openpharmacophore.ComplexBindingSite

class openpharmacophore.ComplexBindingSite(protein, ligand)

Bases: AbstractBindingSite

Class to extract and find chemical features in the binding site of a protein-ligand complex.

Parameters:

• protein (openpharmacophore.Protein)

• ligand (openpharmacophore.Ligand)

Methods

get_atoms	Get the indices of the atoms in the binding site.
get_chem_feats	Get the chemical features of the binding site at the specified frame.
get_residues	Get the indices of the residues in the protein that correspond to the binding site.
to_rdkit	Returns the binding site as an rdkit molecule.

get_atoms(frame)

Get the indices of the atoms in the binding site. This will include the ligand atoms as well.

Parameters:

frame (int)

Returns:

Array with the atom indices

Return type:

np.ndarray

get_chem_feats(frame, types=None)

Get the chemical features of the binding site at the specified frame.

Parameters:

• frame (int)

• types (set[str], optional) – Types of features to search for. If none all feat types will be used.

Return type:

ChemFeatContainer

get_residues(frame)

Get the indices of the residues in the protein that correspond to the binding site.

The binding site is defined as the sphere with centroid at the ligand centroid with a radius of ligand maximum extent plus a cutoff distance.

Parameters:

frame (int)

Returns:

Indices of the residues that encompass the binding site

Return type:

list[int]

to_rdkit()

Returns the binding site as an rdkit molecule.

Return type:

rdkit.Chem.Mol