Nothing
context("Testing overlap functions")
test_that("Overlap functions", {
## Simple test with PDB ID 1HEL
file <- system.file("examples/1hel.pdb",package="bio3d")
invisible(capture.output(pdb.a <- read.pdb(file)))
file <- system.file("examples/1dpx.pdb",package="bio3d")
invisible(capture.output(pdb.b <- read.pdb(file)))
## Calculate modes with default arguments
invisible(capture.output(modes <- nma(pdb.a, inds=NULL, ff='calpha',
mass=FALSE, temp=300.0)))
ca.inds.a <- atom.select(pdb.a, "calpha", verbose=FALSE)
ca.inds.b <- atom.select(pdb.b, "calpha", verbose=FALSE)
## Set new coordinates of pdb.b
xyz.b <- fit.xyz(pdb.a$xyz, pdb.b$xyz,
fixed.inds=ca.inds.a$xyz,
mobile.inds=ca.inds.b$xyz)
pdb.b$xyz <- xyz.b
## difference vector
dv <- difference.vector(rbind(pdb.a$xyz[ca.inds.a$xyz],
pdb.b$xyz[ca.inds.b$xyz]))
o1 <- overlap(modes, dv, nmodes=(modes$natoms*3)-6)
expect_that(o1$overlap.cum[(modes$natoms*3)-6],
equals(1, tolerance=1e-6))
expect_that(o1$overlap.cum[1], equals(0.2786508, tolerance=1e-6))
o2 <- overlap(modes$U[,7:26], dv)
expect_that(all((round(o1$overlap[1:20] - o2$overlap, 10)==0)),
equals(TRUE))
## Calculate modes with default arguments
invisible(capture.output(modes.b <- nma(pdb.b, inds=NULL, ff='calpha',
mass=FALSE, temp=300.0)))
r <- rmsip(modes, modes.b)
expect_that(r$overlap[1,1], equals(0.704, tolerance=1e-6))
expect_that(r$overlap[1,2], equals(0.286, tolerance=1e-6))
expect_that(r$overlap[2,1], equals(0.289, tolerance=1e-6))
}
)
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