Calculate matrices of simulated exchange required for obtaining empirical distribution.
get_HD_matrices(
sequence,
transition_probs,
experiment_times,
times_to_record,
n_molecules = 100
)amino acid sequence of a peptide as a character vector
list of probabilities of exchange returned by the
get_exchange_probabilities function
numeric vector of times at which exchange will happen
numeric vector of times for which deuteration level measurement should be made
number of peptide molecules
Matrices are stored in a list of matrices (HD_matrices) -
each matrix for the respective time point of the measurement times.
At each time point in the time sequence:
change H to D with probability \(P(H -> D)\) in each entry of
the matrix from the previous iteration,
change D to H with probability \(P(D -> H)\) in each entry of
the matrix from the previous iteration.