get.fingerprint {rcdk} | R Documentation |
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.
get.fingerprint(molecule, type = 'standard', depth=6, size=1024)
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 |
Objects of class fingerprint, from the fingerprint
package
Rajarshi Guha (rguha@indiana.edu)
## 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')