morfeus.pyramidalization module

Pyramidalization code.

class morfeus.pyramidalization.Pyramidalization(coordinates, atom_index, neighbor_indices=None, elements=None, radii=None, radii_type='pyykko', excluded_atoms=None, method='distance', scale_factor=1.2)[source]

Bases: object

Calculates and stores results of pyramidalization and alpha angle.

As described in Struct. Chem. 1991, 2, 107 and alternatively according to bond angles as in J. Comput. Chem. 2012, 33 (27), 2173–2179.

Parameters:

  • coordinates (ArrayLike2D) – Coordinates (Å)

  • atom_index (int) – Index of pyramidalized atom (1-indexed)

  • neighbor_indices (list[int]) – Indices of neighbors to pyramidalized atom

  • elements (Iterable[int] | Iterable[str] | None) – Elements as atomic symbols or numbers

  • radii (ArrayLike1D | None) – Covalent radii used to determine connectivity (Å)

  • radii_type (str) – Covalent radii type: ‘pyykko’

  • excluded_atoms (Sequence[int] | None) – Indices of atoms to exclude

  • method (str) – Method for detecting neighbors: ‘connectivity’ or ‘distance’. Ignored if neighbor_indices is given.

  • scale_factor (float)

alpha

Average alpha angle (degrees)

Type:

float

alphas

Alpha angles for all permutations of neighbors (degrees)

Type:

Any

neighbor_indices

Indices of neighbors to pyramidalized atom

Type:

list[int]

P_angle

Pyramidalization according to Gavrish

Type:

float

P

Pyramidalization according to Radhakrishnan

Type:

float

print_report()[source]

Print report of results.

Return type:

None

morfeus.pyramidalization.cli(file)[source]

CLI for pyramidalization.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any