tests/testthat/test_accdpx.R

In ptm: Analyses of Protein Post-Translational Modifications

library(ptm)
context("ACC and SASA Computations")


## ---------------------------------------------- ##
#               Testing mkdssp                     #
## ---------------------------------------------- ##
test_that("mkdssp() works properly", {

  skip_on_cran()
  skip_on_travis()

  a <- mkdssp('2xqq', method = 'ptm')
  b <- mkdssp('2xqq', method = 'bio3d')
  c <- mkdssp('./pdb/1u8f.pdb', method = 'ptm')
  d <- mkdssp('./pdb/1u8f.pdb', method = 'bio3d')
  e <- mkdssp('xxxx', method = 'bio3d')
  f <- mkdssp('xxxx', method = 'ptm')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 371)
    expect_equal(ncol(a), 8)
    expect_true('ss' %in% names(a))
    expect_gt(sum(a$sasa), 10000)
  }

  if (!is.null(b)){
    expect_is(b, 'sse')
    expect_equal(length(b), 9)
    expect_gte(length(b$sse), 371)
    expect_gt(sum(b$acc), 10000)
  }

  if (!is.null(c)){
    expect_is(c, 'data.frame')
    expect_equal(nrow(c), 1332)
    expect_equal(ncol(c), 8)
    expect_true('ss' %in% names(c))
    expect_gt(sum(c$sasa), 40000)
  }

  if (!is.null(d)){
    expect_is(d, 'sse')
    expect_equal(length(d), 9)
    expect_gte(length(d$sse), 1332)
    expect_gt(sum(d$acc), 40000)
  }

  expect_is(e, 'NULL')
  expect_is(f, 'NULL')
})


## ---------------------------------------------- ##
#             Testing acc.dssp                     #
## ---------------------------------------------- ##
test_that("acc.dssp() works properly",{

  skip_on_cran()
  skip_on_travis()

  a <- acc.dssp('./pdb/1u8f.pdb')
  b <- acc.dssp('./pdb/1u8f.pdb', aa = 'M')

  d <- acc.dssp('./pdb/1u8f.pdb', aa = 'S')
  e <- acc.dssp('./pdb/1u8f.pdb', aa = 'O')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 1332)
    expect_equal(ncol(a), 11)
    expect_true('P' %in% unique(a$chain))
  }

  if (!is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b), 36)
    expect_equal(ncol(b), 11)
    expect_true('Q' %in% unique(b$chain))
  }

  if (!is.null(d)){
    expect_is(d, 'data.frame')
    expect_equal(nrow(d), 84)
    expect_equal(ncol(d), 11)
    expect_true('O' %in% unique(d$chain))
  }


  a <- acc.dssp('6lu7')
  b <- acc.dssp('6lu7', aa = 'M')

  d <- acc.dssp('6lu7', aa = 'K')
  e <- acc.dssp('xxxx')


  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 309)
    expect_equal(ncol(a), 11)
    expect_true('A' %in% unique(a$chain))
  }

  if (!is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b), 10)
    expect_equal(ncol(b), 11)
    expect_true('A' %in% unique(b$chain))
  }


  if (!is.null(d)){
    expect_is(d, 'data.frame')
    expect_equal(nrow(d), 11)
    expect_equal(ncol(d), 11)
    expect_true('A' %in% unique(d$chain))
  }

  expect_is(e, 'NULL')


  a <- acc.dssp('1h9d') # pdb contain non-protein chains

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 504)
    expect_equal(ncol(a), 11)
  }
})


## ---------------------------------------------- ##
#             Testing get.area                     #
## ---------------------------------------------- ##
test_that("get.area() works properly",{

  skip_on_cran()
  skip_on_travis()

  a <- get.area('3cwm')
  b <- get.area("./pdb/1u8f.pdb")
  c <- get.area("./pdb/1u8f.pdb", keepfiles = TRUE)
  e <- get.area('xxxx')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 2929)
    expect_equal(ncol(a), 5)
    expect_true('areaenergy' %in% names(a))
  }

  if (!is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b), 10092)
    expect_equal(ncol(b), 5)
    expect_true('resno' %in% names(b))
  }

  if (!is.null(c)){
    expect_is(c, 'data.frame')
    expect_equal(nrow(c), 10092)
    expect_equal(ncol(c), 5)
    expect_true('resid' %in% names(c))
    expect_true(file.exists('./pdb/1u8f_getarea.Rda'))
    expect_true(file.exists('./pdb/1u8f_getarea.txt'))
  }

  expect_is(e, 'NULL')
})
file.remove('./pdb/1u8f_getarea.Rda')
file.remove('./pdb/1u8f_getarea.txt')


## ---------------------------------------------- ##
#                 Testing dpx                      #
## ---------------------------------------------- ##
test_that("dpx() works properly",{

  skip_on_cran()
  skip_on_travis()

  a <- dpx('3cwm')
  b <- dpx('./pdb/1u8f.pdb')
  c <- dpx('xxxx')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 2929)
    expect_equal(ncol(a), 9)
    expect_gt(sum(a$dpx), 1)
  }

  if (!is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b), 10092)
    expect_equal(ncol(b), 9)
    expect_gt(sum(b$dpx), 1)
  }

  expect_is(c, 'NULL')

})


## ---------------------------------------------- ##
#                 Testing atom.dpx                 #
## ---------------------------------------------- ##
test_that("atom.dpx() works properly",{

  skip_on_cran()
  skip_on_travis()

  a <- atom.dpx('1hxp')
  b <- atom.dpx('./pdb/1u8f.pdb')
  c <- atom.dpx('xxxx')
  d <- atom.dpx('./whateversoever.xxxx.pdb')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 5354)
    expect_equal(ncol(a), 9)
    expect_gt(sum(a$delta_dpx), 1)
  }

  if (!is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b),10092)
    expect_equal(ncol(b), 9)
    expect_gt(sum(b$delta_dpx), 1)
  }

  expect_is(c, 'NULL')
  expect_is(d, 'NULL')
})

## ---------------------------------------------- ##
#                 Testing res.dpx                  #
## ---------------------------------------------- ##
test_that("res.dpx() works properly",{

  skip_on_cran()
  skip_on_travis()

  a <- res.dpx('1hxp')
  b <- res.dpx('./pdb/1u8f.pdb')
  c <- res.dpx('1cll', aa = 'M')
  d <- res.dpx('xxxx')
  e <- res.dpx('1cll', aa = 'O')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 669)
    expect_equal(ncol(a), 10)
    expect_gt(sum(a$max_dpx_complex), sum(a$max_dpx_chain))
  }

  if (!is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b), 1332)
    expect_equal(ncol(b), 10)
    expect_gt(sum(b$max_dpx_complex), sum(b$max_dpx_chain))
  }

  if (!is.null(c)){
    expect_is(c, 'data.frame')
    expect_equal(nrow(c),9)
    expect_equal(ncol(c), 10)
    expect_gte(c$max_dpx_chain[1], c$min_dpx_chain[1])
  }

  expect_is(d, 'NULL')
  expect_is(e, 'NULL')
})

## ---------------------------------------------- ##
#             Testing stru.part                    #
## ---------------------------------------------- ##
test_that("stru.part() works properly",{

  skip_on_cran()
  skip_on_travis()

  a <- stru.part(pdb = '2xqq')
  b <- stru.part(pdb = '2xqq', cutoff = 0.05)
  c <- stru.part('./pdb/1u8f.pdb')
  d <- stru.part(pdb = 'xxxx')

  if (!is.null(a)){
    expect_is(a, 'data.frame')
    expect_equal(nrow(a), 371)
    expect_equal(ncol(a), 9)
    expect_equal(as.numeric(table(a$str)['surface']), 96)
    expect_equal(as.numeric(table(a$str)['interior']), 104)
    expect_equal(as.numeric(table(a$str)['rim']), 68)
    expect_equal(as.numeric(table(a$str)['support']), 34)
    expect_equal(as.numeric(table(a$str)['core']), 69)
  }

  if (!is.null(a) & !is.null(b)){
    expect_is(b, 'data.frame')
    expect_equal(nrow(b), 371)
    expect_equal(ncol(b), 9)
    expect_gt(as.numeric(table(b$str)['surface']), as.numeric(table(a$str)['surface']))
    expect_lt(as.numeric(table(b$str)['interior']), as.numeric(table(a$str)['interior']))
    expect_gt(as.numeric(table(b$str)['rim']), as.numeric(table(a$str)['rim']))
    expect_lt(as.numeric(table(b$str)['support']), as.numeric(table(a$str)['support']))
  }

  if (!is.null(c)){
    expect_is(c, 'data.frame')
    expect_equal(nrow(c), 1332)
    expect_equal(ncol(c), 9)
    expect_equal(as.numeric(table(c$str)['surface']), 358)
    expect_equal(as.numeric(table(c$str)['interior']), 615)
    expect_equal(as.numeric(table(c$str)['rim']), 92)
    expect_equal(as.numeric(table(c$str)['support']), 114)
    expect_equal(as.numeric(table(c$str)['core']), 153)
  }

  expect_is(d, 'NULL')
})