readRmoleculeset: Generating an Rmoleculeset from an SDF file

Description Usage Arguments Value Author(s)

View source: R/utility.R

Description

This function uses the ChemmineR package to read an SDF file and converts it into an Rmoleculeset that can be used as input for the kernel functions sd2gram, sd2gramSpectrum, ..., sd2gram3Dpharma.

Usage

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  readRmoleculeset(sdfFileName, detectArom = TRUE,
    bound = Inf, type = 2)

Arguments

sdfFileName

The name of the SDF file containing the molecules.

detectArom

If the molecules in the SDF file have no annotated aromatic bonds, the ChemmineR function rings is used for detecting aromaticity. (Default = TRUE).

bound

Detection of aromaticity can be time consuming if the molecules are large. Detection is only done if the number of atoms is below the given number. (Default = Inf).

type

Experimental parameter to switch between to types of the function. (Default = 2).

Value

An instance of Rmoleculeset.

Author(s)

Guenter Klambauer <[email protected]>


Rchemcpp documentation built on May 2, 2018, 3:16 a.m.