def __init__(
self,
step_size=0.1,
distance_threshold=1.5,
scale_steps=False,
):
"""
Initialize an instance of :class:`.PeriodicCollapser`.
Parameters
----------
step_size : :class:`float`, optional
The relative size of the step to take during collapse in
Angstrom.
distance_threshold : :class:`float`, optional
Distance between distinct building blocks to use as
threshold for halting collapse in Angstrom.
scale_steps : :class:`bool`, optional
Whether to scale the step of each distinct building block
by its relative distance from the molecules centroid.
"""
self._optimizer = mch.Collapser(
step_size=step_size,
distance_threshold=distance_threshold,
scale_steps=scale_steps,
)
def collapser():
return mch.Collapser(
step_size=0.05,
distance_threshold=1.5,
scale_steps=True,
)
mch_mol = mch.Molecule(
atoms=(mch.Atom(
id=atom.get_id(),
element_string=atom.__class__.__name__,
) for atom in cage.get_atoms()),
bonds=(mch.Bond(id=i,
atom_ids=(
bond.get_atom1().get_id(),
bond.get_atom2().get_id(),
)) for i, bond in enumerate(cage.get_bonds())),
position_matrix=cage.get_position_matrix(),
)
optimizer = mch.Collapser(
step_size=0.05,
distance_threshold=1.2,
scale_steps=True,
)
subunits = get_subunits(mol=cage)
# Get all steps.
mch_mol, mch_result = optimizer.get_trajectory(
mol=mch_mol,
bond_pair_ids=stk_long_bond_ids,
subunits=subunits,
)
cage = cage.with_position_matrix(mch_result.get_final_position_matrix())
cage.write('coll_poc_opt.mol')
with open('coll_opt.out', 'w') as f:
f.write(mch_result.get_log())