morfeus.cone_angle module

Cone angle code.

class morfeus.cone_angle.ConeAngle(elements, coordinates, atom_1, radii=None, radii_type='crc', method='libconeangle')[source]

Bases: object

Calculates and stores the results of exact cone angle calculation.

As described in J. Comput. Chem. 2013, 34, 1189.

Parameters:

  • elements (Iterable[int] | Iterable[str]) – Elements as atomic symbols or numbers

  • coordinates (ArrayLike2D) – Coordinates (Å)

  • atom_1 (int) – Index of central atom (1-inexed)

  • radii (ArrayLike1D | None) – vdW radii (Å)

  • radii_type (str) – Type of vdW radii: ‘alvarez’, ‘bondi’, ‘crc’ or ‘truhlar’

  • method (str) – Method of calculation: ‘internal’ or ‘libconeangle’ (default)

cone_angle

Exact cone angle (degrees)

Type:

float

tangent_atoms

Atoms tangent to cone (1-indexed)

Type:

list[int]

Raises:

  • RunTimeError – If cone angle could not be found by internal algorithm

  • ValueError – If atoms within vdW radius of central atom or if exception happened with libconeangle or if wrong method chosen

Parameters:

  • elements (Iterable[int] | Iterable[str])

  • coordinates (ArrayLike2D)

  • atom_1 (int)

  • radii (ArrayLike1D | None)

  • radii_type (str)

  • method (str)

print_report()[source]

Prints report of results.

Return type:

None

morfeus.cone_angle.cli(file)[source]

CLI for cone angle.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any