calcDrugFPSim: Calculate Drug Molecule Similarity Derived by Molecular...

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Description

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".

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: √(a + b)

• Dice: aka Sorensen, Czekanowski, Hodgkin-Richards - c/0.5[(a+c) + (b+c)]

• Cosine: aka Ochiai, Carbo - c/√((a + c)(b + c))

• Hamming: aka Manhattan, taxi-cab, city-block distance - (a + b)

Value

The numeric similarity value.

Author(s)

Nan Xiao <https://nanx.me>

References

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

Examples

mols = readMolFromSDF(system.file('compseq/tyrphostin.sdf', package = 'Rcpi'))


fp1 = extractDrugEstate(mols[[1]])
fp2 = extractDrugEstate(mols[[2]])
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'tanimoto')
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'euclidean')
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'cosine')
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'dice')
calcDrugFPSim(fp1, fp2, fptype = 'compact', metric = 'hamming')

fp3 = extractDrugEstateComplete(mols[[1]])
fp4 = extractDrugEstateComplete(mols[[2]])
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'tanimoto')
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'euclidean')
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'cosine')
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'dice')
calcDrugFPSim(fp3, fp4, fptype = 'complete', metric = 'hamming')

Example output

OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
   4048890
Try using the -Djava.io.tmpdir= option to select an alternate temp location.

[1] 0.5
[1] 0.9678372
[1] 0.6804138
[1] 0.6666667
[1] 0.06329114
[1] 0.5
[1] 0.9678372
[1] 0.6804138
[1] 0.6666667
[1] 0.06329114

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.