Rcpp_Rmoleculeset-class {Rchemcpp} | R Documentation

## Class `"Rcpp_Rmoleculeset"`

### 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)

[Package Rchemcpp version 2.20.1 Index]