get.fingerprint: Generate molecular fingerprints

In rcdk: Interface to the 'CDK' Libraries

Generate molecular fingerprints

Description

'get.fingerprint' returns a 'fingerprint' object representing molecular fingerprint of the input molecule.

Usage

get.fingerprint(
  molecule,
  type = "standard",
  fp.mode = "bit",
  depth = 6,
  size = 1024,
  substructure.pattern = character(),
  circular.type = "ECFP6",
  verbose = FALSE
)

Arguments

molecule	A jobjRef object to an IAtomContaine
type	The type of fingerprint. Possible values are: standard - Considers paths of a given length. The default is but can be changed. These are hashed fingerprints, with a default length of 1024 extended - Similar to the standard type, but takes rings and atomic properties into account into account graph - Similar to the standard type by simply considers connectivity hybridization - Similar to the standard type, but only consider hybridization state maccs - The popular 166 bit MACCS keys described by MDL estate - 79 bit fingerprints corresponding to the E-State atom types described by Hall and Kier pubchem - 881 bit fingerprints defined by PubChem kr - 4860 bit fingerprint defined by Klekota and Roth shortestpath - A fingerprint based on the shortest paths between pairs of atoms and takes into account ring systems, charges etc. signature - A feature,count type of fingerprint, similar in nature to circular fingerprints, but based on the signature descriptor circular - An implementation of the ECFP6 (default) fingerprint. Other circular types can be chosen by modifying the circular.type parameter. substructure - Fingerprint based on list of SMARTS pattern. By default a set of functional groups is tested.
fp.mode	The style of fingerprint. Specifying "'bit'" will return a binary fingerprint, "'raw'" returns the the original representation (usually sequence of integers) and "'count'" returns the fingerprint as a sequence of counts.
depth	The search depth. This argument is ignored for the 'pubchem', 'maccs', 'kr' and 'estate' fingerprints
size	The final length of the fingerprint. This argument is ignored for the 'pubchem', 'maccs', 'kr', 'signature', 'circular' and 'estate' fingerprints
substructure.pattern	List of characters containing the SMARTS pattern to match. If the an empty list is provided (default) than the functional groups substructures (default in CDK) are used.
circular.type	Name of the circular fingerprint type that should be computed given as string. Possible values are: 'ECFP0', 'ECFP2', 'ECFP4', 'ECFP6' (default), 'FCFP0', 'FCFP2', 'FCFP4' and 'FCFP6'.
verbose	Verbose output if TRUE

Value

an S4 object of class fingerprint-class or featvec-class, which can be manipulated with the fingerprint package.

Author(s)

Rajarshi Guha ([e-mail])

Examples

## 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')
## get Substructure fingerprint for functional group fragments
fps <- lapply(mols, get.fingerprint, type='substructure')

## get Substructure count fingerprint for user defined fragments
mol1 <- parse.smiles("c1ccccc1CCC")[[1]]
smarts <- c("c1ccccc1", "[CX4H3][#6]", "[CX2]#[CX2]")
fps <- get.fingerprint(mol1, type='substructure', fp.mode='count',
    substructure.pattern=smarts)

## get ECFP0 count fingerprints 
mol2 <- parse.smiles("C1=CC=CC(=C1)CCCC2=CC=CC=C2")[[1]]
fps <- get.fingerprint(mol2, type='circular', fp.mode='count', circular.type='ECFP0')

rcdk documentation built on July 9, 2023, 7:27 p.m.