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 grid_rmin: float = 0: Minimum radius around atom for constructing shells

field use_radii: Literal['bondi_orig', 'bondi', 'mantina', 'alvarez', 'msk'] = 'msk': Name of the radius set to use

field vdw_point_density: float = 1.0: Point density in the generated grid shells

field vdw_radii: Dict[str, float] [Required]: 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)

generate_grid(molecule, client=None)[source]

Generate VdW surface points

Parameters

molecule (Union[str, int, Dict[str, Any], qcelemental.models.Molecule, qcfractal.interface.models.records.ResultRecord]) –
client (Optional[qcfractal.interface.client.FractalClient]) –

Return type

numpy.ndarray

static generate_unit_sphere(n_points)[source]

Get coordinates of n points on a unit sphere.

Adapted from GAMESS.

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

numpy.ndarray

get_vdwradii_for_elements(symbols)[source]

Return an array of VdW radii for the specified elements