get.fingerprint {rcdk}R Documentation

Evaluate Fingerprints

Description

This function evaluates fingerprints of a specified type for a set of molecules or a single molecule. Depending on the nature of the fingerprint, parameters can be specified. Currently five different fingerprints can be specified:

Depending on whether the input is a single IAtomContainer object, a list or single vector is returned. Each element of the list is an S4 object of class fingerprint, which can be manipulated with the fingerprint package.

Usage

    get.fingerprint(molecule, type = 'standard', depth=6, size=1024)

Arguments

molecule An IAtomContainer object that can be obtained by loading them from disk or drawing them in the editor.
type The type of fingerprint. Alternatives include 'extended', 'graph', 'maccs', 'estate'
depth The search depth. This argument is ignored for the 'maccs' and 'estate' fingerprints
size The length of the fingerprint bit string. This argument is ignored for the 'maccs' and 'estate' fingerprints

Value

Objects of class fingerprint, from the fingerprint package

Author(s)

Rajarshi Guha (rguha@indiana.edu)

See Also

load.molecules

Examples

## get some molecules
sp <- get.smiles.parser()
smiles <- c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1','C1CCC1CC(CN(C)(C))CC(=O)CC')
mols <- sapply(smiles, parse.smiles, parser=sp)

## get a single fingerprint using the standard
## (hashed, path based) fingerprinter
fp <- get.fingerprint(mols[[1]])

## get MACCS keys for all the molecules
fps <- lapply(mols, get.fingerprint, type='maccs')

[Package rcdk version 2.9.2 Index]