qp.cluster.spheres

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:

• 0. No capping. (Default)

• 1. Cap with hydrogens.

• 2. 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	Check whether a backbone atom already has sufficient bonded neighbors.
check_disulfide	Detect whether a cysteine residue is involved in a disulfide bond.
complete_oligomer	Ensure that partially included oligomeric ligands are fully added.
compute_charge	Computes the total charge of coordinating AAs
count_residues	Counts the frequency of coordinating residues
extract_clusters	Extract active site coordination spheres using Voronoi tessellation.
fill_dummy	Fill dummy atoms in a point cloud
format_plot	General plotting parameters for the Kulik Lab.
get_center_residues	Find all center residues in a model and optionally merge nearby ones.
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	Return the unit vector pointing from atom1 to atom2.
make_res_key	Format a residue as a 'RESNAME_CHAINID' string key (e.g., 'FE_A199').
merge_centers	Recursively merge center residues that are within a distance cutoff.
plot_voronoi_2d	Plot a 2D Voronoi diagram from the atomic coordinates, excluding unbounded vertices and filtering by x and y thresholds.
prune_atoms	Prune residues from the cluster to meet the max atom count constraint.
residue_in_ligands	Check whether a residue matches any key in the ligand charge dictionary.
scale_hydrogen	Replaces an atom with hydrogen, rescaling the original bond length
visualize_dummy	Write dummy atom positions to an XYZ file for debugging.
voronoi	Compute the Voronoi tessellation of a protein structure.
write_pdbs	Write coordination sphere to PDB file.

Classes

CenterResidue