Clustering

generate_clusters(df, field_name, sim_df, threshold=0.4, verbose=0, cluster_algorithm='greedy_incremental')

Generates clusters from a DataFrame.

Parameters:

Name	Type	Description	Default
df	DataFrame	DataFrame with entities to cluster.	required
field_name	str	Name of the field with the entity information (e.g., protein_sequence or structure_path), defaults to 'sequence'.	required
threshold	float	Similarity value above which entities will be considered similar, defaults to 0.4	0.4
sim_df	DataFrame	DataFrame with similarities (metric) between query and target, it is the product of calculate_similarity function	required
verbose	int	How much information will be displayed. Options: - 0: Errors, - 1: Warnings, - 2: All Defaults to 0	0
cluster_algorithm	str	Clustering algorithm to use. Options: - CDHIT or greedy_incremental - greedy_cover_set - connected_components Defaults to "CDHIT".	'greedy_incremental'

Returns:

Type	Description
pd.DataFrame	DataFrame with entities and the cluster they belong to.

Raises:

Type	Description
NotImplementedError	Clustering algorithm is not supported