fp2bit {ChemmineR} | R Documentation

## Convert base 64 fingerprints to binary

### Description

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.

### Usage

    fp2bit(x, type = 3, fptag = "PUBCHEM_CACTVS_SUBSKEYS")

### Arguments

`x` | Object of class `SDFset`, `matrix` or `character`
`type` | If set to `1`, the results are returned as binary `matrix`. If set to `2`, the results are returned as `character` strings in a named vector. If set to `3` (default), the results are returned as `FPset` object.
`fptag` | Name tag in SDF data block where the PubChem fingerprints are stored. Default is set to "PUBCHEM_CACTVS_SUBSKEYS".

### Details

...

### Value

`matrix`, `character` or `FPset`

### Author(s)

Thomas Girke

### References

See PubChem fingerprint specification at: ftp://ftp.ncbi.nih.gov/pubchem/specifications/pubchem_fingerprints.txt

### See Also

Functions: `fpSim`

### Examples

    ## 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)

[Package ChemmineR version 3.40.0 Index]