AA57OLMatrix            Overlapping Matrix for 57 amino acid and
                        secondary structure combinations.
AA57OLWeights           Overlapping weights for 57 amino acid and
                        secondary structure combinations.
AvgCov.t                Average covariance across three secondary
                        structures for all amino acid typings
                        (including oxidized cystine).
CAMuTable               Mean chemical shift values for alpha carbon .
CASdTable               Standard deviation of chemical shift values for
                        alpha carbon .
CBMuTable               Mean chemical shift values for beta carbon .
CBSdTable               Standard deviation of chemical shift values for
                        beta carbon .
CarbonCov.t             Covariance values of chemical shifts of alpha
                        and beta carbons.
ID                      RefDB ID included in the BaMORC package.
RefDB.StatCA            Statistics of chemical shifts values of alpha
                        carbons from RefDB.
RefDB.StatCB            Statistics of chemical shifts values of beta
                        carbons from RefDB.
RefDB_data              RefDB object
aaCodes1Letter19        Single-letter amino acid naming convention.
aaCodes1Letter20        Single-letter amino acid naming convention.
aaCodes3Letter1stCap    Three-letter amino acid naming convention with
                        first letter capitalized.
aaCodes3LetterAllCap.v
                        Three-letter amino acid naming convention with
                        all letters capitalized.
aaFreq                  Pre-defined amino acid frequency data.
bamorc                  Calculates the referencing correction value.
calculate_aa_prob       Calculates an amino acid typing probability.
calculate_chi_squared_stat
                        Calculates a chi squared statistic(s).
calculate_mse           Calculates mean squared error
calculate_rcf           Calculates the relative cumulative frequency
                        for amino acid and secondary structure.
chemicalShifts          Pre-defined sample chemical shifts data.
cname                   All the amino acids and secondary structures
                        combinations for easy access.
inverseMatrices         inverseMatrices.
jpred_fetcher           Using JPred Mass-submission scheduler program
                        to submit protein sequence and return secondary
                        structure results.
read_db_file            'read_db_file()' reads in data from existing
                        database that included in the BaMORC package.
                        This database was extracted from RefDB
                        database.
read_nmrstar_file       Extracts data from BMRB STAR 3.0 file.
                        'read_nmrstar_file()' parses BMRB STAR 3.0
                        file. It will extract sequence information and
                        chemical shifts for both alpha and beta
                        carbons.
read_raw_file           Extracts data from a protein NMR experimental
                        peak list. 'read_raw_file()' function reads in
                        a user provided protein NMR experimental peak
                        list. It currently supports file format in csv,
                        txt with deliminator of comma, whitespace or
                        semicolon. Note: please don't leave space
                        between sequence and chemical shifts data,
                        otherwise it will report error.
unassigned_bamorc       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.
