stko.Optimizer

class stko.Optimizer(*args, **kwargs)

Bases: Protocol

A base class for optimizers.

Optimizers are objects used to optimize molecules. Each optimizer is initialized with some settings and can optimize a molecule with optimize().

import stk
import stko

mol = stk.BuildingBlock('NCCCN', [stk.PrimaryAminoFactory()])
mmff = stko.MMFF()
mol = mmff.optimize(mol)

# Optimizers also work with ConstructedMolecule objects.
polymer = stk.ConstructedMolecule(
    topology_graph=stk.polymer.Linear(
        building_blocks=(mol, ),
        repeating_unit='A',
        num_repeating_units=3,
    )
)
etkdg = stko.ETKDG()
polymer = etkdg.optimize(polymer)

Sometimes it is desirable to chain multiple optimizations, one after another. For example, before running an optimization, it may be desirable to embed a molecule first, to generate an initial structure. OptimizerSequence may be used for this.

# Create a new optimizer which chains the previously defined
# mmff and etkdg optimizers.
optimizer_sequence = stko.OptimizerSequence(etkdg, mmff)

# Run each optimizer in sequence.
polymer = optimizer_sequence.optimize(polymer)

Making New Optimizers:

New optimizers can be made by simply making a class which defines a optimize() method. The method must take 1 mandatory mol parameter. optimize() will take the mol and change its structure in whatever way it likes. Beyond this there are no requirements. New optimizers can be added into the optimizers submodule or into a new submodule.

Methods

optimize

Optimize mol.

optimize(mol)

Optimize mol.

Parameters:

mol (MoleculeT) – The molecule to be optimized.

Returns:

The optimized molecule.

Return type:

MoleculeT