# Generate molecular fingerprints `get.fingerprint` returns a `fingerprint` object representing molecular fingerprint of the input molecule. ```r 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` ## Returns an S4 object of class `fingerprint-class` or `featvec-class`, which can be manipulated with the fingerprint package. ## Examples ```r ## 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') ``` ## Author(s) Rajarshi Guha (rajarshi.guha@gmail.com )

get.fingerprint function