Calculates the referencing correction value for unassigned protein NMR peaklists. unassigned_bamorc() will analyze unassigned protein NMR spectra, first groups the peaklist via SSC, then estimates the secondary structure via JPred, finally using BaMORC core function to calculate the reference correction value.

unassigned_bamorc(peakList_file_loc, sequence,
  secondary_structure = NULL, from = -5, to = 5,
  ssc = "moseleybioinformaticslab/ssc",
  para = "--plformat=sparky --stype=HNcoCACB --dims=H,N,CA/CB --rdims=H,N")

Arguments

peakList_file_loc

NMR HNCACB file location

sequence

sequence string of protein of interest

secondary_structure

string of secondary structure if available

from

the lower bound of the optimization

to

the upper bound of the optimization

ssc

location of ssc docker image

para

parameter input for ssc function (no need to change)

Value

Reference correction value.

Examples

sequence = "RPAFCLEPPYAGPGKARIIRYFYNAAAGAAQAFVYGGVRAKRNNFASAADALAACAAA" sample_data_generator(input_type = "ssc_sample") peakList_file_loc = "./bpti_HNcoCACB.txt"
# NOT RUN { unassigned_bamorc(peakList_file_loc, sequence, secondary_structure=NULL, from=-5, to=5, ssc="moseleybioinformaticslab/ssc", para="--plformat=sparky --stype=HNcoCACB --dims=H,N,CA/CB --rdims=H,N") # }
# Expected result should be around (due to randomness): 0.0007890328 unlink("./bpti_HNcoCACB.txt")