qp.cluster.spheres_bad¶

Extract active site coordination sphere clusters

Usage:

>>> from qp.cluster import spheres

>>> spheres.extract_clusters(
...     "path/to/PDB.pdb",
...     "path/to/out/dir/",
...     center_residues=["FE", "FE2"], # List of resnames of the residues to use as the cluster center
...     sphere_count=2,              # Number of spheres to extract
...     ligands=["AKG"]       # PDB IDs of additional ligands
... )

Extracting clusters leaves open valences in the outermost sphere. Capping may be performed by specifying capping in spheres.extract_clusters:

1. No capping. (Default)
1. Cap with hydrogens.
1. Cap with ACE/NME groups.

Functions

`box_outlier_thres`	Compute the threshold for the boxplot outlier detection method
`build_heavy`	Cap with ACE/NME, building based on the upstream or downstream residue
`build_hydrogen`	Cap with hydrogen, building based on the upstream or downstream residue
`calc_dist`	Calculate the Euclidean distance between two points
`cap_chains`	Cap chain breaks for a set of extracted residues
`check_NC`	Check if a nitrogen / carbon atom in the first sphere is coordinated.
`check_atom_valence`
`complete_oligomer`
`compute_charge`	Computes the total charge of coordinating AAs
`count_residues`	Counts the frequency of coordinating residues
`extract_clusters`	Extract active site coordination spheres.
`fill_dummy`	Fill dummy atoms in a point cloud
`get_center_residues`
`get_grid`	Compute the grid's parameter for a given 1D point list
`get_grid_coord_idx`	Compute a point's position in a 1D grid
`get_next_neighbors`	Iteratively determines spheres around a given starting atom
`get_normalized_vector`
`make_res_key`
`merge_centers`
`plot_voronoi_2d`	Plot a 2D Voronoi diagram from the atomic coordinates.
`plot_voronoi_3d`	Plot a 3D Voronoi diagram from the atomic coordinates, excluding dummy atoms.
`prune_atoms`	Prune residues from the cluster model to meet the max atom count constraint, while keeping specified ligands and co-factors.
`residue_in_ligands`
`scale_hydrogen`	Replaces an atom with hydrogen, rescaling the original bond length
`voronoi`	Computes the Voronoi tessellation of a protein structure.
`write_pdbs`	Write coordination sphere to PDB file.