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test.frag1 <- function() {
m <- parse.smiles("c1(ccc(cc1C)CCC(C(CCC)C2C(C2)CC)C3C=C(C=C3)CC)C")[[1]]
do.aromaticity(m)
set.atom.types(m)
f <- get.murcko.fragments(m, as.smiles=TRUE, min.frag.size = 6, single.framework = TRUE)
checkEquals(length(f), 1)
checkEquals(length(f[[1]]$rings), 1)
checkEquals(f[[1]]$rings, "c1ccccc1")
checkEquals(f[[1]]$frameworks, "c1ccc(cc1)CCC(CC2CC2)C3C=CC=C3")
}
test.frag2 <- function() {
ms <- parse.smiles(c('c1(ccc(cc1C)CCC(C(CCC)C2C(C2)CC)C3C=C(C=C3)CC)C',
'c1ccc(cc1)c2c(oc(n2)N(CCO)CCO)c3ccccc3',
'COc1ccc(cc1OCc2ccccc2)C(=S)N3CCOCC3'))
lapply(ms, do.aromaticity)
lapply(ms, set.atom.types)
f <- get.murcko.fragments(ms, as.smiles=TRUE, min.frag.size = 6, single.framework = TRUE)
checkEquals(length(f), 3)
fworks <- unlist(lapply(f, function(x) length(x$frameworks)))
checkTrue(all(fworks == 1))
}
test.frag3 <- function() {
ms <- parse.smiles(c('c1(ccc(cc1C)CCC(C(CCC)C2C(C2)CC)C3C=C(C=C3)CC)C',
'c1ccc(cc1)c2c(oc(n2)N(CCO)CCO)c3ccccc3',
'COc1ccc(cc1OCc2ccccc2)C(=S)N3CCOCC3'))
lapply(ms, do.aromaticity)
lapply(ms, set.atom.types)
f <- get.murcko.fragments(ms, as.smiles=FALSE, min.frag.size = 6, single.framework = TRUE)
checkEquals(length(f), 3)
fworks <- unlist(lapply(f, function(x) unlist(lapply(x$frameworks, .jclass))))
checkTrue(all(fworks == "org.openscience.cdk.silent.AtomContainer2"))
}
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