cgexplore.optimisation.CGOMMOptimizer

class cgexplore.optimisation.CGOMMOptimizer(fileprefix, output_dir, max_iterations=None, atom_constraints=None, platform=None)

Bases: object

Optimiser of CG models using OpenMM.

Methods

calculate_energy	Calculate energy of a system.
calculate_energy_decomposition	Calculate energy of a system.
optimize	Optimize a molecule.
read_final_energy_decomposition	Read the final energy decomposition in an output file.

Parameters:

• fileprefix (str)

• output_dir (Path)

• max_iterations (int | None)

• atom_constraints (Iterable[tuple[int, int]] | None)

• platform (str | None)

calculate_energy(assigned_system)

Calculate energy of a system.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

float

calculate_energy_decomposition(assigned_system)

Calculate energy of a system.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

dict[str, float]

optimize(assigned_system)

Optimize a molecule.

Parameters:

assigned_system (AssignedSystem | MartiniSystem)

Return type:

Molecule

read_final_energy_decomposition()

Read the final energy decomposition in an output file.

Return type:

dict[str, tuple[float, str]]