7. Utility Functions

MDSimsEval.utils.complement_residues(ligand_list_full, ligand_list_selected)

Given a list of ligands and a list of ligands selected from the previous list, return the ligands included in the first but not the second list.

Parameters

  • ligand_list_full – A list of List[AnalysisActorClass] containing the full set of ligands

  • ligand_list_selected – A list of List[AnalysisActorClass] containing a subset of the ligand_list_full

Returns

A list of List[AnalysisActorClass] containing the complement of the two sets above

MDSimsEval.utils.create_analysis_actor_dict(root_directory)

Reads the simulations (topologies, trajectories and sasa.xvg, salts if available) and stores them in a dictionary structure. The dictionary structure called analysis_actors_dict is the core structure that our functions take as an argument.

Example:
from MDSimsEval.utils import create_analysis_actor_dict
analysis_actors_dict = create_analysis_actor_dict('path_to_data_directory/')

analysis_actors_dict['Agonists'][0].info()
Out:
    <<< Info of 5-MeOT >>>
    Number of Frames: 2500
    Number of Atoms: 4743
    Number of Residues: 291
Parameters

root_directory (str) – The path of the input directory having the expected structure on the documentation

Returns

analysis_actors_dict:

Dict(
    "Agonists": List[AnalysisActor.class]
    "Antagonists": List[AnalysisActor.class]
  )

MDSimsEval.utils.render_corr_df(corr_df, filepath, reversed=False)

Renders and saves a correlation heatmap which is visually interpretable.

rmsf corr figure missing

Correlation heatmap, click for higher resolution.

Note

In order to save the image as .png you must install wkhtmltopdf via sudo apt-get install wkhtmltopdf on your machine. Else the output will be in a .html file and can be viewed using any browser.

Parameters

  • corr_df (pd.DataFrame) – A DataFrame of pairwise correlations

  • filepath (str) – The full path the heatmap save location eg. /dir1/dir2/name_of_file

  • reversed (boolean) – If you want the coolwarm colormap to be inversed