def convert_to_xyz(self,
xyz_filename=None,
generate_tcl=True,
tcl_with_grid=False,
particle_radii=None,
color_ids=None,
draw_box=False):
"""
Converts this trajectory to a xyz file that can be read into VMD. Assuming the TCL script was generated, the
trajectory can be visualized by `vmd -e traj.xyz.tcl`.
:param xyz_filename: the output file name, if None, the filename with an .xyz extension will be used
:param generate_tcl: generates a tcl script that can be used alongside with the xyz file
:param tcl_with_grid: enables a grid view inside VMD
:param particle_radii: map particle radii for visualization purposes, e.g., `{"A": 10., "B": .1}`
:param color_ids: map particle type names to tcl/vmd color ids, e.g., `{"A": 0, "B": 5}`, default uses
consecutive numbering
:param draw_box: if True, will use box size from trajectory file and make vmd draw the edges of the box
"""
from readdy.api.utils import convert_trajectory_to_xyz as to_xyz
if draw_box:
bs = tuple(self._general.box_size)
else:
bs = None
to_xyz(self._filename,
self._name,
xyz_filename=xyz_filename,
generate_tcl=generate_tcl,
tcl_with_grid=tcl_with_grid,
particle_radii=particle_radii,
color_ids=color_ids,
box_size=bs)
def convert_to_xyz(self, xyz_filename=None, generate_tcl=True, tcl_with_grid=False, particle_radii=None):
"""
Converts this trajectory to a xyz file that can be read into VMD. Assuming the TCL script was generated, the
trajectory can be visualized by `vmd -e traj.xyz.tcl`.
:param xyz_filename: the output file name, if None, the filename with an .xyz extension will be used
:param generate_tcl: generates a tcl script that can be used alongside with the xyz file
:param tcl_with_grid: enables a grid view inside VMD
:param particle_radii: map particle radii for visualization purposes, e.g., `{"A": 10., "B": .1}`
"""
from readdy.api.utils import convert_trajectory_to_xyz as to_xyz
to_xyz(self._filename, self._name, xyz_filename=xyz_filename, generate_tcl=generate_tcl,
tcl_with_grid=tcl_with_grid, particle_radii=particle_radii)
def convert_to_xyz(self,
xyz_filename=None,
generate_tcl=True,
tcl_with_grid=False,
particle_radii=None):
"""
Converts this trajectory to a xyz file that can be read into VMD. Assuming the TCL script was generated, the
trajectory can be visualized by `vmd -e traj.xyz.tcl`.
:param xyz_filename: the output file name, if None, the filename with an .xyz extension will be used
:param generate_tcl: generates a tcl script that can be used alongside with the xyz file
:param tcl_with_grid: enables a grid view inside VMD
:param particle_radii: map particle radii for visualization purposes, e.g., `{"A": 10., "B": .1}`
"""
from readdy.api.utils import convert_trajectory_to_xyz as to_xyz
to_xyz(self._filename,
self._name,
xyz_filename=xyz_filename,
generate_tcl=generate_tcl,
tcl_with_grid=tcl_with_grid,
particle_radii=particle_radii)