From 6937e41d317b953d8246203814500166dbe89470 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 13 Oct 2020 11:26:03 +0200 Subject: Temporarily remove @example tags Due to r-lib/roxygen2#1158 --- man/chent.Rd | 273 +++++++++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 256 insertions(+), 17 deletions(-) (limited to 'man/chent.Rd') diff --git a/man/chent.Rd b/man/chent.Rd index 29fba70..a1a5fe8 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -1,20 +1,19 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/chent.R -\docType{class} \name{chent} \alias{chent} \title{An R6 class for chemical entities with associated data} -\format{An \code{\link{R6Class}} generator object} -\usage{ -chent +\format{ +An \code{\link{R6Class}} generator object } \description{ The class is initialised with an identifier. Chemical information is retrieved from the internet. Additionally, it can be generated using RDKit if RDKit and its python bindings are installed and configured for use with PythonInR. } -\section{Fields}{ - +\keyword{data} +\section{Public fields}{ +\if{html}{\out{
}} \describe{ \item{\code{identifier}}{The identifier that was used to initiate the object, with attribute 'source'} @@ -50,18 +49,258 @@ configured for use with PythonInR} \item{\code{soil_sorption}}{Dataframe of soil sorption data} \item{\code{PUF}}{Plant uptake factor} -}} +} +\if{html}{\out{
}} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-new}{\code{chent$new()}} +\item \href{#method-try_pubchem}{\code{chent$try_pubchem()}} +\item \href{#method-get_pubchem}{\code{chent$get_pubchem()}} +\item \href{#method-get_rdkit}{\code{chent$get_rdkit()}} +\item \href{#method-get_chyaml}{\code{chent$get_chyaml()}} +\item \href{#method-add_p0}{\code{chent$add_p0()}} +\item \href{#method-add_cwsat}{\code{chent$add_cwsat()}} +\item \href{#method-add_PUF}{\code{chent$add_PUF()}} +\item \href{#method-add_TP}{\code{chent$add_TP()}} +\item \href{#method-add_transformation}{\code{chent$add_transformation()}} +\item \href{#method-add_soil_degradation}{\code{chent$add_soil_degradation()}} +\item \href{#method-add_soil_ff}{\code{chent$add_soil_ff()}} +\item \href{#method-add_soil_sorption}{\code{chent$add_soil_sorption()}} +\item \href{#method-pdf}{\code{chent$pdf()}} +\item \href{#method-png}{\code{chent$png()}} +\item \href{#method-emf}{\code{chent$emf()}} +\item \href{#method-clone}{\code{chent$clone()}} +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-new}{}}} +\subsection{Method \code{new()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$new( + identifier, + smiles = NULL, + smiles_source = "user", + inchikey = NULL, + inchikey_source = "user", + pubchem = TRUE, + pubchem_from = c("name", "smiles", "inchikey"), + rdkit = TRUE, + template = NULL, + chyaml = TRUE +)}\if{html}{\out{
}} +} -\examples{ -oct <- chent$new("1-octanol", smiles = "CCCCCCCCO") -print(oct) -if (!is.null(oct$Picture)) { - plot(oct) } -caffeine <- chent$new("caffeine") -print(caffeine) -if (!is.null(caffeine$Picture)) { - plot(caffeine) +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-try_pubchem}{}}} +\subsection{Method \code{try_pubchem()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-get_pubchem}{}}} +\subsection{Method \code{get_pubchem()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-get_rdkit}{}}} +\subsection{Method \code{get_rdkit()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-get_chyaml}{}}} +\subsection{Method \code{get_chyaml()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$get_chyaml( + repo = c("wd", "local", "web"), + chyaml = paste0(URLencode(self$identifier), ".yaml") +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_p0}{}}} +\subsection{Method \code{add_p0()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_cwsat}{}}} +\subsection{Method \code{add_cwsat()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_PUF}{}}} +\subsection{Method \code{add_PUF()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_PUF( + PUF = 0, + source = "focus_generic_gw_2014", + page = 41, + remark = "Conservative default value" +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_TP}{}}} +\subsection{Method \code{add_TP()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_transformation}{}}} +\subsection{Method \code{add_transformation()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_transformation( + study_type, + TP_identifier, + max_occurrence, + remark = "", + source = NA, + pages = NA +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}} +\subsection{Method \code{add_soil_degradation()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_soil_degradation( + soils, + DT50_mod, + DT50_mod_ref, + type = NA, + country = NA, + pH_orig = NA, + pH_medium = NA, + pH_H2O = NA, + perc_OC = NA, + temperature = NA, + moisture = NA, + category = "lab", + formulation = NA, + model = NA, + chi2 = NA, + remark = "", + source, + page = NA +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}} +\subsection{Method \code{add_soil_ff()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}} +\subsection{Method \code{add_soil_sorption()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$add_soil_sorption( + soils, + Kf, + Kfoc, + N, + type = NA, + pH_orig = NA, + pH_medium = NA, + pH_H2O = NA, + perc_OC = NA, + perc_clay = NA, + CEC = NA, + remark = "", + source, + page = NA +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-pdf}{}}} +\subsection{Method \code{pdf()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$pdf( + file = paste0(self$identifier, ".pdf"), + dir = "structures/pdf", + template = NULL +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-png}{}}} +\subsection{Method \code{png()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$png( + file = paste0(self$identifier, ".png"), + dir = "structures/png", + antialias = "gray" +)}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-emf}{}}} +\subsection{Method \code{emf()}}{ +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{
}} +} + +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{chent$clone(deep = FALSE)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{deep}}{Whether to make a deep clone.} +} +\if{html}{\out{
}} +} } } -\keyword{data} -- cgit v1.2.1