protex.system.ProtexSystem

class protex.system.ProtexSystem(simulation: Simulation, templates: ProtexTemplates, simulation_for_parameters: Simulation | None = None, fast: bool = True)

Bases: object

Defines the full system, performs the MD steps and offers an interface for protonation state updates.

Parameters:

• simulation – the OpenMM simulation object

• templates – An instance of the IonicLiquidTemplates class

• simulation_for_parameters – another OpenMM simulation object, set up with a psf that contains all possible forms (protonated and deprotonated) of all species, needed for finding the parameters of the other form during an update

• fast – If True indices list for all forces for each residue will be made once at initilaizaiton of ProtexSystem, and then used for finding the indices during an update. If False, the whole forces.getNumExceptions and similar calls will be used for each update and each residue, which is way slower

Methods

dump	Pickle the current ProtexSystem object.
force_is_valid	Check if the given force name is covered.
get_current_number_of_each_residue_type	Get a dictionary with the resname and the current number of residues belonging to that name.
load	Load pickled protex system.
loadCheckpoint	Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.
loadState	Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.
load_updates	Load the current update values from a yaml file, which was generated using "save_updates".
saveCheckpoint	Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.
saveState	Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.
save_updates	Save the current update values into a yaml file.
update_context	Update the context for the given force.
write_psf	Write a new psf file, which reflects the occured transfer events and changed residues to load the written psf create a new ionic_liquid instance and load the new psf via OpenMM.

Attributes

COVERED_FORCES
IGNORED_FORCES
UNCOVERED_FORCES

dump(fname: str) → None

Pickle the current ProtexSystem object.

Parameters:

fname (str) – The file name to store the object

classmethod force_is_valid(name: str) → bool

Check if the given force name is covered.

get_current_number_of_each_residue_type() → dict[str, int]

Get a dictionary with the resname and the current number of residues belonging to that name.

Returns:

resname: number of residues

Return type:

dict[str, int]

static load(fname: str, simulation: Simulation, simulation_for_parameters: Simulation | None = None) → ProtexSystem

Load pickled protex system.

Parameters:

• fname (str) – The file name to load

• simulation (openmm.app.simulation.Simulation) – An already generated OpenMM simulation object, needed to initialize the ProtesSystem instance

• simulation_for_parameters (openmm.app.simulation.Simulation, optional) – An OpenMM simulation object, which contains all possible residues needed if the simulation object does not contain all possible residues, by default None

Returns:

A new instance of the ProtexSystem

Return type:

ProtexSystem

loadCheckpoint(file) → None

Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.

Parameters:

file (string or file) – a File-like object to load the checkpoint from, or alternatively a filename

loadState(file) → None

Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.

Parameters:

file (string or file) – a File-like object to load the state from, or alternatively a filename

load_updates(file) → None

Load the current update values from a yaml file, which was generated using “save_updates”.

Parameters:

file (string or file)

saveCheckpoint(file) → None

Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.

Parameters:

file (string or file) – a File-like object to write the checkpoint to, or alternatively a filename

saveState(file) → None

Wrapper method which just calls the underlying same function on the simulation object of the ionic liquid object.

Parameters:

file (string or file) – a File-like object to write the state to, or alternatively a filename

save_updates(file) → None

Save the current update values into a yaml file. Used to have the current probability values.

Parameters:

file (string or file)

update_context(name: str)

Update the context for the given force.

Parameters:

name (str) – The name of the force to update

write_psf(old_psf_infname: str, new_psf_outfname: str, psf_for_parameters: str | None = None) → None

Write a new psf file, which reflects the occured transfer events and changed residues to load the written psf create a new ionic_liquid instance and load the new psf via OpenMM.

Parameters:

• old_psf_infname – Name of the old psf_file, which serves for the basic strucutre, same number of atoms, same bonds, angles, …

• new_psf_outfname – Name of the new psf that will be written

• psf_for_parameters – Optional psf file which contains all possible molecules/states, if they are not represented by the old_psf_infname. I.e. one species gets protonated and is not present anymore, this file can be used to have all potential states.

Return type:

None