psiresp.grid.GridOptions
- pydantic model psiresp.grid.GridOptions[source]
Options for setting up the grid for ESP computation
- Fields:
- field grid_rmax: float = -1
Maximum radius around atom for constructing shells. If set to -1, no points are clipped.
- field use_radii: Literal['bondi_orig', 'bondi', 'mantina', 'alvarez', 'msk'] = 'msk'
Name of the radius set to use
- field vdw_radii: Dict[str, float] [Optional]
Dictionary of specific VDW radii to override the radii the use_radii set
- field vdw_scale_factors: List[float] = [1.4, 1.6, 1.8, 2.0]
Scale factors used to generate grid shells
- generate_connolly_spheres(radii)[source]
Compute Connolly spheres of specified radii and density around each atom.
- Parameters:
radii (1D numpy.ndarray of floats) – scaled radii of elements
- Returns:
points – cartesian coordinates of points
- Return type:
list of numpy.ndarray of shape (N, 3)
- static generate_unit_sphere(n_points)[source]
Get coordinates of n points on a unit sphere.
Adapted from GAMESS.
- Parameters:
n_points (int) – maximum number of points
- Returns:
coordinates – cartesian coordinates of points
- Return type:
np.ndarray
- get_hash()
- get_shell_within_bounds(radii, coordinates)[source]
Filter shell points to lie between inner_bound and outer_bound
- Parameters:
radii (numpy.ndarray) – This has shape (N,) where N is the number of atoms
spheres (numpy.ndarray) – This has shape (N, M, 3)
coordinates (numpy.ndarray) – This has shape (N, 3)
- Returns:
with shape (L, 3)
- Return type:
- property all_vdw_radii
- property effective_rmax