path: root/man/chent.Rd

% 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.
}
\examples{
caffeine <- chent$new("caffeine")
print(caffeine)
if (!is.null(caffeine$Picture)) {
  plot(caffeine)
}
oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
print(oct)
}
\section{Public fields}{
\if{html}{\out{<div class="r6-fields">}}
\describe{
\item{\code{identifier}}{(\code{character(1)})\cr
The identifier that was used to initiate the object, with attribute 'source'}

\item{\code{inchikey}}{(\code{character(1)})\cr
InChI Key, with attribute 'source'}

\item{\code{smiles}}{(\code{character()})\cr
SMILES code(s), with attribute 'source'}

\item{\code{mw}}{(\code{numeric(1)})\cr
Molecular weight, with attribute 'source'}

\item{\code{pubchem}}{(\code{list()})\cr
List of information retrieved from PubChem}

\item{\code{rdkit}}{List of information obtained with RDKit}

\item{\code{mol}}{<rdkit.Chem.rdchem.Mol> object}

\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{PUF}}{Plant uptake factor}

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

\item{\code{TPs}}{List of transformation products as chent objects}

\item{\code{transformations}}{Data frame of observed transformations}

\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}
}
\if{html}{\out{</div>}}
}
\section{Methods}{
\subsection{Public methods}{
\itemize{
\item \href{#method-chent-new}{\code{chent$new()}}
\item \href{#method-chent-try_pubchem}{\code{chent$try_pubchem()}}
\item \href{#method-chent-get_pubchem}{\code{chent$get_pubchem()}}
\item \href{#method-chent-get_rdkit}{\code{chent$get_rdkit()}}
\item \href{#method-chent-get_chyaml}{\code{chent$get_chyaml()}}
\item \href{#method-chent-add_p0}{\code{chent$add_p0()}}
\item \href{#method-chent-add_cwsat}{\code{chent$add_cwsat()}}
\item \href{#method-chent-add_PUF}{\code{chent$add_PUF()}}
\item \href{#method-chent-add_TP}{\code{chent$add_TP()}}
\item \href{#method-chent-add_transformation}{\code{chent$add_transformation()}}
\item \href{#method-chent-add_soil_degradation}{\code{chent$add_soil_degradation()}}
\item \href{#method-chent-add_soil_ff}{\code{chent$add_soil_ff()}}
\item \href{#method-chent-add_soil_sorption}{\code{chent$add_soil_sorption()}}
\item \href{#method-chent-pdf}{\code{chent$pdf()}}
\item \href{#method-chent-png}{\code{chent$png()}}
\item \href{#method-chent-emf}{\code{chent$emf()}}
\item \href{#method-chent-clone}{\code{chent$clone()}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-new"></a>}}
\if{latex}{\out{\hypertarget{method-chent-new}{}}}
\subsection{Method \code{new()}}{
Creates a new instance of this \link[R6:R6Class]{R6} class.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$new(
  identifier,
  smiles = NULL,
  inchikey = NULL,
  pubchem = TRUE,
  pubchem_from = c("name", "smiles", "inchikey"),
  rdkit = TRUE,
  template = NULL,
  chyaml = FALSE
)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{identifier}}{Identifier to be stored in the object}

\item{\code{smiles}}{Optional user provided SMILES code}

\item{\code{inchikey}}{Optional user provided InChI Key}

\item{\code{pubchem}}{Should an attempt be made to retrieve chemical
information from PubChem via the webchem package?}

\item{\code{pubchem_from}}{Possibility to select the argument
that is used to query pubchem}

\item{\code{rdkit}}{Should an attempt be made to retrieve chemical
information from a local rdkit installation via python
and the reticulate package?}

\item{\code{template}}{An optional SMILES code to be used as template for RDKit}

\item{\code{chyaml}}{Should we look for a identifier.yaml file in the working
directory?}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-try_pubchem"></a>}}
\if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}}
\subsection{Method \code{try_pubchem()}}{
Try to get chemical information from PubChem
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{query}}{Query string to be passed to \link[webchem:get_cid]{get_cid}}

\item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid}}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-get_pubchem"></a>}}
\if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}}
\subsection{Method \code{get_pubchem()}}{
Get chemical information from PubChem for a known PubChem CID
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{pubchem_cid}}{CID}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-get_rdkit"></a>}}
\if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}}
\subsection{Method \code{get_rdkit()}}{
Get chemical information from RDKit if available
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{template}}{An optional SMILES code to be used as template for RDKit}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-get_chyaml"></a>}}
\if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}}
\subsection{Method \code{get_chyaml()}}{
Obtain information from a YAML file
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{repo}}{Should the file be looked for in the current working
directory, a local git repository under \verb{~/git/chyaml}, or from
the web (not implemented).}

\item{\code{chyaml}}{The filename to be looked for}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_p0"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_p0}{}}}
\subsection{Method \code{add_p0()}}{
Add a vapour pressure
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{p0}}{The vapour pressure in Pa}

\item{\code{T}}{Temperature}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{page}}{The page from which the information was taken}

\item{\code{remark}}{A remark}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_cwsat"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}}
\subsection{Method \code{add_cwsat()}}{
Add a water solubility
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{cwsat}}{The water solubility in mg/L}

\item{\code{T}}{Temperature}

\item{\code{pH}}{pH value}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{page}}{The page from which the information was taken}

\item{\code{remark}}{A remark}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_PUF"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}}
\subsection{Method \code{add_PUF()}}{
Add a plant uptake factor
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{PUF}}{The plant uptake factor, a number between 0 and 1}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{page}}{The page from which the information was taken}

\item{\code{remark}}{A remark}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_TP"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_TP}{}}}
\subsection{Method \code{add_TP()}}{
Add a transformation product to the internal list
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object}

\item{\code{smiles}}{Optional user provided SMILES code}

\item{\code{pubchem}}{Should chemical information be obtained from PubChem?}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_transformation"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}}
\subsection{Method \code{add_transformation()}}{
Add a line in the internal dataframe holding observed transformations
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{study_type}}{A characterisation of the study type}

\item{\code{TP_identifier}}{An identifier of one of the transformation products
in \code{self$TPs}}

\item{\code{max_occurrence}}{The maximum observed occurrence of the
transformation product, expressed as a fraction of the amount that would
result from stochiometric transformation}

\item{\code{remark}}{A remark}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{pages}}{The pages from which the information was taken}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_soil_degradation"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}}
\subsection{Method \code{add_soil_degradation()}}{
Add a line in the internal dataframe holding modelling DT50 values
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{soils}}{Names of the soils}

\item{\code{DT50_mod}}{The modelling DT50 in the sense of regulatory pesticide
fate modelling}

\item{\code{DT50_mod_ref}}{The normalised modelling DT50 in the sense of
regulatory pesticide fate modelling}

\item{\code{type}}{The soil type}

\item{\code{country}}{The country (mainly for field studies)}

\item{\code{pH_orig}}{The pH stated in the study}

\item{\code{pH_medium}}{The medium in which this pH was measured}

\item{\code{pH_H2O}}{The pH extrapolated to pure water}

\item{\code{perc_OC}}{The percentage of organic carbon in the soil}

\item{\code{temperature}}{The temperature during the study in degrees Celsius}

\item{\code{moisture}}{The moisture during the study}

\item{\code{category}}{Is it a laboratory ('lab') or field study ('field')}

\item{\code{formulation}}{Name of the formulation applied, if it was not
the technical active ingredient}

\item{\code{model}}{The degradation model used for deriving \code{DT50_mod}}

\item{\code{chi2}}{The relative error as defined in FOCUS kinetics}

\item{\code{remark}}{A remark}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{page}}{The page from which the information was taken}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_soil_ff"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}}
\subsection{Method \code{add_soil_ff()}}{
Add one or more formation fractions for degradation in soil
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{target}}{The identifier(s) of the transformation product}

\item{\code{soils}}{The soil name(s) in which the transformation was observed}

\item{\code{ff}}{The formation fraction(s)}

\item{\code{remark}}{A remark}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{page}}{The page from which the information was taken}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}}
\if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}}
\subsection{Method \code{add_soil_sorption()}}{
Add soil sorption data
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{soils}}{Names of the soils}

\item{\code{Kf}}{The sorption constant in L/kg, either linear (then \code{N} is 1)
or according to Freundlich}

\item{\code{Kfoc}}{The constant from above, normalised to soil organic carbon}

\item{\code{N}}{The Freundlich exponent}

\item{\code{type}}{The soil type}

\item{\code{pH_orig}}{The pH stated in the study}

\item{\code{pH_medium}}{The medium in which this pH was measured}

\item{\code{pH_H2O}}{The pH extrapolated to pure water}

\item{\code{perc_OC}}{The percentage of organic carbon in the soil}

\item{\code{perc_clay}}{The percentage of clay in the soil}

\item{\code{CEC}}{The cation exchange capacity}

\item{\code{remark}}{A remark}

\item{\code{source}}{An acronym specifying the source of the information}

\item{\code{page}}{The page from which the information was taken}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-pdf"></a>}}
\if{latex}{\out{\hypertarget{method-chent-pdf}{}}}
\subsection{Method \code{pdf()}}{
Write a PDF image of the structure
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{file}}{The file to write to}

\item{\code{dir}}{The directory to write the file to}

\item{\code{template}}{An optional SMILES code to be used as template for RDKit}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-png"></a>}}
\if{latex}{\out{\hypertarget{method-chent-png}{}}}
\subsection{Method \code{png()}}{
Write a PNG image of the structure
\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>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{file}}{The file to write to}

\item{\code{dir}}{The directory to write the file to}

\item{\code{antialias}}{Passed to \link[grDevices:png]{png}}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-emf"></a>}}
\if{latex}{\out{\hypertarget{method-chent-emf}{}}}
\subsection{Method \code{emf()}}{
Write an EMF image of the structure using \link[devEMF:emf]{emf}
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{file}}{The file to write to}

\item{\code{dir}}{The directory to write the file to}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-chent-clone"></a>}}
\if{latex}{\out{\hypertarget{method-chent-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>}}
}
}
}