morfeus.bite_angle module#

Bite angle code.

class morfeus.bite_angle.BiteAngle(coordinates, metal_index, ligand_index_1, ligand_index_2, ref_atoms=None, ref_vector=None)[source]#

Bases: object

Performs and stores the results of a bite angle calculation.

The bite angle can become ‘inverted’ if it goes beyond 180°. This cannot be detected automatically, so the user has to supply a reference vector that should point in the ‘direction’ of the ligand. As a convenience, the vector can be constructed automatically from the metal atom to the geometric mean of a set of ‘ref_atoms’.

Parameters:

  • coordinates (ArrayLike2D) – Coordinates (Å)

  • metal_index (int) – Index of metal atom (1-indexed)

  • ligand_index_1 (int) – Index of first ligand atom (1-indexed)

  • ligand_index_2 (int) – Index of second ligand atom (1-indexed)

  • ref_vector (ArrayLike1D | None) – Reference vector for determining inverted bite angle

  • ref_atoms (Iterable[int] | None) – Reference atoms for determnining inverted bite angle (1-indexed)

angle#

Bite angle (degrees)

Type:

float

inverted#

Whether angle is ‘inverted’

Type:

bool

morfeus.bite_angle.cli(file)[source]#

CLI for bite angle.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any