Source code for

Output support for X3D and X3DOM file types.
X3DOM outputs to html that display 3-d manipulatable atoms in
modern web browsers and jupyter notebooks.

from import covalent_radii
from import jmol_colors
from ase.utils import writer
import xml.etree.ElementTree as ET
from xml.dom import minidom
import numpy as np

[docs]@writer def write_x3d(fd, atoms, format='X3D', style=None): """Writes to html using X3DOM. Args: filename - str or file-like object, filename or output file object atoms - Atoms object to be rendered format - str, either 'X3DOM' for web-browser compatibility or 'X3D' to be readable by Blender. `None` to detect format based on file extension ('.html' -> 'X3DOM', '.x3d' -> 'X3D') style - dict, css style attributes for the X3D element """ X3D(atoms).write(fd, datatype=format, x3d_style=style)
[docs]@writer def write_html(fd, atoms): """Writes to html using X3DOM. Args: filename - str or file-like object, filename or output file object atoms - Atoms object to be rendered """ write_x3d(fd, atoms, format='X3DOM')
class X3D: """Class to write either X3D (readable by open-source rendering programs such as Blender) or X3DOM html, readable by modern web browsers. """ def __init__(self, atoms): self._atoms = atoms def write(self, fileobj, datatype, x3d_style=None): """Writes output to either an 'X3D' or an 'X3DOM' file, based on the extension. For X3D, filename should end in '.x3d'. For X3DOM, filename should end in '.html'. Args: datatype - str, output format. 'X3D' or 'X3DOM' x3d_style - dict, css style attributes for the X3D element """ # convert dictionary of style attributes to a css string if x3d_style is None: x3d_style = {} x3dstyle = " ".join(f'{k}="{v}";' for k, v in x3d_style.items()) if datatype == 'X3DOM': template = X3DOM_template elif datatype == 'X3D': template = X3D_template else: raise ValueError(f'datatype not supported: {datatype}') scene = x3d_atoms(self._atoms) document = template.format(scene=pretty_print(scene), style=x3dstyle) print(document, file=fileobj) def x3d_atom(atom): """Represent an atom as an x3d, coloured sphere.""" x, y, z = atom.position r, g, b = jmol_colors[atom.number] radius = covalent_radii[atom.number] material = element('material', diffuseColor=f'{r} {g} {b}') appearance = element('appearance', child=material) sphere = element('sphere', radius=f'{radius}') shape = element('shape', children=(appearance, sphere)) return translate(shape, x, y, z) def x3d_wireframe_box(box): """x3d wireframe representation of a box (3x3 array). To draw a box, spanned by vectors a, b and c, it is necessary to draw 4 faces, each of which is a parallelogram. The faces are: (start from) , (vectors spanning the face) 1. (0), (a, b) 2. (c), (a, b) # opposite face to 1. 3. (0), (a, c) 4. (b), (a, c) # opposite face to 3.""" # box may not be a cube, hence not just using the diagonal a, b, c = box faces = [ wireframe_face(a, b), wireframe_face(a, b, origin=c), wireframe_face(a, c), wireframe_face(a, c, origin=b), ] return group(faces) def wireframe_face(vec1, vec2, origin=(0, 0, 0)): """x3d wireframe representation of a face spanned by vec1 and vec2.""" x1, y1, z1 = vec1 x2, y2, z2 = vec2 material = element('material', diffuseColor='0 0 0') appearance = element('appearance', child=material) points = [ (0, 0, 0), (x1, y1, z1), (x1 + x2, y1 + y2, z1 + z2), (x2, y2, z2), (0, 0, 0), ] points = ' '.join(f'{x} {y} {z}' for x, y, z in points) coordinates = element('coordinate', point=points) lineset = element('lineset', vertexCount='5', child=coordinates) shape = element('shape', children=(appearance, lineset)) x, y, z = origin return translate(shape, x, y, z) def x3d_atoms(atoms): """Convert an atoms object into an x3d representation.""" atom_spheres = group([x3d_atom(atom) for atom in atoms]) wireframe = x3d_wireframe_box(atoms.cell) cell = group((wireframe, atom_spheres)) # we want the cell to be in the middle of the viewport # so that we can (a) see the whole cell and (b) rotate around the center # therefore we translate so that the center of the cell is at the origin cell_center = atoms.cell.diagonal() / 2 cell = translate(cell, *(-cell_center)) # we want the cell, and all atoms, to be visible # - sometimes atoms appear outside the cell # - sometimes atoms only take up a small part of the cell # location of the viewpoint therefore takes both of these into account: # the scene is centered on the cell, so we find the furthest point away # from the cell center, and use this to determine the # distance of the viewpoint points = np.vstack((atoms.positions, atoms.cell[:])) max_xyz_extent = get_maximum_extent(points - cell_center) # the largest separation between two points in any of x, y or z max_dim = max(max_xyz_extent) # put the camera twice as far away as the largest extent pos = f'0 0 {max_dim * 2}' # NB. viewpoint needs to contain an (empty) child to be valid x3d viewpoint = element('viewpoint', position=pos, child=element('group')) return element('scene', children=(viewpoint, cell)) def element(name, child=None, children=None, **attributes) -> ET.Element: """Convenience function to make an XML element. If child is specified, it is appended to the element. If children is specified, they are appended to the element. You cannot specify both child and children.""" # make sure we don't specify both child and children if child is not None: assert children is None, 'Cannot specify both child and children' children = [child] else: children = children or [] element = ET.Element(name, **attributes) for child in children: element.append(child) return element def translate(thing, x, y, z): """Translate a x3d element by x, y, z.""" return element('transform', translation=f'{x} {y} {z}', child=thing) def group(things): """Group a (list of) x3d elements.""" return element('group', children=things) def pretty_print(element: ET.Element, indent: int = 2): """Pretty print an XML element.""" byte_string = ET.tostring(element, 'utf-8') parsed = minidom.parseString(byte_string) prettied = parsed.toprettyxml(indent=' ' * indent) # remove first line - contains an extra, un-needed xml declaration lines = prettied.splitlines()[1:] return '\n'.join(lines) def get_maximum_extent(xyz): """Get the maximum extent of an array of 3d set of points.""" return np.max(xyz, axis=0) - np.min(xyz, axis=0) X3DOM_template = """\ <html> <head> <title>ASE atomic visualization</title> <link rel="stylesheet" type="text/css" \ href=""></link> <script type="text/javascript" \ src=""></script> </head> <body> <X3D {style}> <!--Inserting Generated X3D Scene--> {scene} <!--End of Inserted Scene--> </X3D> </body> </html> """ X3D_template = """\ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE X3D PUBLIC "ISO//Web3D//DTD X3D 3.2//EN" \ ""> <X3D profile="Interchange" version="3.2" \ xmlns:xsd="" \ xsd:noNamespaceSchemaLocation=\ "" {style}> <!--Inserting Generated X3D Scene--> {scene} <!--End of Inserted Scene--> </X3D> """