spindry.Spinner

class spindry.Spinner(step_size, rotation_step_size, num_conformers, max_attempts=1000, potential_function=None, beta=2, random_seed=1000)[source]

Bases: object

Generate host-guest conformations by rotating guest.

A Metroplis MC algorithm is applied to perform rigid translations and rotations of the guest, relative to the host.

Methods

`compute_potential`	Compute the potential of a supramolecule.
`get_conformers`	Get conformers of supramolecule.
`get_final_conformer`	Get final conformer of supramolecule.

Parameters:

step_size (float)
rotation_step_size (float)
num_conformers (int)
max_attempts (int)
potential_function (Potential | None)
beta (float)
random_seed (int | None)

compute_potential(supramolecule)[source]

Compute the potential of a supramolecule.

Parameters:: supramolecule (SupraMolecule)
Return type:: float

get_conformers(supramolecule, movable_components=None, verbose=False)[source]

Get conformers of supramolecule.

Parameters:

supramolecule (SupraMolecule) – The supramolecule to optimize.
movable_components (tuple[int, ...] | None) – Components of supramolecule to move during simulation.
verbose (bool) – True to print some extra information.

Yields:

conformer –

SupraMolecule: The host-guest supramolecule.

Return type:

abc.Iterable[mch.Molecule]

get_final_conformer(supramolecule, movable_components=None)[source]

Get final conformer of supramolecule.

Parameters:

supramolecule (SupraMolecule) – The supramolecule to optimize.
movable_components (tuple[int, ...] | None) – Components of supramolecule to move during simulation. If None, then moved components are selected randomly, and the largest component (host) is not moved.

Returns:

The host-guest supramolecule.

Return type:

conformer