BioSimSpace.Notebook.View

class BioSimSpace.Notebook.View(handle)

A class for handling interactive molecular visualisations.

__init__(handle)

Constructor.

Parameters:handle (Process, System) – A handle to a process or system.

Methods

__init__(handle) Constructor.
molecule([index, gui]) View a specific molecule.
molecules([indices, gui]) View specific molecules.
nViews() Return the number of views.
reload([index, gui]) Reload a particular view.
reset() Reset the object, clearing all view files.
savePDB(file[, index]) Save a specific view as a PDB file.
system([gui]) View the entire molecular system.
molecule(index=0, gui=True)

View a specific molecule.

Parameters:
  • index (int) – The molecule index.
  • gui (bool) – Whether to display the gui.
molecules(indices=None, gui=True)

View specific molecules.

Parameters:
  • indices ([int], range) – A list of molecule indices.
  • gui (bool) – Whether to display the gui.
nViews()

Return the number of views.

Returns:num_views – The number of views.
Return type:int
reload(index=None, gui=True)

Reload a particular view.

Parameters:
  • index (int) – The view index.
  • gui (bool) – Whether to display the gui.
reset()

Reset the object, clearing all view files.

savePDB(file, index=None)

Save a specific view as a PDB file.

Parameters:
  • file (str) – The name of the file to write to.
  • index (int) – The view index.
system(gui=True)

View the entire molecular system.

Parameters:gui (bool) – Whether to display the gui.