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Radii Assignment

Utility functions for determining the van der Waals of atoms in a molecule. It provides two functions that achieve the same goal but in different ways; the first one iterates over the atoms in the molecule which can be time-consuming, while the second one utilizes a vectorized operation for faster performance.

assign_radii 

assign_radii(mol)

Get the van der Waals for each atom in the molecule.

Parameters:

Name Type Description Default
mol MolType

The OBMol object for which to determine the van der Waals radii.

 required

Returns:

Type Description
radii_array

An array of shape (n_atoms,) containing the van der Waals radii for each atom in the molecule.
Source code in lahuta/utils/radii.py 
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def assign_radii(mol: MolType) -> NDArray[np.float32]:
    """Get the van der Waals for each atom in the molecule.


    Args:
        mol (MolType): The OBMol object for which to determine the van der Waals radii.

    Returns:
        (radii_array):  An array of shape (n_atoms,) containing the van der Waals \
                        radii for each atom in the molecule.
    """
    atom_radii = np.zeros(mol.NumAtoms(), dtype=float)
    for atom in ob.OBMolAtomIter(mol):
        atom_radii[atom.GetId()] = ob.GetVdwRad(atom.GetAtomicNum())
    return atom_radii

v_radii_assignment 

v_radii_assignment(elements)

Determine the van der Waals radii for each atom in the molecule using vectorized operation.

This function is a faster alternative to 'assign_radii' as it utilizes numpy's vectorized operations for improved performance when dealing with large molecules.

Parameters:

Name Type Description Default
elements NDArray[str_]

An array of atomic element symbols.

 required

Returns:

Type Description
NDArray[float32]

NDArray[np.float32]: An array of shape (n_atoms, ) where each element is the van der Waals radius.
Source code in lahuta/utils/radii.py 
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def v_radii_assignment(elements: NDArray[np.str_]) -> NDArray[np.float32]:
    """Determine the van der Waals radii for each atom in the molecule using vectorized operation.

    This function is a faster alternative to 'assign_radii' as it utilizes numpy's vectorized operations
    for improved performance when dealing with large molecules.

    Args:
        elements: An array of atomic element symbols.

    Returns:
        NDArray[np.float32]: An array of shape (n_atoms, ) where each element is the van der Waals radius.
    """
    vdwradii: dict[str, int] = {k.capitalize(): v for k, v in MDA_VDW_RADII.items()}

    def v_capitalize(array: NDArray[np.str_], mapping: dict[str, int]) -> NDArray[np.float32]:
        vfunc = np.vectorize(mapping.get, otypes=[np.float32])
        radii: NDArray[np.float32] = vfunc(array)
        return radii

    return v_capitalize(elements, vdwradii)