% 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{ oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) print(oct) if (!is.null(oct$Picture)) { plot(oct) } caffeine <- chent$new("caffeine") print(caffeine) if (!is.null(caffeine$Picture)) { plot(caffeine) } } \section{Public fields}{ \if{html}{\out{
}} \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}}{ 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 Add a transformation product to the internal list} \item{\code{transformations}}{Data frame of observed transformations Add a line in the internal dataframe holding observed transformations} \item{\code{soil_degradation}}{Dataframe of modelling DT50 values Add a line in the internal dataframe holding modelling DT50 values} \item{\code{soil_ff}}{Dataframe of formation fractions} \item{\code{soil_sorption}}{Dataframe of soil sorption data Add soil sorption data} } \if{html}{\out{
}} } \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$clone()}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-new}{}}} \subsection{Method \code{new()}}{ Creates a new instance of this \link[R6:R6Class]{R6} class. Try to get chemical information from PubChem \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c("name", "smiles", "inchikey"), rdkit = TRUE, template = NULL, chyaml = FALSE )}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} \subsection{Method \code{try_pubchem()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{query}}{Query string to be passed to \link[webchem:get_cid]{get_cid}} \item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid} Get chemical information from PubChem for a known PubChem CID} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}} \subsection{Method \code{get_pubchem()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{pubchem_cid}}{CID} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} \subsection{Method \code{get_rdkit()}}{ Get chemical information from RDKit if available Obtain information from a YAML file \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{template}}{An optional SMILES code to be used as template for RDKit} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}} \subsection{Method \code{get_chyaml()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$get_chyaml( repo = c("wd", "local", "web"), chyaml = paste0(URLencode(self$identifier), ".yaml") )}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{repo}}{Should the file be looked for in the current working directory, a local git repository under \verb{~/git/chyaml}, or from the web (not implemented).} \item{\code{chyaml}}{The filename to be looked for Add a vapour pressure} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} \subsection{Method \code{add_p0()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{p0}}{The vapour pressure in Pa Add a water solubility} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}} \subsection{Method \code{add_cwsat()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{cwsat}}{The water solubility in mg/L Add a plant uptake factor} \item{\code{T}}{Temperature} \item{\code{pH}}{pH value} \item{\code{source}}{An acronym specifying the source of the information} \item{\code{page}}{The page from which the information was taken} \item{\code{remark}}{A remark} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} \subsection{Method \code{add_PUF()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_PUF( PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value" )}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_TP}{}}} \subsection{Method \code{add_TP()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object} \item{\code{smiles}}{Optional user provided SMILES code} \item{\code{pubchem}}{Should chemical information be obtained from PubChem?} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} \subsection{Method \code{add_transformation()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = "", source = NA, pages = NA )}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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$TPs}} \item{\code{max_occurrence}}{The maximum observed occurrence of the transformation product, expressed as a fraction of the amount that would result from stochiometric transformation} \item{\code{remark}}{A remark} \item{\code{source}}{An acronym specifying the source of the information} \item{\code{pages}}{The pages from which the information was taken} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}} \subsection{Method \code{add_soil_degradation()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$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{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} \subsection{Method \code{add_soil_ff()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{target}}{The identifier(s) of the transformation product} \item{\code{soils}}{The soil name(s) in which the transformation was observed} \item{\code{ff}}{The formation fraction(s)} \item{\code{remark}}{A remark} \item{\code{source}}{An acronym specifying the source of the information} \item{\code{page}}{The page from which the information was taken} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}} \subsection{Method \code{add_soil_sorption()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$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{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-pdf}{}}} \subsection{Method \code{pdf()}}{ Write a PDF image of the structure Write a PNG image of the structure \subsection{Usage}{ \if{html}{\out{
}}\preformatted{chent$pdf( file = paste0(self$identifier, ".pdf"), dir = "structures/pdf", template = NULL )}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-chent-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{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \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{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \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{
}}\preformatted{chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")}\if{html}{\out{
}} } \subsection{Arguments}{ \if{html}{\out{
}} \describe{ \item{\code{file}}{The file to write to} \item{\code{dir}}{The directory to write the file to} } \if{html}{\out{
}} } } \if{html}{\out{
}} \if{html}{\out{}} \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{
}}\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{
}} } } }