getCDKlogPsAndRT: Use rcdk to calculate AlogP and XlogP from SMILES and...

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

A small wrapper function to calculate AlogP and XlogP with rcdk from a SMILES code (as getCDKlogPs) plus estimate retention times using a simple linear model. Default model was calculated on 810 Eawag reference standards and is only valid for this Xbridge chromatographic program.

Usage

getCDKlogPsAndRT <- function(smiles,kekulise=TRUE,model=c(3.654,1.6225),quiet=TRUE)

Arguments

smiles	Valid SMILES code used to perform calculation.
kekulise	Default TRUE performs aromaticity detection prior to calculation. FALSE interprets the SMILES "as is". Can result in dramatically different logP values.
model	A vector of length 2 containing the intercept and slope for the model. Default values c(3.654,1.6225) arise from the standard Eawag non-target chromatographic program on 810 standards.

Value

Returns the resulting AlogP, XlogP and RT estimated from XlogP values in a list. Default model returns RT in minutes.

Author(s)

Emma Schymanski <[e-mail]>

See Also

parse.smiles, get.alogp, get.xlogp, getCDKlogPs.

Examples

getCDKlogPsAndRT("c1ccccc1")
getCDKlogPsAndRT("c1ccccc1",kekulise=FALSE)
getCDKlogPsAndRT("c1ccc2c(c1)[nH]nn2")
getCDKlogPsAndRT("c1ccc2c(c1)[nH]nn2",kekulise=FALSE)

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.