def particles(self, filename='pytim_part.vtk', group=None, sequence=False):
""" Write to vtk files the particles in a group.
:param str filename: the file name
:param bool sequence: if true writes a sequence of files adding
the frame to the filename
:param AtomGroup group: if None, writes the whole universe
>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)
>>> # writes on part.vtk
>>> inter.writevtk.particles('part.vtk')
>>> # writes on part.<frame>.vtk
>>> inter.writevtk.particles('part.vtk',sequence=True)
"""
inter = self.interface
if sequence is True:
filename = vtk.consecutive_filename(inter.universe, filename)
if group is None:
group = inter.universe.atoms
self._dump_group(group, filename)
def density(self, filename='pytim_dens.vtk', sequence=False):
""" Write to vtk files the volumetric density:
:param str filename: the file name
:param bool sequence: if true writes a sequence of files adding the frame to the filename
>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> interface = pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)
>>> interface.writevtk.density('dens.vtk') # writes on dens.vtk
>>> interface.writevtk.density('dens.vtk',sequence=True) # writes on dens.<frame>.vtk
"""
inter = self.interface
if sequence == True:
filename = vtk.consecutive_filename(inter.universe, filename)
vtk.write_scalar_grid(filename, inter.ngrid, inter.spacing,
inter.density_field)
def surface(self, filename='pytim_surf.vtk', sequence=False):
""" Write to vtk files the triangulated surface:
:param str filename: the file name
:param bool sequence: if true writes a sequence of files adding the frame to the filename
>>> import MDAnalysis as mda
>>> import pytim
>>> from pytim.datafiles import MICELLE_PDB
>>> u = mda.Universe(MICELLE_PDB)
>>> g = u.select_atoms('resname DPC')
>>> interface = pytim.WillardChandler(u, group=g, alpha=3.0, mesh=2.0)
>>> interface.writevtk.surface('surf.vtk') # writes on surf.vtk
>>> interface.writevtk.surface('surf.vtk',sequence=True) # writes on surf.<frame>.vtk
"""
inter = self.interface
vertices = inter.triangulated_surface[0]
faces = inter.triangulated_surface[1]
normals = inter.triangulated_surface[2]
if sequence == True:
filename = vtk.consecutive_filename(inter.universe, filename)
vtk.write_triangulation(filename, vertices[::, ::-1], faces,
normals)