sd2gram3Dspectrum {Rchemcpp} | R Documentation

## sd2gram3Dspectrum - Similarity of molecules by fast approximations of the pharmacophore kernel

### Description

This tool implements the six discrete approximations of the pharmacophore kernel presented in "The pharmacophore kernel for virtual screening with support vector machines" (Mahe, 2006).

### Usage

      sd2gram3Dspectrum(sdf, sdf2, chargesFileName = "",
        chargesFileName2 = "",
        kernelType = c("3Pspectrum", "3Pbinary", "3Ptanimoto", "2Pspectrum", "2Pbinary", "2Ptanimoto"),
        depthMax = as.integer(3), nBins = as.integer(20),
        distMin = 0, distMax = 20, flagRemoveH = FALSE,
        morganOrder = as.integer(0), chargesThreshold = 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 format. If specified the molecules of the first file will be compared with the molecules of this second file. Default = "missing".
`chargesFileName` | A character with the name of the file containing the atom charges. Default = missing.
`chargesFileName2` | A character with the name of the file containing the atom charges. Default = missing.
`kernelType` | Type of kernel to be used. Possible choices are 3-points spectrum kernel ("3Pspectrum"), 3-points binary kernel ("3Pbinary"), 3-points Tanimoto kernel ("3Ptanimoto"), 2-points spectrum kernel ("2Pspectrum"), 2-points binary kernel ("2Pbinary"), 2-points Tanimoto kernel ("2Ptanimoto"). Default = "3Pspectrum".
`depthMax` | The maximal length of the molecular fragments. Default = 3.
`nBins` | number of bins used to discretize the inter-atomic lengths. An adequate value for the number of bins is between 20 and 30. Default = 20.
`distMin` | minimum distance for inter-atomic distance range. Default = 0.
`distMax` | maximum distance in angstrom for inter-atomic distance range. Default = 20.
`chargesThreshold` | specifies a threshold above which partial charges are considered as positive/negative. By default this threshold is zero, and every positive (resp. negative) partial charge is seen as a positive (resp. negative) charge. However, it might be interesting to consider a threshold of 0.2 for example, in which case only partial charges greater than 0.2 (resp. smaller than -0.2) would be seen as positive (resp. negative). Default = 0.
`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.
`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

### References

(Mahe, 2006) – P. Mahe, L. Ralaivola, V. Stoven, and J.-P. Vert. The pharmacophore kernel for virtual screening with support vector machines. Technical Report, HAL:ccsd-00020066, Ecole des Mines de Paris, March 2006.

### Examples

    sdfolder <- system.file("extdata",package="Rchemcpp")
    sdf <- list.files(sdfolder,full.names=TRUE,pattern="tiny")
    K <- sd2gram3Dspectrum(sdf)

[Package Rchemcpp version 2.24.0 Index]