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/rcdk/man/getfp.Rd

http://github.com/rajarshi/cdkr
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 1\name{get.fingerprint}
 2\alias{get.fingerprint}
 3\title{
 4  Evaluate Fingerprints
 5}
 6\description{
 7  This function evaluates fingerprints of a specified type for a set of molecules or
 8  a single molecule. Depending on the nature of the fingerprint,
 9  parameters can be specified. Currently five different fingerprints
10  can be specified:
11  \itemize{
12  \item standard - Considers paths of a given length. The default is
13  but can be changed. These are hashed fingerprints, with a
14  default length of 1024
15  \item extended - Similar to the standard type, but takes rings and
16   atomic properties into account into account
17  \item graph - Similar to the standard type by simply considers connectivity
18  \item hybridization - Similar to the standard type, but only consider hybridization state
19  \item maccs - The popular 166 bit MACCS keys described by MDL
20  \item estate - 79 bit fingerprints corresponding to the E-State atom types described by Hall and Kier
21  \item pubchem - 881 bit fingerprints defined by PubChem
22  \item kr - 4860 bit fingerprint defined by Klekota and Roth
23  \item shortestpath - A fingerprint based on the shortest paths between pairs of atoms and takes into account ring systems, charges etc.
24  \item signature - A feature,count type of fingerprint, similar in nature to circular fingerprints, but based on the signature 
25    descriptor
26  \item circular - An implementation of the ECFP6 fingerprint
27  }
28
29  Depending on whether the input is a single \code{IAtomContainer}
30  object, a list or single vector is returned. Each element of the list 
31  is an S4 object of class \code{\link{fingerprint-class}} or \code{\link{featvec-class}}, 
32  which can be manipulated with the fingerprint package.
33}
34\usage{
35    get.fingerprint(molecule, type = 'standard', 
36                    fp.mode = 'bit', depth=6, size=1024, verbose=FALSE)
37}
38\arguments{
39  \item{molecule}{An \code{IAtomContainer} object that can be obtained
40    by loading them from disk or drawing them in the editor.
41  }
42  \item{type}{The type of fingerprint. See description for possible values. The default is the standard
43  binary fingerprint.}
44  \item{fp.mode}{The type of fingerprint to return. Possible values are 'bit', 'raw', and 'count'. The 'raw' mode will  
45  return a \code{featvec-class} type of fingerprint, representing fragments and their count of occurence in the molecule.
46  The 'count' mode is similar, except that it returns hash values of fragments and their count of occurence.
47  While any of these values can be specified, a given fingerprint implementation may not implement all of them, and in 
48  those cases the return value is NULL.}
49  \item{depth}{The search depth. This argument is ignored for the
50  'pubchem', 'maccs', 'kr' and 'estate' fingerprints}
51  \item{size}{The length of the fingerprint bit string. This argument is ignored for the
52  'pubchem', 'maccs', 'kr', 'signature', 'circular' and 'estate' fingerprints}
53  \item{verbose}{If \code{TRUE}, exceptions, if they occur, will be printed}
54}
55\value{
56  Objects of class \code{\link{fingerprint-class}} or \code{\link{featvec-class}}, from the \code{fingerprint} package. If there is a problem
57  during fingerprint calculation, \code{NULL} is returned.
58}
59\examples{
60## get some molecules
61sp <- get.smiles.parser()
62smiles <- c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1','C1CCC1CC(CN(C)(C))CC(=O)CC')
63mols <- parse.smiles(smiles)
64
65## get a single fingerprint using the standard
66## (hashed, path based) fingerprinter
67fp <- get.fingerprint(mols[[1]])
68
69## get MACCS keys for all the molecules
70fps <- lapply(mols, get.fingerprint, type='maccs')
71
72## get Signature fingerprint
73## feature, count fingerprinter
74fps <- lapply(mols, get.fingerprint, type='signature', fp.mode='raw')
75}      
76
77\seealso{
78  \code{\link{load.molecules}}
79}
80
81\references{
82Faulon et al, \href{http://dx.doi.org/10.1021/ci020345w}{The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR studies}, \emph{J. Chem. Inf. Comput. Sci.}, 2003, \emph{43}, 707-720. 	
83}
84
85\keyword{programming}
86
87\author{Rajarshi Guha (\email{rajarshi.guha@gmail.com})}