol_cells.push(c1); // Find linked atoms var link1 = this._bondmat[a1]; for (let i in link1) { var a2 = parseInt(i); var link12 = link1[i]; //