API Documentation for bindingmodes
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.. py:class:: BindingModeProcesser(pdb_md, ligand, peptide, special, ligand_rings, interaction_list, threshold, total_frames)

    A class that processes protein-ligand interaction data for a given molecular dynamics (MD) simulation trajectory.
    The class performs multiple analyses on interaction data, such as filtering interactions based on frequency, 
    generating fingerprints according to the combination of interactions present in frames creating specific binding modes.

    :ivar str pdb_md: The path to the molecular dynamics (MD) PDB file for the protein-ligand complex.
    :ivar str ligand: The ligand information (e.g., name or structure).
    :ivar str or None peptide: The peptide chain ID, if applicable, or None if not considered.
    :ivar bool special: Special handling or unique identifiers related to the ligand or protein.
    :ivar list ligand_rings: List of ligand ring information used for hydrophobic interaction detection.
    :ivar pd.DataFrame interaction_list: DataFrame containing the interactions for the trajectory frames.
    :ivar float threshold: The threshold for filtering interactions based on their occurrence frequency.
    :ivar int total_frames: The total number of frames in the molecular dynamics simulation trajectory.
    :ivar dict unique_columns_rings_grouped: A dictionary containing the grouped interactions based on frames.
    :ivar pd.DataFrame interactions_all: DataFrame containing all interaction data processed.
    :ivar dict unique_data_all: Dictionary of unique data generated for all interactions across all frames.
    :ivar dict unique_data: Dictionary of unique data generated based on filtered interactions and threshold.

    .. py:method:: _gather_interactions(df)

        Process a DataFrame with the protein-ligand interaction and generate column names for each unique interaction.

        :param pd.DataFrame df: DataFrame that contains the interaction data for the whole trajectory.
        :returns: A dictionary with the keys being 'FRAME' numbers and values being dictionaries containing row indices and their corresponding unique column names for interactions.
        :rtype: dict

    .. py:method:: _process_interaction_wraper(interaction_list, threshold)

        Apply filtering and interaction enumeration to an interaction DataFrame.

        :param pd.DataFrame interaction_list: Interaction data obtained from the MD simulation.
        :param float threshold: Threshold for interaction occurrence (as a fraction of total frames).
        :returns: 
            - **interaction_list** (*pd.DataFrame*): Modified DataFrame including new interaction columns that contain the filtered values.
            - **unique_data** (*dict*): Dictionary containing unique filtered interaction names.
        :rtype: tuple[pd.DataFrame, dict]

    .. py:method:: _filtering_values(threshold, df)

        Filter and append values (interactions) to a DataFrame based on occurrence counts.

        :param float threshold: A threshold value that is used for filtering of the values (interactions) based upon the occurence count.
        :param pd.DataFrame df: DataFrame to which the filtered values (interactions) will be added.
        :returns: A list of values, with unique values and their corresponding occurence counts.
        :rtype: list of str

    .. py:method:: _unique_data_generation(filtered_values)

        Generate a dictionary conataing the unique interactions from a list of filtered values obtained by filtering_values.

        :param list of str filtered_values: A list of values, where the unique interactions are extracted from.
        :returns: A dictionary containing the filtered unique interactions.
        :rtype: dict

    .. py:method:: _df_iteration_numbering(df, unique_data)

        Loop through the DataFrame and assign the values 1 and 0 to the rows, depending if the corresponding interaction from unique data is present.

        :param pd.DataFrame df: DataFrame which has the interaction data for all of the frames.
        :param dict unique_data: Dictionary that contains the unique interactions obtained from unique_data_generation.
        :returns: None. Modifies the input DataFrame in-place by appending columns corresponding to recurring interactions.
        :rtype: None