Nothing
context("Testing dssp()")
test_that("SSE assignment still works", {
skip_on_cran()
skip_on_travis()
if(!check.utility('dssp')) {
skip('Need DSSP installed to run this test')
}
## Simple test with PDB ID 1HEL
invisible(capture.output(pdb <- read.pdb("3ERJ")))
sse <- dssp(pdb)
## helices
sse.stored <- c(17, 37, 58, 101, 19, 37, 58, 101)
expect_that(as.numeric(sse$helix$start), equals(sse.stored))
sse.stored <- c(18, 9, 14, 8, 16, 10, 13, 7)
expect_that(as.numeric(sse$helix$length), equals(sse.stored))
## sheet
sse.stored <- c(3, 50, 75, 93, 3, 50, 75, 93 )
expect_that(as.numeric(sse$sheet$start), equals(sse.stored))
sse.stored <- c(8, 6, 4, 8, 8, 6, 4, 8)
expect_that(as.numeric(sse$sheet$length), equals(sse.stored))
## With RESNO=FALSE
sse <- dssp(pdb, resno=FALSE)
## helices
sse.stored <- c(16, 36, 57, 100, 134, 152, 173, 216)
expect_that(as.numeric(sse$helix$start), equals(sse.stored))
sse.stored <- c(rep("A", 4), rep("B", 4))
expect_that(as.character(sse$helix$chain), equals(sse.stored))
## sheet
sse.stored <- c(2, 49, 74, 92, 118, 165, 190, 208)
expect_that(as.numeric(sse$sheet$start), equals(sse.stored))
sse.stored <- c(rep("A", 4), rep("B", 4))
expect_that(as.character(sse$sheet$chain), equals(sse.stored))
## With FULL=TRUE
sse <- dssp(pdb, full=TRUE)
expect_that(sum(as.numeric(sse$hbonds[,"BP1"]), na.rm=T), equals(2127))
expect_that(sum(as.numeric(sse$hbonds[,"BP2"]), na.rm=T), equals(1355))
expect_that(sum(as.numeric(sse$hbonds[,"NH-O.1"]), na.rm=T), equals(12017))
expect_that(sum(as.numeric(sse$hbonds[,"E1"]), na.rm=T), equals(-315.8))
expect_that(sum(as.numeric(sse$hbonds[,"O-HN.1"]), na.rm=T), equals(13347))
expect_that(sum(as.numeric(sse$hbonds[,"E2"]), na.rm=T), equals(-313.4))
expect_that(sum(as.numeric(sse$hbonds[,"NH-O.2"]), na.rm=T), equals(11859))
expect_that(sum(as.numeric(sse$hbonds[,"E3"]), na.rm=T), equals(-51.2))
expect_that(sum(as.numeric(sse$hbonds[,"O-HN.2"]), na.rm=T), equals(13076))
expect_that(sum(as.numeric(sse$hbonds[,"E4"]), na.rm=T), equals(-53.6))
expect_that(length(which(sse$hbonds[,"Chain1"]=="A")), equals(112))
expect_that(length(which(sse$hbonds[,"Chain1"]=="B")), equals(105))
expect_that(length(which(sse$hbonds[,"Chain2"]=="A")), equals(115))
expect_that(length(which(sse$hbonds[,"Chain3"]=="B")), equals(108))
expect_that(length(which(sse$hbonds[,"Chain4"]=="A")), equals(116))
}
)
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