get_exchange_probabilities: Get probability of an exchange (HD and DH)

In hadexversum/powerHDX: Efficient Simulation of HDX-MS Data and Tools for the Statistical Analysis

Get probability of an exchange (HD and DH)

Description

Calculate probabilities of exchanges that are required to simulate the exchange process.

Usage

get_exchange_probabilities(HD_rate, DH_rate, time_step, protection_factor)

Arguments

HD_rate	rate of hydrogen-deuterium exchange calculated via get_exchange_rates
DH_rate	rate of deuterium-hydrogen exchange (back-exchange) calculated via get_exchange_rates
time_step	size of a single time step of a simulation
protection_factor	protection factor. If a single number of provided, same protection factor will be assumed for each amide. Default value: 1 (indicates that the exchange rate is equal to the intristic exchange rate)

Details

he process is defined as a series of steps from the time sequence, and each step depends on the state in the previous one. Therefore, the probabilities of changing the state are conditional probabilities - probabilities of particular state in k+1^th step given particular state in k^th step. For i^th amino acid probabilities are calculated as follows

P_i( H -> D ) = 1 - exp((-kcHD_i * time_step)/protection_factor)

P_i( D -> H ) = 1 - exp((-kcDH_i * time_step)/protection_factor)

P_i( H -> H ) = 1 - P_i( H -> D )

P_i( D -> D ) = 1 - P_i( D -> H )

where the last two equations describe the probabilities of staying in the same state.

Value

a list of four vectors: vector HD for probabilities P_i( H -> D ), vector DH for probabilities P_i( D -> H ), vector HH for probabilities P_i( H -> H ) and vector DD for probabilities P_i( D -> D).

hadexversum/powerHDX documentation built on Aug. 31, 2022, 7:47 p.m.