def test_check_nbextension(self):
with TemporaryDirectory() as d:
f = u'ƒ.js'
src = pjoin(d, f)
touch(src)
install_nbextension(src)
assert check_nbextension(f, self.ipdir)
assert check_nbextension([f], self.ipdir)
assert not check_nbextension([f, pjoin('dne', f)], self.ipdir)
def test_check_nbextension(self):
with TemporaryDirectory() as d:
f = u'ƒ.js'
src = pjoin(d, f)
touch(src)
install_nbextension(src)
assert check_nbextension(f, self.ipdir)
assert check_nbextension([f], self.ipdir)
assert not check_nbextension([f, pjoin('dne', f)], self.ipdir)
def test_check_nbextension(self):
with TemporaryDirectory() as d:
f = u"ƒ.js"
src = pjoin(d, f)
touch(src)
install_nbextension(src, user=True)
assert check_nbextension(f, user=True)
assert check_nbextension([f], user=True)
assert not check_nbextension([f, pjoin("dne", f)], user=True)
def test_check_nbextension(self):
with TemporaryDirectory() as d:
f = u'ƒ.js'
src = pjoin(d, f)
touch(src)
install_nbextension(src, user=True)
nbext = pjoin(self.ipdir, u'nbextensions')
assert check_nbextension(f, nbext)
assert check_nbextension([f], nbext)
assert not check_nbextension([f, pjoin('dne', f)], nbext)
def __init__(self, install_assets=False, *args, **kwargs):
'''
Each time an instance is created:
- if the nbextension is not installed...
- copy all assets in `static` to the current profile's nbextensions
- automagically load any css
'''
if install_assets or not check_nbextension([nbextension]):
# copy the static files to a namespaced location in `nbextensions`
install_nbextension(static)
# magically-named files css/SomeWidgetView.css
magic_style = os.path.join(static, 'css', '%s.css' % self._view_name)
styles = getattr(self, '_view_styles', [])
if os.path.exists(magic_style):
styles.append('css/%s.css' % self._view_name)
styles = [
'/nbextensions/%s/%s' % (nbextension, style)
for style in styles
]
# tell the front-end to request the assets
display(Javascript('', css=styles))
# always call the parent constructor!
super(InstallerMixin, self).__init__(*args, **kwargs)
def __init__(self, install_assets=False, *args, **kwargs):
'''
Each time an instance is created:
- if the nbextension is not installed...
- copy all assets in `static` to the current profile's nbextensions
- automagically load any css
'''
if install_assets or not check_nbextension([nbextension]):
# copy the static files to a namespaced location in `nbextensions`
install_nbextension(static, user=True)
# magically-named files css/SomeWidgetView.css
magic_style = os.path.join(static, 'css', '%s.css' % self._view_name)
styles = getattr(self, '_view_styles', [])
if os.path.exists(magic_style):
styles.append('css/%s.css' % self._view_name)
styles = [
'/nbextensions/%s/%s' % (nbextension, style) for style in styles
]
# tell the front-end to request the assets
display(Javascript('', css=styles))
# always call the parent constructor!
super(InstallerMixin, self).__init__(*args, **kwargs)
def _repr_html_(self):
"""For IPython notebook, renders 3D pybel.Molecule webGL objects."""
# Returning None defers to _repr_svg_
if not ipython_3d:
return None
# If the javascript files have not yet been loaded, do so
# IPython >=2.0 does this by copying into ~/.ipython/nbextensions
filename = "imolecule.min.js"
local_path = os.path.join("nbextensions", filename)
remote_path = ("https://rawgit.com/openbabel/contributed/master/web/"
"imolecule/build/imolecule.min.js")
# Try using IPython >=2.0 to install js locally from website
try:
from IPython.html.nbextensions import (install_nbextension,
check_nbextension)
if not check_nbextension(local_path):
install_nbextension(remote_path, verbose=0)
except:
pass
# Some exposed parameters. Leaving this unfunctionalized for now.
size = (400, 300)
drawing_type = "ball and stick"
camera_type = "perspective"
# Clone molecule
mol = self.clone
# Infer structure in cases where the input format has no specification
if not mol.OBMol.HasNonZeroCoords():
mol.make3D()
mol.OBMol.Center()
# Convert the relevant parts of `self` into JSON for rendering
table = ob.OBElementTable()
atoms = [{"element": table.GetSymbol(atom.atomicnum),
"location": atom.coords}
for atom in mol.atoms]
bonds = [{"atoms": [bond.GetBeginAtom().GetIndex(),
bond.GetEndAtom().GetIndex()],
"order": bond.GetBondOrder()}
for bond in ob.OBMolBondIter(mol.OBMol)]
mol = {"atoms": atoms, "bonds": bonds}
if hasattr(mol, "unitcell"):
uc = mol.unitcell
mol["unitcell"] = [[v.GetX(), v.GetY(), v.GetZ()]
for v in uc.GetCellVectors()]
# Support for previous naming scheme
mol["periodic_connections"] = mol["unitcell"]
json_mol = json.dumps(mol, separators=(",", ":"))
# Try using local copy. If that fails, use remote copy.
div_id = uuid.uuid4()
return """<div id="molecule_%s"></div>
<script type="text/javascript">
requirejs.config({baseUrl: "/",
paths: {imolecule: ['%s', '%s']}});
require(['imolecule'], function () {
var $d = $('#molecule_%s');
$d.width(%d); $d.height(%d);
$d.imolecule = jQuery.extend({}, imolecule);
$d.imolecule.create($d, {drawingType: '%s',
cameraType: '%s'});
$d.imolecule.draw(%s);
$d.resizable({
aspectRatio: %d / %d,
resize: function (evt, ui) {
$d.imolecule.renderer.setSize(ui.size.width,
ui.size.height);
}
});
});
</script>""" % (div_id, local_path[:-3], remote_path[:-3],
div_id, size[0], size[1], drawing_type,
camera_type, json_mol, size[0], size[1])
