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Generate molecular fingerprints

Source: R/fingerprint.R
get.fingerprint.Rd

`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

Rajarshi Guha (rajarshi.guha@gmail.com)

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')