Nothing
test.match1 <- function()
{
m <- parse.smiles('CCCCc1cccc(Cl)c1')[[1]]
q <- 'cCl'
checkTrue(matches(q,m))
}
test.match2 <- function()
{
m <- parse.smiles('CCCCc1cccc(Cl)c1')[[1]]
q <- 'CCCCc'
checkTrue(matches(q,m))
}
test.match3 <- function()
{
m1 <- parse.smiles('CCCCc1cccc(Cl)c1')[[1]]
m2 <- parse.smiles('CC(N)(N)CC=O')[[1]]
q <- '[CD2]'
checkTrue(all(matches(q,list(m1,m2))))
checkEquals(2, length(matches(q,list(m1,m2))))
}
test.match4 <- function()
{
smiles <- c('CCC', 'c1ccccc1', 'C(C)(C=O)C(CCNC)C1CC1C(=O)')
mols <- sapply(smiles, parse.smiles)
mappings <- matches("CCCC", mols, TRUE)
checkEquals(3, length(mappings))
checkTrue(!mappings[[1]]$match)
checkTrue(!mappings[[2]]$match)
checkTrue(mappings[[3]]$match)
checkTrue(is.null(mappings[[1]]$mapping))
checkTrue(is.null(mappings[[2]]$mapping))
checkEquals(13, length(mappings[[3]]$mapping))
m <- sapply(mappings[[3]]$mapping, function(x) length(x))
checkTrue(all(m == 4))
}
test.mcs1 <- function() {
mols <- parse.smiles(c("NCc1ccccc1OC(=N)CCN", "c1ccccc1OC(=N)"))
lapply(mols, do.aromaticity)
lapply(mols, set.atom.types)
mcs <- get.mcs(mols[[1]], mols[[2]], TRUE)
checkEquals("org.openscience.cdk.silent.AtomContainer2", .jclass(mcs))
checkEquals(9, get.atom.count(mcs))
}
test.mcs3 <- function() {
mols <- parse.smiles(c("c1cccc(COC(=O)NC(CC(C)C)C(=O)NC(CCc2ccccc2)C(=O)COC)c1", "c1cccc(COC(=O)NC(CC(C)C)C(=O)NCC#N)c1"))
lapply(mols, do.aromaticity)
lapply(mols, set.atom.types)
mcs <- get.mcs(mols[[1]], mols[[2]], TRUE)
checkEquals("org.openscience.cdk.silent.AtomContainer2", .jclass(mcs))
checkEquals(21, get.atom.count(mcs))
}
test.mcs2 <- function() {
mols <- parse.smiles(c("NCc1ccccc1OC(=N)CCN", "c1ccccc1OC(=N)"))
lapply(mols, do.aromaticity)
lapply(mols, set.atom.types)
mcs <- get.mcs(mols[[1]], mols[[2]], FALSE)
checkTrue(inherits(mcs, "matrix"))
checkEquals(9, nrow(mcs))
checkEquals(2, ncol(mcs))
}
test.aromaticity.match <- function() {
smiles <- c("CCC", "c1ccccc1", "C(C)(C=O)C(CCNC)C1CC1C(=O)")
mols <- parse.smiles(smiles)
query <- "[#6]=O"
doesMatch <- matches(query, mols)
checkTrue(all(doesMatch == c(FALSE,FALSE,TRUE)))
}
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