def __call__(self, f):
try:
xyz_reader = XYZReader(f)
molecule = xyz_reader.get_first_molecule()
except IOError:
raise FilterError("Could not read the first frame from the XYZ file. Incorrect file format.")
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
title = molecule.title.strip()
if len(title) > 0:
universe.name = title
Atom = context.application.plugins.get_node("Atom")
Point = context.application.plugins.get_node("Point")
for index, number, symbol, coordinate in zip(xrange(molecule.size), molecule.numbers, xyz_reader.symbols, molecule.coordinates):
extra = {"index": index}
transl = Translation(coordinate)
if number == 0:
atom = Point(name=symbol, extra=extra, transformation=transl)
else:
atom = Atom(name=symbol, number=number, extra=extra, transformation=transl)
universe.add(atom)
geometries = []
for title, coordinates in xyz_reader:
geometries.append(coordinates)
return [universe, folder]
def __call__(self, f):
try:
xyz_reader = XYZReader(f)
molecule = xyz_reader.get_first_molecule()
except IOError:
raise FilterError(
"Could not read the first frame from the XYZ file. Incorrect file format."
)
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
title = molecule.title.strip()
if len(title) > 0:
universe.name = title
Atom = context.application.plugins.get_node("Atom")
Point = context.application.plugins.get_node("Point")
for index, number, symbol, coordinate in zip(xrange(molecule.size),
molecule.numbers,
xyz_reader.symbols,
molecule.coordinates):
extra = {"index": index}
transl = Translation(coordinate)
if number == 0:
atom = Point(name=symbol, extra=extra, transformation=transl)
else:
atom = Atom(name=symbol,
number=number,
extra=extra,
transformation=transl)
universe.add(atom)
geometries = []
for title, coordinates in xyz_reader:
geometries.append(coordinates)
return [universe, folder]
