The ihm.multi_state_scheme Python module

class ihm.multi_state_scheme.MultiStateScheme(name, details=None, connectivities=None, relaxation_times=None)

MultiStateScheme collects information about a collection of multiple states, that can form a connected/ordered scheme. A special case is a kinetic scheme, for which kinetic rates and relaxation times are available.

Parameters:

• name (str) – The name of the multi-state scheme.

• details (str) – Details on the scheme.

• connectivities (List of Connectivity) – A list of connectivities that belong to the scheme.

• relaxation_times (List of RelaxationTime) – A list of relaxation times not assigned to specific connectivities, but to the scheme

add_connectivity(connectivity)

Add a connectivity to the scheme.

Parameters:

connectivity (Connectivity) – The connectivity to add to the scheme

add_relaxation_time(relaxation_time)

Add a relaxation time to the scheme. This relaxation time is not assigned to a connectivity.

Parameters:

relaxation_time (RelaxationTime) – The relaxation time to add to the scheme.

get_connectivities()

Return the connectivities assigned to a scheme

get_relaxation_times()

Return the relaxation times assigned to a scheme

get_states()

Return the states involved in a scheme

class ihm.multi_state_scheme.Connectivity(begin_state, end_state=None, details=None, dataset_group=None, kinetic_rate=None, relaxation_time=None)

A connectivity between states. Used to describe the directed edge of graph. If no end_state is given, the state is not connected to another state. This could be the case for states where no connection to other states could be resolved.

Parameters:

• begin_state (ihm.model.State) – The start state of the connectivity.

• end_state (ihm.model.State) – The end state of the connectivity. Can be None in case of states that are not connected to others.

• details – Details to the connectivity.

• dataset_group (ihm.dataset.DatasetGroup) – The DatasetGroup that was used to obtain information on the connectivity.

• kinetic_rate (KineticRate) – A kinetic rate assigned to the connectivity.

• relaxation_time (RelaxationTime) – A relaxation time assigned to the connectivity.

class ihm.multi_state_scheme.EquilibriumConstant(value, unit=None)

Base class for an equilibrium constant. This class handles the case that none of the derived classes is applicable.

Parameters:

• value (float) – The value of the equilibrium constant

• unit (str) – Unit of the equilibrium constant. Depending on what the process describes, a unit might be applicable or not

class ihm.multi_state_scheme.PopulationEquilibriumConstant(value, unit=None)

An equilibrium constant determined from population

class ihm.multi_state_scheme.KineticRateEquilibriumConstant(value, unit=None)

An equilibrium constant determined from kinetic rates as kAB/kBA

class ihm.multi_state_scheme.KineticRate(transition_rate_constant=None, equilibrium_constant=None, details=None, dataset_group=None, file=None)

A base class for a kinetic rate that can be assigned to a connectivity. The kinetic rate could be a transition_rate_constant or an equilibrium_constant. Alternatively, both could be provided.

Parameters:

• transition_rate_constant (float) – A transition rate constant describing the exchange between two states. Unit: per second.

• equilibrium_constant (EquilibriumConstant or PopulationEquilibriumConstant or KineticRateEquilibriumConstant) – An equilibrium constant describing the exchange between two states

• details (str) – Details on the kinetic rate.

• dataset_group (ihm.dataset.DatasetGroup) – The DatasetGroup used to determine the kinetic rate.

• file (ihm.location.OutputFileLocation) – External file containing measurement data for the kinetic rate.

class ihm.multi_state_scheme.RelaxationTime(value, unit, amplitude=None, details=None, dataset_group=None, file=None)

A relaxation time determined for a scheme. The relaxation time can either be connected to a specific connectivity in the scheme or to the scheme in general if no assignment is possible.

Parameters:

• value (float) – The relaxation time.

• unit (str) – The unit of the relaxation time. Options are [‘seconds’,’milliseconds’, microseconds’]

• amplitude (float) – The amplitude of the relaxation time if determined.

• details (str) – Details on the relaxation time.

• dataset_group (ihm.dataset.DatasetGroup) – DatasetGroup used to determine the relaxation time.

• file (ihm.location.OutputFileLocation) – An external file containing measurement data for the relaxation time.

property unit

The unit of the relaxation time.