sd2gramSpectrum {Rchemcpp} | R Documentation

## sd2gramSpectrum - Similarity of molecules by walk-based graph kernels

### Description

This function computes several walk-based graph kernel functions based on finite length walks and a fast implementation for input SDF file(s).

### Usage

      sd2gramSpectrum(sdf, sdf2,
        kernelType = c("spectrum", "tanimoto", "minmaxTanimoto", "marginalized", "lambda"),
        margKernelEndProbability = 0.1, lambdaKernelLambda = 1,
        depthMax = as.integer(3), onlyDepthMax = FALSE,
        flagRemoveH = FALSE, morganOrder = as.integer(0),
        silentMode = FALSE, returnNormalized = TRUE,
        detectArom = FALSE)

### Arguments

`sdf` | File containing the molecules. Must be in MDL file format (MOL and SDF files). For more information on the file format see http://en.wikipedia.org/wiki/Chemical_table_file.
`sdf2` | A second file containing molecules. Must also be in SDF. If specified the molecules of the first file will be compared with the molecules of this second file. Default = "missing".
`kernelType` | Type of kernel to be used. Options are "spectrum (Spectrum kernel) , "tanimoto" (Tanimoto kernel), "minmaxTanimoto" (MinMax Tanimoto kernel), "marginalized (Marginalized kernel approximation) and "lambda" (LambdaK kernel). See vignette for details. Default = "spectrum".
`margKernelEndProbability` | The ending probability for the marginalized kernel. Default = 0.1.
`lambdaKernelLambda` | The lambda parameter of the LambdaK kernel. Default = 1.0.
`depthMax` | The maximal length of the molecular fragments. Default = 3.
`onlyDepthMax` | Whether fragments up to the given length should be used or only fragments of the given length. Default = FALSE.
`flagRemoveH` | A logical that indicates whether H-atoms should be removed or not. Default = FALSE
`morganOrder` | The order of the DeMorgan indices to be used. If set to zero no DeMorgan indices are used. The higher the order the more different types of atoms exist and consequently the more dissimilar will be the molecules. Default = 0.
`silentMode` | Whether or not the program should print progress reports to the standart output. Default = FALSE.
`returnNormalized` | A logical specifying whether a normalized kernel matrix should be returned. Default = TRUE.
`detectArom` | Whether aromatic rings should be detected and aromatic bonds should a special bond type. If large molecules are in the data set the detection of aromatic rings can be very time-consuming. (Default = FALSE).

### Value

A numeric matrix containing the similarity values between the molecules.

### Author(s)

Michael Mahr <rchemcpp@bioinf.jku.at> c++ function written by Jean-Luc Perret and Pierre Mahe

### Examples

    sdfolder <- system.file("extdata",package="Rchemcpp")
    sdf <- list.files(sdfolder,full.names=TRUE,pattern="tiny")
    K <- sd2gramSpectrum(sdf)

[Package Rchemcpp version 2.20.1 Index]