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Diffstat (limited to 'man/chent.Rd')
| -rw-r--r-- | man/chent.Rd | 428 |
1 files changed, 361 insertions, 67 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index a1a5fe8..ba47feb 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -7,26 +7,40 @@ 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. +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$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE) +print(oct) } -\keyword{data} \section{Public fields}{ \if{html}{\out{<div class="r6-fields">}} \describe{ -\item{\code{identifier}}{The identifier that was used to initiate the object, with attribute 'source'} +\item{\code{identifier}}{(\code{character(1)})\cr +The identifier that was used to initiate the object, with attribute 'source'} + +\item{\code{inchikey}}{(\code{character(1)})\cr +InChI Key, with attribute 'source'} -\item{\code{inchikey}}{InChI Key, with attribute 'source'} +\item{\code{smiles}}{(\code{character()})\cr +SMILES code(s), with attribute 'source'} -\item{\code{smiles}}{SMILES code, with attribute 'source'} +\item{\code{mw}}{(\code{numeric(1)})\cr +Molecular weight, with attribute 'source'} -\item{\code{mw}}{Molecular weight, with attribute 'source'} +\item{\code{pubchem}}{(\code{list()})\cr +List of information retrieved from PubChem} -\item{\code{pubchem}}{List of information retreived from PubChem} +\item{\code{rdkit}}{List of information obtained with RDKit} -\item{\code{rdkit}}{List of information obtained with RDKit, if installed and -configured for use with PythonInR} +\item{\code{mol}}{<rdkit.Chem.rdchem.Mol> object} \item{\code{svg}}{SVG code} @@ -40,91 +54,147 @@ configured for use with PythonInR} \item{\code{cwsat}}{Water solubility in mg/L} +\item{\code{PUF}}{Plant uptake factor} + \item{\code{chyaml}}{List of information obtained from a YAML file} +\item{\code{TPs}}{List of transformation products as chent objects} + +\item{\code{transformations}}{Data frame of observed transformations} + \item{\code{soil_degradation}}{Dataframe of modelling DT50 values} \item{\code{soil_ff}}{Dataframe of formation fractions} \item{\code{soil_sorption}}{Dataframe of soil sorption data} - -\item{\code{PUF}}{Plant uptake factor} } \if{html}{\out{</div>}} } \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{chent$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()}} +\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$clone()}} } } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-new"></a>}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{<a id="method-chent-new"></a>}} +\if{latex}{\out{\hypertarget{method-chent-new}{}}} \subsection{Method \code{new()}}{ +Creates a new instance of this \link[R6:R6Class]{R6} class. \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$new( identifier, smiles = NULL, - smiles_source = "user", inchikey = NULL, - inchikey_source = "user", pubchem = TRUE, pubchem_from = c("name", "smiles", "inchikey"), rdkit = TRUE, template = NULL, - chyaml = TRUE + 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-try_pubchem"></a>}} -\if{latex}{\out{\hypertarget{method-try_pubchem}{}}} +\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$try_pubchem(query, from = "name")}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{query}}{Query string to be passed to \link[webchem:get_cid]{get_cid}} + +\item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid}} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-get_pubchem"></a>}} -\if{latex}{\out{\hypertarget{method-get_pubchem}{}}} +\if{html}{\out{<a id="method-chent-get_pubchem"></a>}} +\if{latex}{\out{\hypertarget{method-chent-get_pubchem}{}}} \subsection{Method \code{get_pubchem()}}{ +Get chemical information from PubChem for a known PubChem CID \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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-get_rdkit"></a>}} -\if{latex}{\out{\hypertarget{method-get_rdkit}{}}} +\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$get_rdkit(template = NULL)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{template}}{An optional SMILES code to be used as template for RDKit} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-get_chyaml"></a>}} -\if{latex}{\out{\hypertarget{method-get_chyaml}{}}} +\if{html}{\out{<a id="method-chent-get_chyaml"></a>}} +\if{latex}{\out{\hypertarget{method-chent-get_chyaml}{}}} \subsection{Method \code{get_chyaml()}}{ +Obtain information from a YAML file \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_chyaml( repo = c("wd", "local", "web"), @@ -132,29 +202,75 @@ configured for use with PythonInR} )}\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-add_p0"></a>}} -\if{latex}{\out{\hypertarget{method-add_p0}{}}} +\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$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{p0}}{The vapour pressure in Pa} + +\item{\code{T}}{Temperature} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} + +\item{\code{remark}}{A remark} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_cwsat"></a>}} -\if{latex}{\out{\hypertarget{method-add_cwsat}{}}} +\if{html}{\out{<a id="method-chent-add_cwsat"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_cwsat}{}}} \subsection{Method \code{add_cwsat()}}{ +Add a water solubility \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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-add_PUF"></a>}} -\if{latex}{\out{\hypertarget{method-add_PUF}{}}} +\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$add_PUF( PUF = 0, @@ -164,20 +280,46 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{PUF}}{The plant uptake factor, a number between 0 and 1} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} + +\item{\code{remark}}{A remark} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_TP"></a>}} -\if{latex}{\out{\hypertarget{method-add_TP}{}}} +\if{html}{\out{<a id="method-chent-add_TP"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_TP}{}}} \subsection{Method \code{add_TP()}}{ +Add a transformation product to the internal list \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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-add_transformation"></a>}} -\if{latex}{\out{\hypertarget{method-add_transformation}{}}} +\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$add_transformation( study_type, @@ -189,11 +331,32 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{study_type}}{A characterisation of the study type} + +\item{\code{TP_identifier}}{An identifier of one of the transformation products +in \code{self$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-add_soil_degradation"></a>}} -\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}} +\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$add_soil_degradation( soils, @@ -217,20 +380,83 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{soils}}{Names of the soils} + +\item{\code{DT50_mod}}{The modelling DT50 in the sense of regulatory pesticide +fate modelling} + +\item{\code{DT50_mod_ref}}{The normalised modelling DT50 in the sense of +regulatory pesticide fate modelling} + +\item{\code{type}}{The soil type} + +\item{\code{country}}{The country (mainly for field studies)} + +\item{\code{pH_orig}}{The pH stated in the study} + +\item{\code{pH_medium}}{The medium in which this pH was measured} + +\item{\code{pH_H2O}}{The pH extrapolated to pure water} + +\item{\code{perc_OC}}{The percentage of organic carbon in the soil} + +\item{\code{temperature}}{The temperature during the study in degrees Celsius} + +\item{\code{moisture}}{The moisture during the study} + +\item{\code{category}}{Is it a laboratory ('lab') or field study ('field')} + +\item{\code{formulation}}{Name of the formulation applied, if it was not +the technical active ingredient} + +\item{\code{model}}{The degradation model used for deriving \code{DT50_mod}} + +\item{\code{chi2}}{The relative error as defined in FOCUS kinetics} + +\item{\code{remark}}{A remark} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_soil_ff"></a>}} -\if{latex}{\out{\hypertarget{method-add_soil_ff}{}}} +\if{html}{\out{<a id="method-chent-add_soil_ff"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} \subsection{Method \code{add_soil_ff()}}{ +Add one or more formation fractions for degradation in soil \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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-add_soil_sorption"></a>}} -\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}} +\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$add_soil_sorption( soils, @@ -250,11 +476,46 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{soils}}{Names of the soils} + +\item{\code{Kf}}{The sorption constant in L/kg, either linear (then \code{N} is 1) +or according to Freundlich} + +\item{\code{Kfoc}}{The constant from above, normalised to soil organic carbon} + +\item{\code{N}}{The Freundlich exponent} + +\item{\code{type}}{The soil type} + +\item{\code{pH_orig}}{The pH stated in the study} + +\item{\code{pH_medium}}{The medium in which this pH was measured} + +\item{\code{pH_H2O}}{The pH extrapolated to pure water} + +\item{\code{perc_OC}}{The percentage of organic carbon in the soil} + +\item{\code{perc_clay}}{The percentage of clay in the soil} + +\item{\code{CEC}}{The cation exchange capacity} + +\item{\code{remark}}{A remark} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-pdf"></a>}} -\if{latex}{\out{\hypertarget{method-pdf}{}}} +\if{html}{\out{<a id="method-chent-pdf"></a>}} +\if{latex}{\out{\hypertarget{method-chent-pdf}{}}} \subsection{Method \code{pdf()}}{ +Write a PDF image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$pdf( file = paste0(self$identifier, ".pdf"), @@ -263,11 +524,23 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{file}}{The file to write to} + +\item{\code{dir}}{The directory to write the file to} + +\item{\code{template}}{An optional SMILES code to be used as template for RDKit} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-png"></a>}} -\if{latex}{\out{\hypertarget{method-png}{}}} +\if{html}{\out{<a id="method-chent-png"></a>}} +\if{latex}{\out{\hypertarget{method-chent-png}{}}} \subsection{Method \code{png()}}{ +Write a PNG image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$png( file = paste0(self$identifier, ".png"), @@ -276,19 +549,40 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{file}}{The file to write to} + +\item{\code{dir}}{The directory to write the file to} + +\item{\code{antialias}}{Passed to \link[grDevices:png]{png}} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-emf"></a>}} -\if{latex}{\out{\hypertarget{method-emf}{}}} +\if{html}{\out{<a id="method-chent-emf"></a>}} +\if{latex}{\out{\hypertarget{method-chent-emf}{}}} \subsection{Method \code{emf()}}{ +Write an EMF image of the structure using \link[devEMF:emf]{emf} \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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-clone"></a>}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\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}{ |