Clustering

Summary This script will generate files to cluster a SubPEx run

calculate_clusters_per_bin(bins, settings)

Calculates the number of clusters per bin. Updates bin in place.

PARAMETER	DESCRIPTION
bins	A dictionary with the bins and the walkers in each bin. TYPE: dict
settings	The settings dictionary. TYPE: dict

create_bin_cpptraj_files(bins, settings, directory)

Creates the cpptraj files for each bin.

PARAMETER	DESCRIPTION
bins	A dictionary with the bins and the walkers in each bin. TYPE: dict
settings	The settings dictionary. TYPE: dict
directory	The directory where the cpptraj files will be created. TYPE: str

create_cpptraj_file_bins(bins, settings, directory, key, selection_string)

Creates the cpptraj file for a bin.

PARAMETER	DESCRIPTION
bins	A dictionary with the bins and the walkers in each bin. TYPE: dict
settings	The settings dictionary. TYPE: dict
directory	The directory where the cpptraj files will be created. TYPE: str
key	The name of the bin. TYPE: str
selection_string	The selection string that will be used. TYPE: str

get_bins_dictionary(west, settings)

Creates a dictionary with the bins and the walkers in each bin.

PARAMETER	DESCRIPTION
west	The west.h5 file as a dictionary. TYPE: dict
settings	The settings dictionary. TYPE: dict

RETURNS	DESCRIPTION
dict	A dictionary with the bins and the walkers in each bin. TYPE: MutableMapping[str, Any]

get_clustering_bins_cpptraj(west, settings, directory)

Creates the input files (sh) for cpptraj to cluster the bins.

PARAMETER	DESCRIPTION
west	The west.h5 file. TYPE: dict
settings	The settings dictionary. TYPE: dict
directory	The directory where the input files will be created. TYPE: str

get_clustering_command_cpptraj(method, num_clusters, selection_string)

Creates the clustering command for cpptraj.

PARAMETER	DESCRIPTION
method	the clustering method to use. Currently, only hierarchical is implemented. TYPE: str
num_clusters	The number of clusters to use. TYPE: int
selection_string	The selection string for cpptraj. TYPE: str

RETURNS	DESCRIPTION
str	The clustering command for cpptraj. TYPE: str

get_clustering_generation_cpptraj(west_file, settings, directory)

Creates the cpptraj files for each bin.

PARAMETER	DESCRIPTION
west_file	The west.h5 file contents. TYPE: dict
settings	The settings dictionary. TYPE: dict
directory	The directory where the cpptraj files will be created. TYPE: str

get_generation_walkers_list(directory_gen)

Gets the list of walkers for a given generation.

PARAMETER	DESCRIPTION
directory_gen	The directory where the generation is. TYPE: str

RETURNS	DESCRIPTION
List[str]	List[str]: The list of walkers.

get_number_clusters_generation(west_file, max_clusters, min_clusters=3)

Gets the number of clusters for each generation.

PARAMETER	DESCRIPTION
west_file	The west.h5 file. TYPE: dict
max_clusters	The maximum number of clusters to use. TYPE: int
min_clusters	The minimum number of clusters to use. Defaults to 3. TYPE: int DEFAULT: 3

RETURNS	DESCRIPTION
List[int]	List[int]: The number of clusters for each generation.

get_selection_cpptraj(filename)

Takes the filename of the selection string used in SubPEx and returns a selection string formated for cpptraj. The selection will take all heavy atoms of each of the residues.

PARAMETER	DESCRIPTION
filename	The filename of the selection string used in SubPEx. TYPE: str

RETURNS	DESCRIPTION
str	The selection string formated for cpptraj. TYPE: str

make_input_file_cpptraj(directory, walkers_list, settings, num_clusters, selection_string)

Creates the input file for cpptraj.

PARAMETER	DESCRIPTION
directory	The directory where the input file will be created. TYPE: str
walkers_list	The list of walkers for the generation. TYPE: List[str]
settings	The settings dictionary. TYPE: dict
selection_string	The selection string for cpptraj. TYPE: str

run_clustering()