sd2gramSpectrum: 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.

Examples

Run this code

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

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