WatCon.WatCon module

WatCon.WatCon.check_conditions(kwargs)[source]
WatCon.WatCon.parse_analysis(filename)[source]

Parse inputs from input file

Parameters:

filename (str) – Path of input file

Returns:

Dictionary of kwargs

Return type:

dict

WatCon.WatCon.parse_arguments()[source]

Parse arguments from command line

WatCon.WatCon.parse_inputs(filename)[source]

Parse inputs from input file

Parameters:

filename (str) – Path of input file

Returns:

  • str

    structure type (static/dynamic)

  • dict

    Dictionary of kwargs

Return type:

tuple

WatCon.WatCon.run_watcon(structure_type, kwargs)[source]

Run WatCon from input file

Parameters:

  • structure_type ({‘static’, ‘dynamic’}) – Type of input structures

  • kwargs (dict) – Key word arguments from parsed input file

Returns:

Results from initialize network

Return type:

tuple

WatCon.WatCon.run_watcon_postanalysis(concatenate=None, input_directory='watcon_output', histogram_metrics=False, residue_interactions=False, reference_topology=None, interaction_cutoff=0.0, calculate_densities=False, density_pdb=None, traj_directory=None, active_region_definition=None, image_output_dir='images', custom_selection=None, water_name=None, cluster_concatenated=False, cluster_method='hdbscan', eps=0.0, n_jobs=1, min_samples=100, cluster_filebase='CLUSTER', calculate_commonality=None, color_by_conservation=None, classify_waters=False, csv_dir='msa_classification')[source]

Run WatCon analysis from input file

Parameters:

  • concatenate (list) – List of files to concatenate when performing analysis. Default is None

  • input_directory (str) – Directory which contains input files. Default is ‘watcon_output’

  • histogram_metrics (bool) – Indicate whether to histogram calculated metrics. Default is False.

  • residue_interactiosn (bool) – Indicate whether to plot bar graphs of water-protein interactions at the residue level. Default is False.

  • reference_topology (str) – Full path to reference topology to be used for residue interaction analysis

  • calculate_densities (bool) – Calculate densities for combined simulation data. Default is False.

  • density_pdb (str) – PDB to use for density calculations. Default is None.

  • traj_directory (str) – Directory containing trajectories to be used when calculating densities. Default is None.

  • active_region_definition (str) – MDAnalysis selection language to define active site when calculating densities. Default is None.

  • image_output_dir (str) – Output directory for images. Default is ‘images’

  • custom_selection (str) – MDAnalysis selection language for classifying custom residues as ‘protein’. Default is None.

  • water_name (str) – Residue name of water (not necessary if water is WAT, SOL, H2O, or HOH). Default is None.

  • cluster_concatenated (bool) – Indicate whether to cluster coordinates across concatenate list. Default is False.

  • cluster_method ({‘hdbscan’, ‘optics’, ‘dbscan’}) – Cluster method (if cluster_concatenated). Default is ‘hdbscan’

  • eps (float) – Eps value for clustering method (if cluster_concatenated). Default is 0.0.

  • min_samples (int) – Min sample value for clustering method (if cluster_concatenated). Default is 100.

  • n_jobs (int) – Number of available cores for clustering

  • cluster_filebase (str) – Base of output files. Default is ‘CLUSTER’. OR Desired clustered pdb to calculate commonality

  • calculate_commonality ({‘bar’, ‘hist’, None}) – Indicate whether to calculate commonality score to a set of clusters and plot either as a bar graph (helpful for discrete static structures) or histogram (helpful for high dimensional dynamic data)

  • color_by_conservation ({‘all’, ‘centers’, ‘connections’, None}) – Color cluster centers by conservation, connections among cluster centers, or neither

  • classify_waters (bool) – Indicate whether to plot distributions of 2-angle calculations. Default is False.

  • csv_dir (str) – Directory containing csvs (for classify_waters)

Return type:

None

Notes

calculate_densities is NOT recommended for static structures due to sparsity in water positions

cluster_concatenated is NOT recommended for collections of large trajectories, calculate_densities is recommended instead

If f”{cluster_filebase}.pdb” already exists and cluster_concatenated == False, then the current clustering pdb will be used for analysis