# Install packages once
#install.packages(c("rcdk", "fingerprint"))
# Load rcdk
library(rcdk)
## Loading required package: rcdklibs
## Loading required package: rJava
## Warning: package 'rJava' was built under R version 4.5.3
dir_path <- "C:\\Users\\xut2\\"
# dir_path_name <- list.files(pattern = ".*csv",dir_path,full.names = T, recursive = T)
# dir_path_name
# data_1 <- read.csv(grep("DICT_ECFP4_1024_20260803.csv",dir_path_name,value = T),header = T,stringsAsFactors = F)
# Example compounds
dat <- data.frame(
compound = c("Aspirin", "Caffeine", "Ibuprofen"),
smiles = c(
"CC(=O)Oc1ccccc1C(=O)O",
"Cn1c(=O)n(C)c2ncn(C)c2c1=O",
"CC(C)Cc1ccc(cc1)C(C)C(=O)O"
)
)
print(dat)
## compound smiles
## 1 Aspirin CC(=O)Oc1ccccc1C(=O)O
## 2 Caffeine Cn1c(=O)n(C)c2ncn(C)c2c1=O
## 3 Ibuprofen CC(C)Cc1ccc(cc1)C(C)C(=O)O
# Convert SMILES strings to molecule objects
mols <- parse.smiles(dat$smiles)
# Generate binary ECFP4 fingerprints
fps <- lapply(mols, function(mol) {
get.fingerprint(
mol,
type = "circular",
fp.mode = "bit",
circular.type = "ECFP4"
)
})
fps
## $`CC(=O)Oc1ccccc1C(=O)O`
## Fingerprint object
## name =
## length = 1024
## folded = FALSE
## source = CDK
## bits on = 20 68 94 96 134 211 226 347 408 456 476 487 508 520 550 626 641 689 705 727 762 886 928 948 968
##
## $`Cn1c(=O)n(C)c2ncn(C)c2c1=O`
## Fingerprint object
## name =
## length = 1024
## folded = FALSE
## source = CDK
## bits on = 67 134 245 262 266 311 316 319 377 404 405 422 461 508 524 576 585 603 686 808 948 968 969 982 995
##
## $`CC(C)Cc1ccc(cc1)C(C)C(=O)O`
## Fingerprint object
## name =
## length = 1024
## folded = FALSE
## source = CDK
## bits on = 20 49 94 107 134 153 207 263 270 281 350 378 508 517 550 558 611 626 647 651 727 790 802 948 968 989
# Convert fingerprints to a binary matrix
ecfp4 <- fingerprint::fp.to.matrix(fps)
ecfp4
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
## [1,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
## [1,] 0 0 0 0 0 1 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 1 0 0 0 0 0 0
## [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38]
## [1,] 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0 0 0
## [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50]
## [1,] 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0 1 0
## [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62]
## [1,] 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0 0 0
## [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74]
## [1,] 0 0 0 0 0 1 0 0 0 0 0 0
## [2,] 0 0 0 0 1 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0 0 0
## [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86]
## [1,] 0 0 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0 0 0
## [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98]
## [1,] 0 0 0 0 0 0 0 1 0 1 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 1 0 0 0 0
## [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 1 0
## [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138]
## [1,] 0 0 0 0 0 1 0 0 0 0
## [2,] 0 0 0 0 0 1 0 0 0 0
## [3,] 0 0 0 0 0 1 0 0 0 0
## [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 1 0 0 0 0 0
## [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177] [,178]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187] [,188]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 1 0
## [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217] [,218]
## [1,] 0 0 1 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227] [,228]
## [1,] 0 0 0 0 0 0 0 1 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237] [,238]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 1 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257] [,258]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267] [,268]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 1 0 0 0 1 0 0
## [3,] 0 0 0 0 1 0 0 0 0 0
## [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277] [,278]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 1 0 0 0 0 0 0 0 0
## [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 1 0 0 0 0 0 0 0
## [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307] [,308]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317] [,318]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 1 0 0 0 0 1 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327] [,328]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 1 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337] [,338]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347] [,348]
## [1,] 0 0 0 0 0 0 0 0 1 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357] [,358]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 1 0 0 0 0 0 0 0 0
## [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367] [,368]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377] [,378]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 1 0
## [3,] 0 0 0 0 0 0 0 0 0 1
## [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387] [,388]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397] [,398]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407] [,408]
## [1,] 0 0 0 0 0 0 0 0 0 1
## [2,] 0 0 0 0 0 1 1 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417] [,418]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426] [,427] [,428]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 1 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,429] [,430] [,431] [,432] [,433] [,434] [,435] [,436] [,437] [,438]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,439] [,440] [,441] [,442] [,443] [,444] [,445] [,446] [,447] [,448]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,449] [,450] [,451] [,452] [,453] [,454] [,455] [,456] [,457] [,458]
## [1,] 0 0 0 0 0 0 0 1 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,459] [,460] [,461] [,462] [,463] [,464] [,465] [,466] [,467] [,468]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 1 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,469] [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477] [,478]
## [1,] 0 0 0 0 0 0 0 1 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,479] [,480] [,481] [,482] [,483] [,484] [,485] [,486] [,487] [,488]
## [1,] 0 0 0 0 0 0 0 0 1 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496] [,497] [,498]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,499] [,500] [,501] [,502] [,503] [,504] [,505] [,506] [,507] [,508]
## [1,] 0 0 0 0 0 0 0 0 0 1
## [2,] 0 0 0 0 0 0 0 0 0 1
## [3,] 0 0 0 0 0 0 0 0 0 1
## [,509] [,510] [,511] [,512] [,513] [,514] [,515] [,516] [,517] [,518]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 1 0
## [,519] [,520] [,521] [,522] [,523] [,524] [,525] [,526] [,527] [,528]
## [1,] 0 1 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 1 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,529] [,530] [,531] [,532] [,533] [,534] [,535] [,536] [,537] [,538]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,539] [,540] [,541] [,542] [,543] [,544] [,545] [,546] [,547] [,548]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,549] [,550] [,551] [,552] [,553] [,554] [,555] [,556] [,557] [,558]
## [1,] 0 1 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 1 0 0 0 0 0 0 0 1
## [,559] [,560] [,561] [,562] [,563] [,564] [,565] [,566] [,567] [,568]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576] [,577] [,578]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 1 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,579] [,580] [,581] [,582] [,583] [,584] [,585] [,586] [,587] [,588]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 1 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,589] [,590] [,591] [,592] [,593] [,594] [,595] [,596] [,597] [,598]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,599] [,600] [,601] [,602] [,603] [,604] [,605] [,606] [,607] [,608]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 1 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,609] [,610] [,611] [,612] [,613] [,614] [,615] [,616] [,617] [,618]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 1 0 0 0 0 0 0 0
## [,619] [,620] [,621] [,622] [,623] [,624] [,625] [,626] [,627] [,628]
## [1,] 0 0 0 0 0 0 0 1 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 1 0 0
## [,629] [,630] [,631] [,632] [,633] [,634] [,635] [,636] [,637] [,638]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,639] [,640] [,641] [,642] [,643] [,644] [,645] [,646] [,647] [,648]
## [1,] 0 0 1 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 1 0
## [,649] [,650] [,651] [,652] [,653] [,654] [,655] [,656] [,657] [,658]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 1 0 0 0 0 0 0 0
## [,659] [,660] [,661] [,662] [,663] [,664] [,665] [,666] [,667] [,668]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,669] [,670] [,671] [,672] [,673] [,674] [,675] [,676] [,677] [,678]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,679] [,680] [,681] [,682] [,683] [,684] [,685] [,686] [,687] [,688]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 1 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,689] [,690] [,691] [,692] [,693] [,694] [,695] [,696] [,697] [,698]
## [1,] 1 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,699] [,700] [,701] [,702] [,703] [,704] [,705] [,706] [,707] [,708]
## [1,] 0 0 0 0 0 0 1 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,709] [,710] [,711] [,712] [,713] [,714] [,715] [,716] [,717] [,718]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,719] [,720] [,721] [,722] [,723] [,724] [,725] [,726] [,727] [,728]
## [1,] 0 0 0 0 0 0 0 0 1 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 1 0
## [,729] [,730] [,731] [,732] [,733] [,734] [,735] [,736] [,737] [,738]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,739] [,740] [,741] [,742] [,743] [,744] [,745] [,746] [,747] [,748]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,749] [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757] [,758]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,759] [,760] [,761] [,762] [,763] [,764] [,765] [,766] [,767] [,768]
## [1,] 0 0 0 1 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,769] [,770] [,771] [,772] [,773] [,774] [,775] [,776] [,777] [,778]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,779] [,780] [,781] [,782] [,783] [,784] [,785] [,786] [,787] [,788]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,789] [,790] [,791] [,792] [,793] [,794] [,795] [,796] [,797] [,798]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 1 0 0 0 0 0 0 0 0
## [,799] [,800] [,801] [,802] [,803] [,804] [,805] [,806] [,807] [,808]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 1
## [3,] 0 0 0 1 0 0 0 0 0 0
## [,809] [,810] [,811] [,812] [,813] [,814] [,815] [,816] [,817] [,818]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,819] [,820] [,821] [,822] [,823] [,824] [,825] [,826] [,827] [,828]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,829] [,830] [,831] [,832] [,833] [,834] [,835] [,836] [,837] [,838]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,839] [,840] [,841] [,842] [,843] [,844] [,845] [,846] [,847] [,848]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,849] [,850] [,851] [,852] [,853] [,854] [,855] [,856] [,857] [,858]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,859] [,860] [,861] [,862] [,863] [,864] [,865] [,866] [,867] [,868]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,869] [,870] [,871] [,872] [,873] [,874] [,875] [,876] [,877] [,878]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,879] [,880] [,881] [,882] [,883] [,884] [,885] [,886] [,887] [,888]
## [1,] 0 0 0 0 0 0 0 1 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,889] [,890] [,891] [,892] [,893] [,894] [,895] [,896] [,897] [,898]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,899] [,900] [,901] [,902] [,903] [,904] [,905] [,906] [,907] [,908]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,909] [,910] [,911] [,912] [,913] [,914] [,915] [,916] [,917] [,918]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,919] [,920] [,921] [,922] [,923] [,924] [,925] [,926] [,927] [,928]
## [1,] 0 0 0 0 0 0 0 0 0 1
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,929] [,930] [,931] [,932] [,933] [,934] [,935] [,936] [,937] [,938]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,939] [,940] [,941] [,942] [,943] [,944] [,945] [,946] [,947] [,948]
## [1,] 0 0 0 0 0 0 0 0 0 1
## [2,] 0 0 0 0 0 0 0 0 0 1
## [3,] 0 0 0 0 0 0 0 0 0 1
## [,949] [,950] [,951] [,952] [,953] [,954] [,955] [,956] [,957] [,958]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,959] [,960] [,961] [,962] [,963] [,964] [,965] [,966] [,967] [,968]
## [1,] 0 0 0 0 0 0 0 0 0 1
## [2,] 0 0 0 0 0 0 0 0 0 1
## [3,] 0 0 0 0 0 0 0 0 0 1
## [,969] [,970] [,971] [,972] [,973] [,974] [,975] [,976] [,977] [,978]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 1 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,979] [,980] [,981] [,982] [,983] [,984] [,985] [,986] [,987] [,988]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 1 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0 0
## [,989] [,990] [,991] [,992] [,993] [,994] [,995] [,996] [,997] [,998]
## [1,] 0 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 1 0 0 0
## [3,] 1 0 0 0 0 0 0 0 0 0
## [,999] [,1000] [,1001] [,1002] [,1003] [,1004] [,1005] [,1006] [,1007]
## [1,] 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0
## [,1008] [,1009] [,1010] [,1011] [,1012] [,1013] [,1014] [,1015] [,1016]
## [1,] 0 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0 0
## [,1017] [,1018] [,1019] [,1020] [,1021] [,1022] [,1023] [,1024]
## [1,] 0 0 0 0 0 0 0 0
## [2,] 0 0 0 0 0 0 0 0
## [3,] 0 0 0 0 0 0 0 0
# Add compound names
rownames(ecfp4) <- dat$compound
ecfp4 <- data.frame(ecfp4)
# View the first 20 fingerprint bits
ecfp4[, 1:20]
## X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 X16 X17 X18 X19
## Aspirin 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## Caffeine 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## Ibuprofen 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## X20
## Aspirin 1
## Caffeine 0
## Ibuprofen 1
write.csv(ecfp4, paste0(dir_path, Sys.Date(), "-ecfp4.csv"), row.names = T)