ls_mlkit.util.nma.nma module

ls_mlkit.util.nma.nma.get_nma_displacement_from_node_coordinates(node_coordinates: Tensor, cutoff_distance: float = 10.0, indexes: list[int] = [6], node_mask: Tensor = None) → Tensor

node_coordinates: shape = (…, n, 3) node_mask: shape = (…, n)

ls_mlkit.util.nma.nma.get_nma_displacement_from_protein_ligand_complex(protein_ca_coordinates: Tensor, ligand_center_of_mass: Tensor, cutoff_distance: float = 10.0, indexes: list[int] = [6], protein_mask: Tensor = None) → Tensor

protein_ca_coordinates: shape = (…, n, 3), ligand_center_of_mass: shape = (…, 3) protein_mask: shape = (…, n)

Returns:

shape = (…, k, n, 3) or (…, n, 3) if k == 1, where k is the number of normal modes, n is the number of atoms, and 3 is the number of coordinates (x, y, z)

Return type:

displacements