Calculate Drug Molecule Similarity Derived by Molecular Fingerprints

Usage

calcDrugFPSim(
  fp1,
  fp2,
  fptype = c("compact", "complete"),
  metric = c("tanimoto", "euclidean", "cosine", "dice", "hamming")
)

Arguments

fp1: The first molecule's fingerprints, could be extracted by extractDrugMACCS(), extractDrugMACCSComplete() etc.
fp2: The second molecule's fingerprints.
fptype: The fingerprint type, must be one of "compact" or "complete".
metric: The similarity metric, one of "tanimoto", "euclidean", "cosine", "dice" and "hamming".

Value

The numeric similarity value.

Details

This function calculate drug molecule fingerprints similarity. Define a as the features of object A, b is the features of object B, c is the number of common features to A and B:

Tanimoto: aka Jaccard - \(c/a+b+c\)
Euclidean: \(\sqrt(a + b)\)
Dice: aka Sorensen, Czekanowski, Hodgkin-Richards - \(c/0.5[(a+c) + (b+c)]\)
Cosine: aka Ochiai, Carbo - \(c/\sqrt((a + c)(b + c))\)
Hamming: aka Manhattan, taxi-cab, city-block distance - \((a + b)\)

References

Gasteiger, Johann, and Thomas Engel, eds. Chemoinformatics. Wiley.com, 2006.

Examples

# \donttest{
mols = readMolFromSDF(system.file('compseq/tyrphostin.sdf', package = 'Rcpi'))
#> Error in loadMolecules(normalizePath(sdffile)): The package "rcdk" is required to load molecular structures

fp1 = extractDrugEstate(mols[[1]])
#> Error in eval(expr, envir, enclos): object 'mols' not found
fp2 = extractDrugEstate(mols[[2]])
#> Error in eval(expr, envir, enclos): object 'mols' not found
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'tanimoto')
#> Error in eval(expr, envir, enclos): object 'fp1' not found
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'euclidean')
#> Error in eval(expr, envir, enclos): object 'fp1' not found
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'cosine')
#> Error in eval(expr, envir, enclos): object 'fp1' not found
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'dice')
#> Error in eval(expr, envir, enclos): object 'fp1' not found
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'hamming')
#> Error in eval(expr, envir, enclos): object 'fp1' not found

fp3 = extractDrugEstateComplete(mols[[1]])
#> Error in eval(expr, envir, enclos): object 'mols' not found
fp4 = extractDrugEstateComplete(mols[[2]])
#> Error in eval(expr, envir, enclos): object 'mols' not found
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'tanimoto')
#> Error in eval(expr, envir, enclos): object 'fp3' not found
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'euclidean')
#> Error in eval(expr, envir, enclos): object 'fp3' not found
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'cosine')
#> Error in eval(expr, envir, enclos): object 'fp3' not found
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'dice')
#> Error in eval(expr, envir, enclos): object 'fp3' not found
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'hamming')# }
#> Error in eval(expr, envir, enclos): object 'fp3' not found