Mutual Information Calculation — mdpath.src.mutual_information

This module contains the class NMICalculator which calculates the Normalized Mutual Information (NMI) for all residue pairs in a given dataset based on the dihedral angle movements over the course of the analysed MD trajectory.

Classes

NMICalculator

class mdpath.src.mutual_information.NMICalculator(df_all_residues: DataFrame, num_bins: int = 35, invert=False)

Bases: object

Calculate Normalized Mutual Information (NMI) between dihedral angle movements of residue pairs.

Attributes:

df_all_residues (pd.DataFrame): DataFrame containing all residues.

num_bins (int): Number of bins to use for histogram calculations. Default is 35.

nmi_df (pd.DataFrame): DataFrame containing the mutual information differences. Is calculated using either GMM or histogram method.

entropy_df (pd.DataFrame): Pandas dataframe with residue and entropy values. Is calculated using either GMM or histogram method.

NMI_calcs()

Extended Normalized Mutual Information and Entropy calculation.