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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{<div class="r6-fields">}}
\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{</div>}}
+}
+\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$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$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{</div>}}
+}
-\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{<hr>}}
+\if{html}{\out{<a id="method-try_pubchem"></a>}}
+\if{latex}{\out{\hypertarget{method-try_pubchem}{}}}
+\subsection{Method \code{try_pubchem()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_pubchem"></a>}}
+\if{latex}{\out{\hypertarget{method-get_pubchem}{}}}
+\subsection{Method \code{get_pubchem()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_rdkit"></a>}}
+\if{latex}{\out{\hypertarget{method-get_rdkit}{}}}
+\subsection{Method \code{get_rdkit()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get_chyaml"></a>}}
+\if{latex}{\out{\hypertarget{method-get_chyaml}{}}}
+\subsection{Method \code{get_chyaml()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$get_chyaml(
+ repo = c("wd", "local", "web"),
+ chyaml = paste0(URLencode(self$identifier), ".yaml")
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_p0"></a>}}
+\if{latex}{\out{\hypertarget{method-add_p0}{}}}
+\subsection{Method \code{add_p0()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_cwsat"></a>}}
+\if{latex}{\out{\hypertarget{method-add_cwsat}{}}}
+\subsection{Method \code{add_cwsat()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_PUF"></a>}}
+\if{latex}{\out{\hypertarget{method-add_PUF}{}}}
+\subsection{Method \code{add_PUF()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF(
+ PUF = 0,
+ source = "focus_generic_gw_2014",
+ page = 41,
+ remark = "Conservative default value"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_TP"></a>}}
+\if{latex}{\out{\hypertarget{method-add_TP}{}}}
+\subsection{Method \code{add_TP()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_transformation"></a>}}
+\if{latex}{\out{\hypertarget{method-add_transformation}{}}}
+\subsection{Method \code{add_transformation()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_transformation(
+ study_type,
+ TP_identifier,
+ max_occurrence,
+ remark = "",
+ source = NA,
+ pages = NA
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_soil_degradation"></a>}}
+\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}}
+\subsection{Method \code{add_soil_degradation()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_degradation(
+ soils,
+ DT50_mod,
+ DT50_mod_ref,
+ type = NA,
+ country = NA,
+ pH_orig = NA,
+ pH_medium = NA,
+ pH_H2O = NA,
+ perc_OC = NA,
+ temperature = NA,
+ moisture = NA,
+ category = "lab",
+ formulation = NA,
+ model = NA,
+ chi2 = NA,
+ remark = "",
+ source,
+ page = NA
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_soil_ff"></a>}}
+\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}}
+\subsection{Method \code{add_soil_ff()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add_soil_sorption"></a>}}
+\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}}
+\subsection{Method \code{add_soil_sorption()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_sorption(
+ soils,
+ Kf,
+ Kfoc,
+ N,
+ type = NA,
+ pH_orig = NA,
+ pH_medium = NA,
+ pH_H2O = NA,
+ perc_OC = NA,
+ perc_clay = NA,
+ CEC = NA,
+ remark = "",
+ source,
+ page = NA
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-pdf"></a>}}
+\if{latex}{\out{\hypertarget{method-pdf}{}}}
+\subsection{Method \code{pdf()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$pdf(
+ file = paste0(self$identifier, ".pdf"),
+ dir = "structures/pdf",
+ template = NULL
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-png"></a>}}
+\if{latex}{\out{\hypertarget{method-png}{}}}
+\subsection{Method \code{png()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$png(
+ file = paste0(self$identifier, ".png"),
+ dir = "structures/png",
+ antialias = "gray"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-emf"></a>}}
+\if{latex}{\out{\hypertarget{method-emf}{}}}
+\subsection{Method \code{emf()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{chent$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
}
}
-\keyword{data}

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