tests/testthat/test_exchange_rates.R

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

#get_F_const
test_that("get_F_const works", {
    F_const <- get_F_const(291.15, 1.9858775)
    expect_equal(F_const, list(Fta = 0.858229011688035,
                               Ftb = 0.830568208785807,
                               Ftw = 0.812624750043961))
    F_const <- get_F_const(300, 1.9858775)
    expect_equal(F_const, list(Fta = 1.75315311725701,
                               Ftb = 1.97727446855674,
                               Ftw = 2.14238917600377))
})

test_that("get_F_const returns error", {
    expect_error(get_F_const(0, 1.9858775))
})


#get_poly_const
test_that("get_poly_const returns error for invalid input", {
    expect_error(get_poly_const("blahblah", "HD"))
    expect_error(get_poly_const("poly", "exchange"))

    expect_error(get_poly_const("HDD"))
    expect_error(get_poly_const("oligo", "poly"))
})

test_that("get_poly_const works", {
    #exchange HD
    poly_const <- get_poly_const("poly", "HD")
    expect_equal(poly_const, list(Ka = 0.694782305783893,
                                  Kb = 187003075.716994,
                                  Kw = 0.00052704627669473))
    oligo_const <- get_poly_const("oligo", "HD")
    expect_equal(oligo_const, list(Ka = 1.62579059553431,
                                   Kb = 252454152.217942,
                                   Kw = 0.000835368348561147))

    #exchange DH
    poly_const <- get_poly_const("poly", "DH")
    expect_equal(poly_const, list(Ka = 0.41864773858493,
                                  Kb = 123551706.883486,
                                  Kw = 0.00041864773858493))
    oligo_const <- get_poly_const("oligo", "DH")
    expect_equal(oligo_const, list(Ka = 0.979635708288736,
                                   Kb = 166794804.292706,
                                   Kw = 0.000663556665657114))
})


#get_pkc
test_that("get_pkc returns proper output", {
    gas_constant <- 1.9858775
    temp_kelvin <- 291.15
    #HD
    pkc_const_HD <- get_pkc(temp_kelvin, gas_constant, exchange = "HD")
    expect_equal(pkc_const_HD, list(asp = 4.44446993365174,
                                    glu = 4.89152093814484,
                                    his = 7.15352450238806))
    #DH
    pkc_const_DH <- get_pkc(temp_kelvin, gas_constant, exchange = "DH")
    expect_equal(pkc_const_DH, list(asp = 3.83589113630567,
                                    glu = 4.29152093814484,
                                    his = 6.73352450238806))
})

test_that("get_pkc returns error in the case of invalid output", {
    expect_error(get_pkc(0, 1.9858775, "HD"))
    expect_error(get_pkc(300, 1.9858775, "blah"))
})


#get_exchange_constants
test_that("get_pkc returns proper output", {
    pH <- 7
    pkc_consts <- list(asp = 4.444469934,
                       glu = 4.891520938,
                       his = 7.153524502)
    k_consts <- list(Ka = 0.6947823058,
                     Kb = 187003075.7,
                     Kw = 0.0005270462767)

    constants <- get_exchange_constants(pH, pkc_consts, k_consts)
    expect_equal(constants, structure(c(0, -0.59, 0.898812310601082, -0.9,
                                        -0.58, -0.54, -0.74, -0.22,
                                        -0.896671812875742, -0.6, -0.47,
                                        -0.296158254546754, -0.91, -0.57, -0.56,
                                        -0.64, -0.52, 0, 0, -0.437992277698594,
                                        -0.79, -0.4, -0.41, -0.739022273362575,
                                        0, 0.957046086760691, 0.511939295200356,
                                        0, 0, -0.32, 0.57903422200311, -0.12,
                                        -0.13, -0.46, -0.58, 0.218176047120386,
                                        0.307518999008732, -0.27, -0.27,
                                        -0.22615670112472, -0.59, -0.13, -0.29,
                                        -0.28, -0.43, -0.194773472023435,
                                        -0.854416534276379, -0.388518934646472,
                                        -0.468073125742265, -0.44, -0.37, -0.3,
                                        -1.32, 0, 0, 0.293, 0,
                                        0.0767122542818456, -0.289554452431933,
                                        0.69, 0.49, 0.62, 0.55,
                                        0.267251569286023, -0.494750659376026,
                                        0.24, 0.06, 0.605773780975473, -0.73,
                                        -0.576252727721677, -0.04,
                                        -0.00895484265292644,
                                        -0.235859464059171, 0, 0, 0.37,
                                        -0.0662579798400606,
                                        -0.41, -0.27, -0.701934483299758, 0,
                                        -1.8, -0.577243550643321, 0, 0, 0.22,
                                        -0.173985160086455, 0.6, 0.32, 0.55,
                                        0.46, 0.17, -0.141795340523512, 0.39,
                                        0.2, 0.657172312134108, -0.23, -0.21,
                                        0.12, 0.11, 0.0631315866300978, -0.24,
                                        0.6, 0.299550285605933, 0.2, -0.11,
                                        0.05, -0.14, 1.62, 0, 0, -0.197),
                                      .Dim = c(28L, 4L
                                        )))
})


#get_exchange_rates

pH <- 9
temperature <- 15
if_corr <- 0


test_that("get_exchange_rates returns proper output for sequence PPAQHI", {
    sequence <- c("P", "P", "A", "Q", "H", "I")

    kcHD <- get_exchange_rates(sequence,
                               exchange = "HD",
                               mol_type = "poly",
                               if_corr = TRUE)
    expect_equal(kcHD, c(0, 0, 147.326618489, 293.955249864, 358.207739345,
                         1.108193501))
    kcDH <- get_exchange_rates(sequence, exchange = "DH", mol_type = "poly")
    expect_equal(kcDH, c(0, 0, 293.955039643536, 586.51741289567,
                         670.603937240368, 2.13099882731867))
})

test_that("get_exchange_rates returns proper
          output for sequence DDENFRLLGNVLVCVLA", {
    sequence = c("D", "D", "E", "N", "F", "R", "L", "L", "G", "N", "V",
                 "L", "V", "C", "V", "L", "A")

    kcHD = get_exchange_rates(sequence, exchange = "HD", mol_type = "poly")
    expect_equal(kcHD, c(0, 1407.51087654392, 20.8210814563502,
                         223.031960198571,  123.715050549506, 140.645500183317,
                         44.8775638262605, 16.673595957583, 116.287643601167,
                         465.88851129825, 42.3006964408419, 19.5897671225677,
                         12.4838205631068, 307.809486916701, 71.8368892252938,
                         19.5897671225677, 0.996051978222705))
    kcDH = get_exchange_rates(sequence, exchange = "DH", mol_type = "poly")
    expect_equal(kcDH, c(0, 7052.16868210585, 104.31246014817, 1117.6409076194,
                         620.042482190375, 704.895521242294, 224.920055772394,
                         83.5657244499878, 582.817360266318, 2334.96787728227,
                         212.005157844969, 98.1811653330133, 62.5671577933202,
                         1542.69797782856, 360.036413599322, 98.1811653330133,
                         4.99207280372255))
})


test_that("get_exchange_rates returns proper output for sequence HA", {
    sequence = c("H", "A")

    kcHD = get_exchange_rates(sequence,
                              exchange = "HD",
                              mol_type = "poly",
                              if_corr = TRUE)
    expect_equal(kcHD, c(0, 248.093621605602))

    kcDH = get_exchange_rates(sequence, exchange = "DH", mol_type = "poly")
    expect_equal(kcDH, c(0, 477.071212028545))
})


test_that("get_exchange_rates returns error in the case of invalid input", {
    sequence = c("P", "P", "A", "Q", "H", "I")
    pH = 9
    temperature = -273.15
    if_corr = 0
    expect_error(get_exchange_rates(sequence, exchange = "HD",
                                    mol_type = "poly",
                                    temperature = temperature),
                 "Assertion on 'temperature == -273.15' failed. Must be FALSE.")
    expect_error(get_exchange_rates(sequence,
                                    exchange = "blah",
                                    mol_type = "poly"))
    expect_error(get_exchange_rates(sequence,
                                    exchange = "DH",
                                    mol_type = 'aaa',
                                    "Assertion on 'mol_type' failed."))
    expect_error(get_exchange_rates(sequence, if_corr = 17),
                 "Assertion on 'if_corr' failed.")
    expect_error(get_exchange_rates(sequence = c()),
                 "Length of sequence must be greater than 0")
})