WatCon.visualize_structures module

Create pdbs and pml files for visualization of water networks

WatCon.visualize_structures.export_graph_to_pdb(graph, output_file)[source]

Generate a PDB file with dummy oxygen atoms at the coordinates of a given graph.

Parameters:

  • graph (networkx.Graph) – The NetworkX graph containing node coordinates.

  • output_file (str) – Name of the output PDB file.

Return type:

None

WatCon.visualize_structures.plot_consevation_angles(cluster_conservation_dict, output_filebase='angle_clusters', output_dir='pymol_projections')[source]

Visualize two-angle water-protein conservation

Parameters:

  • cluster_conservation_dict (dict) – Dictionary obtained from WatCon.find_conserved_networks.identify_clustered_angles()

  • output_filebase (str, optional) – Filename base (no extension) for outputted .pml file. Default is ‘angle_clusters’

  • output_dir (str, optional) – Name of output directory. Default is ‘pymol_projections’

Return type:

None

WatCon.visualize_structures.project_clusters(coordinate_list, filename_base='CLUSTER', b_factors=None)[source]

Generate a PDB file to visualize cluster centers.

Parameters:

  • coordinate_list (array-like, dict) – List of coordinates representing cluster centers.

  • filename_base (str) – Naming scheme to use for the outputted PDB file.

  • b_factors (array-like, optional) – Optional list of values to replace the B-factor column.

Return type:

None

WatCon.visualize_structures.pymol_project_oxygen_network(network, filename='STATE.pml', out_path='pymol_projections', active_region_only=False, water_only=False)[source]

Generate a PyMOL (.pml) file to visualize the calculated network.

Parameters:

  • network (WaterNetwork) – The WaterNetwork object representing the network.

  • filename (str) – Name of the output .pml file.

  • out_path (str) – Directory where the output file will be saved.

  • active_region_only (bool, optional) – Whether to include only active site connections. Default is False.

  • water_only (bool, optional) – Whether to show only water-water connections. Default is False.

Return type:

None

WatCon.visualize_structures.save_xyz(network, filename='STATE.xyz')[source]

Generate an XYZ file containing graph coordinates.

Parameters:

  • network (WaterNetwork) – The WaterNetwork object containing graph data.

  • filename (str) – Name of the output XYZ file.

Return type:

None