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test.fp <- function() {
mol <- parse.smiles("CCCCC")[[1]]
fp <- get.fingerprint(mol, type='maccs')
checkTrue(length(fp@bits) > 0)
fp <- get.fingerprint(mol, type='kr')
checkTrue(length(fp@bits) > 0)
fp <- get.fingerprint(mol, type='shortestpath')
checkTrue(length(fp@bits) > 0)
}
# Substructure test are inspired by the test for the substructure fingerprints in CDK
test.fp.substructures.binary <- function() {
# Default patterns: functional groups
mol <- parse.smiles("c1ccccc1CCC")[[1]]
fp <- get.fingerprint(mol, type="substructure", fp.mode="bit")
fp_bits <- fingerprint::fp.to.matrix(list(fp))
checkEquals(length(fp), 307)
checkEquals(fp_bits[1], 1)
checkEquals(fp_bits[2], 1)
checkEquals(fp_bits[274], 1)
checkEquals(fp_bits[101], 0)
# User defined patterns
smarts <- c("c1ccccc1", "[CX4H3][#6]", "[CX2]#[CX2]")
mol <- parse.smiles("c1ccccc1CCC")[[1]]
fp <- get.fingerprint(mol, type="substructure", fp.mode="bit",
substructure.pattern = smarts)
fp_bits <- fingerprint::fp.to.matrix(list(fp))
checkEquals(length(fp), 3)
checkEquals(length(fp@bits), 2)
checkEquals(fp_bits[1], 1)
checkEquals(fp_bits[2], 1)
checkEquals(fp_bits[3], 0)
mol <- parse.smiles("C=C=C")[[1]]
fp <- get.fingerprint(mol, type="substructure", fp.mode="bit",
substructure.pattern = smarts)
fp_bits <- fingerprint::fp.to.matrix(list(fp))
checkEquals(length(fp), 3)
checkEquals(length(fp@bits), 0)
for (i_fp in 1:3) {
checkEquals(fp_bits[i_fp], 0)
}
# Check for aromatic ring
smarts <- "a:1:a:a:a:a:a1"
mol <- parse.smiles("C1=CC=CC(=C1)CCCC2=CC=CC=C2")[[1]]
set.atom.types(mol)
do.aromaticity(mol)
fp <- get.fingerprint(mol, type="substructure", fp.mode="bit",
substructure.pattern = smarts)
fp_bits <- fingerprint::fp.to.matrix(list(fp))
checkEquals(length(fp), 1)
checkEquals(fp_bits[1], 1)
}
test.fp.substructures.count <- function() {
# Default patterns: functional groups
mol <- parse.smiles("c1ccccc1CCC")[[1]]
fp <- get.fingerprint(mol, type="substructure", fp.mode="count")
checkEquals(length(fp), 307)
checkTrue(fingerprint::count(fp@features[[1]]) > 0)
checkTrue(fingerprint::count(fp@features[[2]]) > 0)
checkTrue(fingerprint::count(fp@features[[274]]) > 0)
checkTrue(fingerprint::count(fp@features[[101]]) == 0)
# User defined patterns
smarts <- c("c1ccccc1", "[CX4H3][#6]", "[CX2]#[CX2]")
mol <- parse.smiles("c1ccccc1CCC")[[1]]
fp <- get.fingerprint(mol, type="substructure", fp.mode="count",
substructure.pattern = smarts)
checkEquals(length(fp), 3)
checkEquals(fingerprint::count(fp@features[[1]]), 1)
checkEquals(fingerprint::count(fp@features[[2]]), 1)
checkEquals(fingerprint::count(fp@features[[3]]), 0)
mol <- parse.smiles("C=C=C")[[1]]
fp <- get.fingerprint(mol, type="substructure", fp.mode="count",
substructure.pattern = smarts)
checkEquals(length(fp), 3)
for (i_fp in 1:3) {
checkEquals(fingerprint::count(fp@features[[i_fp]]), 0)
}
# Check for aromatic ring
smarts <- "a:1:a:a:a:a:a1"
mol <- parse.smiles("C1=CC=CC(=C1)CCCC2=CC=CC=C2")[[1]]
set.atom.types(mol)
do.aromaticity(mol)
fp <- get.fingerprint(mol, type="substructure", fp.mode="count",
substructure.pattern = smarts)
checkEquals(length(fp), 1)
checkEquals(fingerprint::count(fp@features[[1]]), 2)
}
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