def write_to_file(self, filename):
"""Write the molecular geometry to a file.
The file format is inferred from the extensions. Currently supported
formats are: ``*.xyz``, ``*.cml``
Argument:
| ``filename`` -- a filename
"""
# TODO: give all file format writers the same API
if filename.endswith('.cml'):
from molmod.io import dump_cml
dump_cml(filename, [self])
elif filename.endswith('.xyz'):
from molmod.io import XYZWriter
symbols = []
for n in self.numbers:
atom = periodic[n]
if atom is None:
symbols.append("X")
else:
symbols.append(atom.symbol)
xyz_writer = XYZWriter(filename, symbols)
xyz_writer.dump(self.title, self.coordinates)
del xyz_writer
else:
raise ValueError("Could not determine file format for %s." %
filename)
def write_to_file(self, filename):
"""Write the molecular geometry to a file.
The file format is inferred from the extensions. Currently supported
formats are: ``*.xyz``, ``*.cml``
Argument:
| ``filename`` -- a filename
"""
# TODO: give all file format writers the same API
if filename.endswith('.cml'):
from molmod.io import dump_cml
dump_cml(filename, [self])
elif filename.endswith('.xyz'):
from molmod.io import XYZWriter
symbols = []
for n in self.numbers:
atom = periodic[n]
if atom is None:
symbols.append("X")
else:
symbols.append(atom.symbol)
xyz_writer = XYZWriter(filename, symbols)
xyz_writer.dump(self.title, self.coordinates)
del xyz_writer
else:
raise ValueError("Could not determine file format for %s." % filename)
def __call__(self, f, universe, folder, nodes=None):
atom_counter = 0
if nodes is None:
nodes = [universe]
molecules = self.collect_molecules(universe)
dump_cml(f, molecules)
def __call__(self, f, universe, folder, nodes=None):
atom_counter = 0
if nodes is None:
nodes = [universe]
molecules = self.collect_molecules(universe)
dump_cml(f, molecules)
