BioSimSpace.Notebook.View#

class BioSimSpace.Notebook.View(handle, property_map={}, is_lambda1=False)[source]#

A class for handling interactive molecular visualisations.

__init__(handle, property_map={}, is_lambda1=False)[source]#

Constructor.

Parameters:

  • handle (Process, System System System str, [str]) – A handle to a process, system, molecule, or molecule container, or the path to molecular input file(s).

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

  • is_lambda1 (bool) – Whether to use the lambda = 1 end state when visualising perturbable molecules. By default, the state at lambda = 0 is used.

Methods

__init__(handle[, property_map, is_lambda1])

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)[source]#

View a specific molecule.

Parameters:

  • index (int) – The molecule index.

  • gui (bool) – Whether to display the gui.

molecules(indices=None, gui=True)[source]#

View specific molecules.

Parameters:

  • indices ([int], range) – A list of molecule indices.

  • gui (bool) – Whether to display the gui.

nViews()[source]#

Return the number of views.

Returns:

num_views – The number of views.

Return type:

int

reload(index=None, gui=True)[source]#

Reload a particular view.

Parameters:

  • index (int) – The view index.

  • gui (bool) – Whether to display the gui.

reset()[source]#

Reset the object, clearing all view files.

savePDB(file, index=None)[source]#

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)[source]#

View the entire molecular system.

Parameters:

gui (bool) – Whether to display the gui.