nuri.desc

nuri.desc.shrake_rupley_sasa(*args, **kwargs)

Overloaded function.

  1. shrake_rupley_sasa(mol: nuri.core._core.Molecule, conf: int = 0, nprobe: int = 92, rprobe: float = 1.4) -> numpy.ndarray[numpy.float64]

Calculate the Solvent-Accessible Surface Area (SASA) of a molecule conformation using the Shrake-Rupley algorithm.

Parameters:

  • mol – The input molecule.

  • conf – The conformation index. If not specified, uses the first conformation.

  • nprobe – The number of probe spheres. Default is 92.

  • rprobe – The radius of the probe spheres. Default is 1.4 angstroms.

Returns:

The calculated SASA values per atom (in angstroms squared).

Raises:

  • IndexError – If the conformation index is out of range.

  • ValueError – If nprobe or rprobe is not positive.

Note

This function does not automatically handle implicit hydrogens. If the molecule contains implicit hydrogens, consider revealing them before calling this function for accurate results (see nuri.core.Molecule.reveal_hydrogens()).

  1. shrake_rupley_sasa(pts: object, radii: object, nprobe: int = 92, rprobe: float = 1.4) -> numpy.ndarray[numpy.float64]

Calculate the Solvent-Accessible Surface Area (SASA) of a molecule conformation using the Shrake-Rupley algorithm.

Parameters:

  • pts – The coordinates of the atoms, as a 2D array of shape (N, 3).

  • radii – The radii of the atoms, as a 1D array of shape (N,).

  • nprobe – The number of probe spheres. Default is 92.

  • rprobe – The radius of the probe spheres. Default is 1.4 angstroms.

Returns:

The calculated SASA values per atom (in angstroms squared).

Raises:

ValueError – If the number of pts and radii do not match, any radii are not positive, nprobe is not positive, or rprobe is not positive.