Calculate probabilities of exchanges that are required to simulate the exchange process.
get_exchange_probabilities(HD_rate, DH_rate, time_step, protection_factor)rate of hydrogen-deuterium exchange calculated via
get_exchange_rates
rate of deuterium-hydrogen exchange (back-exchange) calculated
via get_exchange_rates
size of a single time step of a simulation
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)
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 \(P_i( D -> D)\).
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.