VinaResult

class biotite.application_v2.autodock.VinaResult(ligand_models: AtomArrayStack, ligand_coord: np.ndarray, flexible_residue_models: AtomArrayStack, receptor_coord: np.ndarray, energies: np.ndarray)

Bases: object

The result of an AutoDock Vina docking run.

Attributes:

ligand_modelsAtomArrayStack

The docked ligand. Each model corresponds to one binding mode. The models are sorted from best to worst predicted binding affinity. The returned structure may contain less atoms than the input structure, as Vina removes nonpolar hydrogen atoms. Furthermore, the returned structure contains AutoDock atom types as element annotation.

ligand_coordndarray, shape=(m,n,3), dtype=float

The coordinates for m binding modes and n atoms of the input ligand. The models are sorted from best to worst predicted binding affinity. Missing coordinates due to the removed nonpolar hydrogen atoms are set to NaN.

flexible_residue_modelsAtomArrayStack

The docked side chains. Each model corresponds to one binding mode. The models are sorted from best to worst predicted binding affinity. If no flexible side chains were defined, this AtomArrayStack contains no atoms. The returned structure may contain less atoms than the input structure, as Vina removes nonpolar hydrogen atoms. Furthermore, the returned structure contains AutoDock atom types as element annotation.

receptor_coordndarray, shape=(m,n,3), dtype=float

The coordinates for m binding modes and n atoms of the input receptor. The models are sorted from best to worst predicted binding affinity. Missing coordinates due to the removed nonpolar hydrogen atoms from flexible side chains are set to NaN. The output is only meaningful, if flexible side chains were defined. Otherwise, the coordinates are simply m repetitions of the input receptor coordinates.

energiesndarray, dtype=float

The predicted binding energies (kcal/mol). The energies are sorted from best to worst.

Gallery

Docking a ligand to a receptor

Docking a ligand to a receptor