Nothing
context("Testing basic PDB structure operation")
test_that("read.mol2() reads a mol2 from zinc", {
## Simple test with aspirin
file <- system.file("examples/aspirin.mol2",package="bio3d")
invisible(capture.output(mol <- read.mol2(file)))
expect_is(mol$atom, "data.frame")
expect_true(inherits(mol, "mol2"))
expect_true(inherits(mol$xyz, "xyz"))
expect_equal(nrow(mol$atom), 20)
expect_equal(nrow(mol$bond), 20)
expect_equal(mol$info[1], 20)
expect_equal(mol$info[2], 20)
expect_equal(sum(mol$atom$elety=="H"), 7)
elena <- c("C1", "C2", "O1", "O2", "C3", "C4", "C5",
"C6", "C7", "C8", "C9", "O3", "O4", "H1", "H2",
"H3", "H4", "H5", "H6", "H7")
expect_equal(mol$atom$elena, elena)
x <- c(-1.4238, -1.3441, -1.4532, -1.1519, -0.9822)
y <- c(-2.5790, -3.9491, -4.7933, -4.2739, -2.8882)
z <- c(0.6434, 0.0976, 0.0938, 0.0032, -0.0844)
expect_equal(mol$atom$x[1:5], x)
expect_equal(mol$atom$y[6:10], y)
expect_equal(mol$atom$z[16:20], z)
})
test_that("read.mol2() reads and stores data properly", {
skip_on_cran()
skip_on_travis()
file <- system.file("examples/aspirin.mol2",package="bio3d")
invisible(capture.output(mol <- read.mol2(file)))
f <- tempfile()
write.mol2(mol, file=f)
mol2 <- read.mol2(f)
expect_equal(mol, mol2)
})
test_that("basic atom select and trim of mol2", {
skip_on_cran()
skip_on_travis()
file <- system.file("examples/aspirin.mol2",package="bio3d")
invisible(capture.output(mol <- read.mol2(file)))
capture.output( sele <- atom.select(mol, "noh") )
expect_equal(length(sele$atom), 13)
capture.output( sele <- atom.select(mol, elety="H") )
expect_equal(length(sele$atom), 7)
capture.output( sele <- atom.select(mol, elena="C1") )
expect_equal(length(sele$atom), 1)
capture.output( sele <- atom.select(mol, resno=1) )
expect_equal(length(sele$atom), 20)
capture.output( sele <- atom.select(mol, "noh") )
mol2 <- trim(mol, sele)
expect_equal(nrow(mol2$atom), 13)
expect_equal(nrow(mol2$bond), 13)
expect_equal(length(mol2$xyz), 39)
xyz <- c(-1.4238, 1.4221, 1.2577, -1.3441, -0.0813)
expect_equal(mol2$xyz[1:5], xyz)
})
test_that("converting mol2 to pdb works", {
skip_on_cran()
skip_on_travis()
file <- system.file("examples/aspirin.mol2",package="bio3d")
invisible(capture.output(mol <- read.mol2(file)))
capture.output( pdb <- as.pdb(mol) )
expect_equal(nrow(pdb$atom), nrow(mol$atom))
expect_equal(pdb$xyz, mol$xyz)
expect_equal(mol$atom$elena, pdb$atom$elety)
expect_equal(mol$atom$x, pdb$atom$x)
expect_equal(mol$atom$charge, pdb$atom$charge)
})
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