gemmi.NeighborSearch class

Classes

class Mark

Methods

def add_atom(self, atom: Atom, n_ch: int, n_res: int, n_atom: int) -> None

Lower-level alternative to populate()

def add_chain(self, chain: Chain, include_h: bool = True) -> None

def dist(self, arg0: Position, arg1: Position, /) -> float

def find_atoms(self, pos: Position, alt: str = '\x00', *, min_dist: float = 0, radius: float = 0) -> VectorMarkPtr

def find_nearest_atom(self, pos: Position, radius: float = inf) -> Mark

def find_neighbors(self, atom: Atom, min_dist: float = 0, max_dist: float = 0) -> VectorMarkPtr

def find_site_neighbors(self, atom: SmallStructure.Site, min_dist: float = 0, max_dist: float = 0) -> VectorMarkPtr

def get_image_transformation(self, arg0: int, /) -> FTransform

def populate(self, include_h: bool = True) -> NeighborSearch

Usually run after constructing NeighborSearch.

Special methods

def __init__(self, model: Model, cell: UnitCell, max_radius: float) -> None

def __init__(self, st: Structure, max_radius: float, model_index: int = 0) -> None

def __init__(self, small_structure: SmallStructure, max_radius: float) -> None

def __repr__(self, /) -> str

Properties

grid_cell: UnitCell get

radius_specified: float get