BioSimSpace.Notebook.View¶
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class
BioSimSpace.Notebook.
View
(handle, property_map={}, is_lambda1=False)¶ A class for handling interactive molecular visualisations.
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__init__
(handle, property_map={}, is_lambda1=False)¶ 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.
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molecule
(index=0, gui=True)¶ View a specific molecule.
- Parameters
index (int) – The molecule index.
gui (bool) – Whether to display the gui.
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molecules
(indices=None, gui=True)¶ View specific molecules.
- Parameters
indices ([int], range) – A list of molecule indices.
gui (bool) – Whether to display the gui.
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nViews
()¶ Return the number of views.
- Returns
num_views – The number of views.
- Return type
int
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reload
(index=None, gui=True)¶ Reload a particular view.
- Parameters
index (int) – The view index.
gui (bool) – Whether to display the gui.
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reset
()¶ Reset the object, clearing all view files.
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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.
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system
(gui=True)¶ View the entire molecular system.
- Parameters
gui (bool) – Whether to display the gui.
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