getfp: Evaluate Fingerprints

Description Usage Arguments Value Author(s) References See Also Examples

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-class or featvec-class, which can be manipulated with the fingerprint package.

Usage

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    get.fingerprint(molecule, type = 'standard', 
                    fp.mode = 'bit', depth=6, size=1024, verbose=FALSE)

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. See description for possible values. The default is the standard binary fingerprint.

fp.mode

The type of fingerprint to return. Possible values are 'bit', 'raw', and 'count'. The 'raw' mode will return a featvec-class type of fingerprint, representing fragments and their count of occurence in the molecule. The 'count' mode is similar, except that it returns hash values of fragments and their count of occurence. While any of these values can be specified, a given fingerprint implementation may not implement all of them, and in those cases the return value is NULL.

depth

The search depth. This argument is ignored for the 'pubchem', 'maccs', 'kr' and 'estate' fingerprints

size

The length of the fingerprint bit string. This argument is ignored for the 'pubchem', 'maccs', 'kr', 'signature', 'circular' and 'estate' fingerprints

verbose

If TRUE, exceptions, if they occur, will be printed

Value

Objects of class fingerprint-class or featvec-class, from the fingerprint package. If there is a problem during fingerprint calculation, NULL is returned.

Author(s)

Rajarshi Guha ([email protected])

References

Faulon et al, The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR studies, J. Chem. Inf. Comput. Sci., 2003, 43, 707-720.

See Also

load.molecules

Examples

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

## 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')

## get Signature fingerprint
## feature, count fingerprinter
fps <- lapply(mols, get.fingerprint, type='signature', fp.mode='raw')

rcdk documentation built on April 30, 2018, 5:03 p.m.