fp2bit {ChemmineR} | R Documentation |
The function converts the base 64 encoded PubChem fingerprints to a binary matrix
or a character
vector. If applied to a SDFset
object, then its data block needs to contain the PubChem fingerprint information.
fp2bit(x, type = 3, fptag = "PUBCHEM_CACTVS_SUBSKEYS")
x |
Object of class |
type |
If set to |
fptag |
Name tag in SDF data block where the PubChem fingerprints are stored. Default is set to "PUBCHEM_CACTVS_SUBSKEYS". |
...
matrix
, character
or FPset
Thomas Girke
See PubChem fingerprint specification at: ftp://ftp.ncbi.nih.gov/pubchem/specifications/pubchem_fingerprints.txt
Functions: fpSim
## Load PubChem SDFset sample data(sdfsample); sdfset <- sdfsample cid(sdfset) <- sdfid(sdfset) ## Convert base 64 encoded fingerprints to FPset object fpset <- fp2bit(sdfset) ## Pairwise compound structure comparisons fpSim(fpset[1], fpset[2]) ## Structure similarity searching: x is query and y is fingerprint database fpSim(x=fpset[1], y=fpset, method="Tanimoto", cutoff=0, top="all") ## Compute fingerprint based Tanimoto similarity matrix simMA <- sapply(cid(fpset), function(x) fpSim(x=fpset[x], fpset, sorted=FALSE)) ## Hierarchical clustering with simMA as input hc <- hclust(as.dist(1-simMA), method="single") ## Plot hierarchical clustering tree plot(as.dendrogram(hc), edgePar=list(col=4, lwd=2), horiz=TRUE)