grid

Usage

The tetrahedral grid: ideal bond directions, angles, and lengths.

Attributes

Name	Description
TETRAHEDRAL_ANGLE	The ideal tetrahedral angle, arccos(-1/3) (about 109.47 degrees), in radians.
XH_LENGTH	Ideal bond length to hydrogen, in Angstroms.
XY_LENGTH	Ideal bond length between heavy atoms, in Angstroms.

TETRAHEDRAL_ANGLE

The ideal tetrahedral angle, arccos(-1/3) (about 109.47 degrees), in radians.

TETRAHEDRAL_ANGLE=float(np.arccos(-1 / 3))

XH_LENGTH

Ideal bond length to hydrogen, in Angstroms.

XH_LENGTH=1.1

XY_LENGTH

Ideal bond length between heavy atoms, in Angstroms.

XY_LENGTH=1.5

Functions

Name	Description
tetrahedral_basis()	Get the four bond directions of a tetrahedral grid.

tetrahedral_basis()

Get the four bond directions of a tetrahedral grid.

Usage

Source

tetrahedral_basis(
    up=(0.0, 0.0, 1.0),
    left=(-1.0, 0.0, 0.0),
)

Direction 0 points along up. Direction 1 lies in the plane of up and left, on the side of left. Directions 2 and 3 follow by rotating direction 1 about up by 120 and 240 degrees (counterclockwise, looking down from the tip of up).

Parameters

up: ArrayLike = (0.0, 0.0, 1.0): Direction 0.
left: ArrayLike = (-1.0, 0.0, 0.0): Direction in the plane of directions 0 and 1. Only its component perpendicular to up matters.

Returns

np.ndarray

Unit vectors, one per row, shape (4, 3). Each pair makes the

tetrahedral angle.

Raises

ValueError: If up is zero or left is parallel to up.

Examples

    >>> basis = tetrahedral_basis()
    >>> basis.round(6).tolist()[:2]

[[0.0, 0.0, 1.0], [-0.942809, 0.0, -0.333333]]