Nothing
context("Testing cmap function")
test_that("cmap() works properly", {
## Simple test with PDB ID 1HEL
file <- system.file("examples/1hel.pdb",package="bio3d")
invisible(capture.output(pdb <- read.pdb(file)))
## Calculate contact map on a small protein
invisible(capture.output(inds <- atom.select(pdb, "protein")))
invisible(capture.output(cm <- cmap(pdb$xyz[, inds$xyz],
grpby=pdb$atom[inds$atom, "resno"], ncore=1)))
expect_equal(length(which(cm==1)), 285)
expect_true(all(is.na(cm[1,1:3])))
expect_equal(cm[1,4], 0)
expect_equal(cm[13,129], 1)
## Check multicore cmap
skip_on_cran()
skip_on_travis()
trjfile <- system.file("examples/hivp.dcd", package="bio3d")
invisible(capture.output(trj <- read.dcd(trjfile)))
invisible(capture.output(cm <- cmap(trj, dcut=6, ncore=1)))
invisible(capture.output(cm.mc <- cmap(trj, dcut=6, ncore=NULL)))
expect_that(cm, equals(cm.mc, tolerance=1e-6))
})
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