% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/chent.R
\name{chent}
\alias{chent}
\title{An R6 class for chemical entities with associated data}
\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.
}
\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'}

\item{\code{inchikey}}{InChI Key, with attribute 'source'}

\item{\code{smiles}}{SMILES code, with attribute 'source'}

\item{\code{mw}}{Molecular weight, with attribute 'source'}

\item{\code{pubchem}}{List of information retreived from PubChem}

\item{\code{rdkit}}{List of information obtained with RDKit, if installed and
configured for use with PythonInR}

\item{\code{svg}}{SVG code}

\item{\code{Picture}}{Graph as a \code{\link{picture}} object obtained using grImport}

\item{\code{Pict_font_size}}{Font size as extracted from the intermediate PostScript file}

\item{\code{pdf_height}}{Height of the MediaBox in the pdf after cropping}

\item{\code{p0}}{Vapour pressure in Pa}

\item{\code{cwsat}}{Water solubility in mg/L}

\item{\code{chyaml}}{List of information obtained from a YAML file}

\item{\code{soil_degradation}}{Dataframe of modelling DT50 values}

\item{\code{soil_ff}}{Dataframe of formation fractions}

\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>}}
}

}
\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>}}
}
}
}