Coords

stereomolgraph.coords.are_planar(points: np.ndarray[tuple[N, THREE], NP_FLOAT], threshold: float = 0.35) → np.bool_

Checks if all atoms are in one plane

Checks if the all atoms are planar within a given threshold. The threshold is the maximal distance of an atom from the plane of three other atoms.

Parameters:

• points (np.ndarray) – coordinates of the atoms

• threshold (float) – maximal distance of atom from plane [Angstrom] (default: 0.35)

Returns:

True if all atoms are planar

Return type:

bool

stereomolgraph.coords.handedness(coords: ndarray[tuple[Literal[4], Literal[3]], NP_FLOAT]) → ndarray[tuple[Literal[1]], dtype[int8]]

Calculates the orientation of the atom 4 from the plane defined by the first three atoms from their coordinates.

Return type:

ndarray[tuple[Literal[1]], dtype[int8]]

class stereomolgraph.coords.Geometry(atom_types: Sequence[int | str] = (), coords: ndarray[tuple[int, int], NP_FLOAT] = array([], shape=(0, 3), dtype=float64))

Represents a molecular geometry, i.e. the coordinates and atom types.

Parameters:

• atom_types (Sequence[int | str]) – tuple of Element objects (default: ())

• coords (ndarray[tuple[int, int], TypeVar(NP_FLOAT, bound= dtype[floating], contravariant=True)]) – Cartesian coordinates of atoms in Angstrom (default: array([], shape=(0, 3), dtype=float64))

classmethod from_xyz_file(path: PathLike[str] | str) → Geometry

Create a Geometry from an XYZ file.

Return type:

Geometry

classmethod from_xyz(xyz_string: str) → Geometry

Create a Geometry from an XYZ-format string.

This mirrors from_xyz_file() but reads from a string instead of a file path.

Return type:

Geometry

classmethod from_xyz_file_multi(path: PathLike[str] | str) → tuple[Geometry, ...]

Create multiple Geometries from an XYZ file containing multiple structures.

Parameters:

path (PathLike[str] | str) – Path to XYZ file containing one or more structures

Return type:

tuple[Geometry, ...]

Returns:

Tuple of Geometry objects

classmethod from_xyz_multi(xyz_string: str) → tuple[Geometry, ...]

Create multiple Geometries from an XYZ-format string containing multiple structures.

Parameters:

xyz_string (str) – XYZ-format string containing one or more structures

Return type:

tuple[Geometry, ...]

Returns:

Tuple of Geometry objects

xyz_str(comment: None | str = None) → str

returns the xyz representation of this geometry as a string

Parameters:

comment (None | str) – comment for 2nd line of xyz file (default: None)

Return type:

str

Returns:

xyz representation of this geometry