Rcpp_Rmoleculeset-class: Class '"Rcpp_Rmoleculeset"'

In Rchemcpp: Similarity measures for chemical compounds

Description

This class is a Rcpp modules wrapper for the chemcpp c++ class "MoleculeSet". It allows reading molecule-files and computing simple comparison-matrices. When calling the function "setComparisonSet" however, the argument object is copied (instead of storing a reference). Please note that only a part of the original chemcpp class "MoleculeSet" is exposed until now.

Extends

chemcpp c++ class "MoleculeSet"

Methods

writeSelfKernelList(...):

Write self kernel list

writeGramMatrix(...):

Write the gram matrix to a file, if one has been computed

setMorganLabels(...):

Set Morgan labels

setMorganChargesLabels(...):

Set Morgan Charges label

setKashimaKernelParam(...):

Set Kashima kernel parameter

setComparisonSetSelf(...):

Set the comparison set to be the set itself; NOTE: this is the preferred way to compare a set with itself, because faster implementations are used for comparison this way

setComparisonSetCopy(...):

Set the comparison set to be a different set of molecules; NOTE: this function copies the object specified as argument

readPartialCharges(...):

Add partial charges from file

numMolecules(...):

Returns the number of contained molecules

normalizeTanimoto_raw(...):

Normalize Tanimoto kernel

normalizeTanimotoMinMax(...):

Normalize Tanimoto min-max kernel

normalizeTanimoto(...):

Normalize Tanimoto kernel

normalizeGram_raw(...):

Normalize the gram-matrix

normalizeGram(...):

Normalize the gram-matrix

noTottersTransform(...):

Transform to avoid totters

initializeSelfKernel(...):

Initialize the self-kernel

initializeGram(...):

Initialize the gram matrix

hideHydrogens(...):

Hide hydrogen atoms in all contained molecules

gramCompute3D(...):

Compute 3D gram

gramCompute(...):

Compute gram

getGramNormal(...):

Return the normalized gram matrix, if one has been computed

getGram(...):

Return the gram matrix, if one has been computed

getComparisonSet(...):

Return A POINTER to the comparison set contained in the set; NOTE: this pointer expires when the set is destroyed or a different comparison set is set

bondsListing(...):

Return a list of all bonds which are present in the set

atomsLabelsListing(...):

Return a list of all atom symbols which are present in the set

addSD2(...):

Load a file containing molecules

addSD(...):

Load a file containing molecules

addMoleculeCopy(...):

Add a copy of a molecule object to the set

addKCF2(...):

Load a file containing molecules

addKCF(...):

Load a file containing molecules

getMolByIndex(...):

Return A POINTER to the molecule specified by the Index (zero-based); NOTE: this pointer expires when the set or the molecules in the set are destroyed

length(...):

Return the number of molecules in the molecule set

Author(s)

Michael Mahr; base class written by Jean-Luc Perret and Pierre Mahe

Examples

sdfolder <- system.file("extdata",package="Rchemcpp")
sdf <- list.files(sdfolder,full.names=TRUE,pattern="small")
set <- new(Rmoleculeset)
set$addSD(sdf, FALSE)

Rchemcpp documentation built on May 6, 2019, 4:58 a.m.