4. Rg and SASA Analysis

Rg and SASA are two correlated metrics which focus on describing how the protein expands or shrinks as frames pass.

The functions in this module are based on frame aggregating techniques per class. For example we will take the Rg of all the agonists on frame x and find the average. We will do that for every frame and end up with an average Rg of the agonists vs the antagonists.

MDSimsEval.rg_sasa_analysis.calculate_average_cols_rg(analysis_actors_dict)

Calculates the mean of Rg of each frame for both classes.

Parameters

analysis_actors_dict – { "Agonists": List[AnalysisActor.class], "Antagonists": List[AnalysisActor.class] }

Returns

Tuple(np.array[#frames], np.array[#frames])

MDSimsEval.rg_sasa_analysis.calculate_average_cols_sasa(analysis_actors_dict)

Calculates the mean of SASA of each frame for both classes.

Parameters

analysis_actors_dict – { "Agonists": List[AnalysisActor.class], "Antagonists": List[AnalysisActor.class] }

Returns

Tuple(np.array[#frames], np.array[#frames])

MDSimsEval.rg_sasa_analysis.rg_sasa_mean_mean_plot(analysis_actors_dict, dir_path, start=0, stop=2500)

Creates a mean of Rg - mean of SASA plot on the specified window with annotations on the plots.


rg sasa mean figure missing

Mean Rg - Mean SASA Plot with ligand name annotations

Parameters

  • analysis_actors_dict – { "Agonists": List[AnalysisActor.class], "Antagonists": List[AnalysisActor.class] }

  • dir_path (str) – The path of the directory the plot will be saved (must end with a /)

  • start (int) – The starting frame of the calculations

  • stop (int) – The stopping frame of the calculations

MDSimsEval.rg_sasa_analysis.rg_sasa_std_std_plot(analysis_actors_dict, dir_path, start=0, stop=2500)

Creates a std of Rg - std of SASA plot on the specified window with annotations on the plots.

Parameters

  • analysis_actors_dict – { "Agonists": List[AnalysisActor.class], "Antagonists": List[AnalysisActor.class] }

  • dir_path (str) – The path of the directory the plot will be saved (must end with a /)

  • start (int) – The starting frame of the calculations

  • stop (int) – The stopping frame of the calculations

MDSimsEval.rg_sasa_analysis.summarize_rg(analysis_actors_dict, dir_path, rolling_window=100)

Creates a plot summarizing how the Rg behaves.


summarizing info rg missing

Summarizing info of Rg for each class (Agonists, Antagonists)

Parameters

  • analysis_actors_dict – { "Agonists": List[AnalysisActor.class], "Antagonists": List[AnalysisActor.class] }

  • dir_path (str) – The path of the directory the plot will be saved (must end with a /)

  • rolling_window (int) – The size of the window for the rolling avg and std

MDSimsEval.rg_sasa_analysis.summarize_sasa(analysis_actors_dict, dir_path, rolling_window=100)

Creates a plot summarizing how the SASA behaves.

Parameters

  • analysis_actors_dict – { "Agonists": List[AnalysisActor.class], "Antagonists": List[AnalysisActor.class] }

  • dir_path (str) – The path of the directory the plot will be saved (must end with a /)

  • rolling_window (int) – The size of the window for the rolling avg and std