"""
Output support for X3D and X3DOM file types.
See http://www.web3d.org/x3d/specifications/
X3DOM outputs to html pages that should display 3-d manipulatable atoms in
modern web browsers.
"""
from __future__ import print_function
from ase.data import covalent_radii
from ase.data.colors import jmol_colors
from ase.utils import basestring
def write_x3d(filename, atoms, format=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')"""
X3D(atoms).write(filename, datatype=format)
def write_html(filename, 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(filename, 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, filename, datatype=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:
filename - str or file-like object, output file name or writer
datatype - str, output format. 'X3D' or 'X3DOM'. If `None`, format
will be determined from the filename"""
# Detect the format, if not stated
if datatype is None:
if filename.endswith('.x3d'):
datatype = 'X3D'
elif filename.endswith('.html'):
datatype = 'X3DOM'
else:
raise ValueError("filename must end in '.x3d' or '.html'.")
# Write the header
w = WriteToFile(filename, 'w')
if datatype == 'X3DOM':
w(0, '')
w(1, '')
w(2, 'ASE atomic visualization')
w(2, '')
w(2, '')
w(2, '')
w(1, '')
w(1, '')
w(2, '')
elif datatype == 'X3D':
w(0, '')
w(0, '')
w(0, '')
else:
raise ValueError("datatype not supported: " + str(datatype))
w(3, '')
for atom in self._atoms:
for indent, line in atom_lines(atom):
w(4 + indent, line)
w(3, '')
if datatype == 'X3DOM':
w(2, '')
w(1, '')
w(0, '')
elif datatype == 'X3D':
w(0, '')
class WriteToFile:
"""Creates convenience function to write to a file."""
def __init__(self, filename, mode='w'):
if isinstance(filename, basestring):
self._f = open(filename, mode)
else:
self._f = filename
def __call__(self, indent, line):
text = ' ' * indent
print('%s%s\n'%(text,line), file=self._f)
def close(self):
self._f.close()
def atom_lines(atom):
"""Generates a segment of X3D lines representing an atom."""
x, y, z = atom.position
lines = [(0, '' % (x, y, z))]
lines += [(1, '')]
lines += [(2, '')]
color = tuple(jmol_colors[atom.number])
color = 'diffuseColor="%.3f %.3f %.3f"' % color
lines += [(3, '' % color)]
lines += [(3, '')]
lines += [(2, '')]
lines += [(2, '' % covalent_radii[atom.number])]
lines += [(2, '')]
lines += [(1, '')]
lines += [(0, '')]
return lines