protex.update.StateUpdate

class protex.update.StateUpdate(updateMethod: Update, prob_function: str = None)

Bases: object

Controls the update scheme and proposes the residues that need an update.

Parameters:

• updateMethod (Update) – The update method to be used. At the moment NaiveMCUpdate or KeepHUpdate.

• prob_function (str = None) – The function to be used for scaling down the transfer probabilities for distances between r_min and r_max. Currently implemented: None (strict cutoff at r_max, ignores r_min), “linear”, “cosine”, and “tanh”.

Methods

dump	Pickle the StateUpdate instance.
get_charges	Get charges of all atoms in the system.
get_num_residues	Deprecated 1.1.
load	Load a pickled StateUpdate instance.
update	Updates the current state using the method defined in the UpdateMethod class.
write_charges	Write current charges to a file.

dump(fname: str) → None

Pickle the StateUpdate instance.

Parameters:

fname (str) – The file name

get_charges() → list

Get charges of all atoms in the system. Deprecated with ChargeReporter.

Returns:

atom_idxs, atom object, charge

Return type:

list

Raises:

RuntimeError – If system does not contain a nonbonded force

get_num_residues() → dict

Deprecated 1.1.

static load(fname: str, updateMethod: Update) → StateUpdate

Load a pickled StateUpdate instance.

Parameters:

• fname (str) – The file name

• updateMethod (Update) – The update method instance

Returns:

An instance of StateUpdate

Return type:

StateUpdate

update(nr_of_steps: int = 2) → list[tuple[Residue, Residue]]

Updates the current state using the method defined in the UpdateMethod class.

Parameters:

nr_of_steps (int, optional) – The number of intermediate \({\lambda}\) states. The default of two means 1 with the initial and one with the final state, so no intermediate states, by default 2

Returns:

A list with all the updated residue tuples

Return type:

list[tuple[Residue, Residue]]

write_charges(filename: str) → None

Write current charges to a file. Deprecated with ChargeReporter.

Parameters:

filename (str) – The name of the file to wrtie the charges to