itcsimlib.model_trap module

Binding models for the undecameric TRAP + tryptophan system, demonstrating the use of models written in C via DLLs.

Using compiled DLLs typically provides an order-of-magnitude increase or better in execution speed over native Python models.

class itcsimlib.model_trap.TRAP_DLL_Model

Bases: itcsimlib.itc_model.ITCModel

A model that uses a shared object library to calculate evolved heats for the TRAP + Tryptophan system.

libpath

A globbable path to the dll, relative to the directory this module is present in.

Type:string

libpath = None

start()

Loads the specified shared library.

Returns:errno – The return code from the DLL, 0 if no error. Return type:integer

stop()

Closes the shared library.

calc(T, concentrations, params)

Converts the arguments to their appropriate ctypes, passes to the DLL, and returns the calculated enthalpies.

Parameters:

• T (float) – The experimental temperature (in Kelvin)
• concentrations (list of dicts) – Concentrations of components from the experiment at each injection point.
• params (list of floats) – Model parameter values

Returns:

The integrated enthalpies at each injection point.

Return type:

list of doubles

Raises:

Exception – If DLL returns a non-zero error code.

Notes

Named components are “TRAP” (lattice) and “Trp” (ligand).

class itcsimlib.model_trap.SK

Bases: itcsimlib.model_trap.TRAP_DLL_Model

A nine-parameter model describing the additive 1997 Saroff-Kiefer model, as published.

Notes

The parameters dG, dGa, and dBa (and their enthalpic and heat capacity counterparts) are correlated and should not be fit simultaneously, as described in Ihms. et al., Biophysical Journal (2017),

libpath = 'model_trap_sk*.so'

Q(T0, T, concentrations)

Returns the total binding heat at each injection predicted by the model and its current parameter values. See parent model for information.

class itcsimlib.model_trap.IK

Bases: itcsimlib.model_trap.TRAP_DLL_Model

A nine-parameter model describing the generalized Kleckner (non-additive) model of binding.

libpath = 'model_trap_ik*.so'

Q(T0, T, concentrations)

Returns the total binding heat at each injection predicted by the model and its current parameter values. See parent model for information.

class itcsimlib.model_trap.IKi

Bases: itcsimlib.model_trap.TRAP_DLL_Model

A nine-parameter model describing the Kleckner (non-additive) model, expressed using an intrinsic binding coeffcient.

libpath = 'model_trap_ik*.so'

Q(T0, T, concentrations)

Returns the total binding heat at each injection predicted by the model and its current parameter values. See parent model for information.

class itcsimlib.model_trap.SKa

Bases: itcsimlib.model_trap.TRAP_DLL_Model

A six-parameter model describing the additive 1997 Saroff-Kiefer model, using an intrinsic binding coefficient to remove correlated terms.

libpath = 'model_trap_ik*.so'

Q(T0, T, concentrations)

Returns the total binding heat at each injection predicted by the model and its current parameter values. See parent model for information.