cg_openmm.thermo.calc

Functions

bootstrap_heat_capacity([frame_begin, ...])	Calculate and plot the heat capacity curve, with uncertainty determined using bootstrapping.
bootstrap_partial_heat_capacities(...[, ...])	Given an array classifying each frame into discrete conformational states, compute the heat capacity curve, and contributions from each conformational class to the heat capacity curve, with uncertainties determined using bootstrapping.
get_cv_FWHM(Cv_values, T_list)	Internal function for getting the full-width half-maximum, melting point, and peak height from a heat capacity vs T dataset.
get_heat_capacity([frame_begin, ...])	Given a .nc output and a number of intermediate states to insert for the temperature list, this function calculates and plots the heat capacity profile.
get_heat_capacity_derivative(Cv, ...[, plotfile])	Fit a heat capacity vs T dataset to cubic spline, and compute derivatives
get_heat_capacity_integral_entropy(Cv, ...)	Fit Cv/T vs T dataset to cubic spline, and compute integrals (delta_S(T)) from T_0 to T_i Note this is the total entropy change from all states upon a temperature change, separate from the entropy of folding.
get_heat_capacity_reeval(U_kln[, ...])	Given an array of re-evaluated energies at a non-simulated set of force field parameters, and a corresponding temperature list, compute heat capacity as a function of temperature.
get_partial_heat_capacities(array_folded_states)	Given an array classifying each frame into discrete conformational states, compute the heat capacity curve, and contributions from each conformational class to the heat capacity curve.
plot_heat_capacity(Cv, dCv, temperature_list)	Given an array of temperature-dependent heat capacity values and the uncertainties in their estimates, this function plots the heat capacity curve.
plot_partial_heat_capacities(Cv_partial, ...)	Given an array of temperature-dependent heat capacity values and the uncertainties in their estimates, this function plots the heat capacity curve.