Rchemcpp (version 2.10.0)

sd2gram3Dpharma: sd2gram3Dpharma - Similarity of molecules by the exact pharmacophore kernel.

Description

This tool implements the (exact version of) pharmacophore kernel for 3D structures of molecules (Mahe, 2006).

Usage

sd2gram3Dpharma(sdf, sdf2, chargesFileName = "", chargesFileName2 = "", edgeKernelType = c("RBF", "triangular"), edgeKernelParameter = 1, atomKernelMatrix = "", flagRemoveH = FALSE, morganOrder = as.integer(0), morganChargesThreshold = 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.

edgeKernelType

Options to specify the kernel function comparing distances between atoms. Choices are "RBF" or "triangular". Default = "RBF".

edgeKernelParameter

Specifies the parameter associated to these kernels. Either the bandwith of the RBF kernel or the cut-off of the triangular kernel. Default = 1.

atomKernelMatrix

A string that sets the similarity measure between atoms that should be used. Default = "missing".

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 types of atoms exist and consequently the more dissimilar will be the molecules. Default = 0.

morganChargesThreshold

specifies a threshold above which partial Morgan 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.

silentMode

Whether or not the program should print progress reports to the standart output. Default = TRUE.

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.

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 <- sd2gram3Dpharma(sdf)