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:
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 fingerprint
Depending on whether the input is a single
object, a list or single vector is returned. Each element of the list
is an S4 object of class
which can be manipulated with the fingerprint package.
The type of fingerprint. See description for possible values. The default is the standard binary fingerprint.
The type of fingerprint to return. Possible values are 'bit', 'raw', and 'count'. The 'raw' mode will
The search depth. This argument is ignored for the 'pubchem', 'maccs', 'kr' and 'estate' fingerprints
The length of the fingerprint bit string. This argument is ignored for the 'pubchem', 'maccs', 'kr', 'signature', 'circular' and 'estate' fingerprints
Objects of class
featvec-class, from the
fingerprint package. If there is a problem
during fingerprint calculation,
NULL is returned.
Rajarshi Guha ([email protected])
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.
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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[]) ## 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')
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