diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/chent.Rd | 403 | ||||
| -rw-r--r-- | man/pai.Rd | 103 | ||||
| -rw-r--r-- | man/plot.chent.Rd | 7 | ||||
| -rw-r--r-- | man/pp.Rd | 77 | ||||
| -rw-r--r-- | man/ppp.Rd | 100 |
5 files changed, 508 insertions, 182 deletions
diff --git a/man/chent.Rd b/man/chent.Rd index a1a5fe8..686d6c7 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -7,26 +7,44 @@ 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{ +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) +} } -\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} @@ -40,51 +58,58 @@ 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{soil_degradation}}{Dataframe of modelling DT50 values} +\item{\code{TPs}}{List of transformation products as chent objects +Add a transformation product to the internal list} -\item{\code{soil_ff}}{Dataframe of formation fractions} +\item{\code{transformations}}{Data frame of observed transformations +Add a line in the internal dataframe holding observed transformations} -\item{\code{soil_sorption}}{Dataframe of soil sorption data} +\item{\code{soil_degradation}}{Dataframe of modelling DT50 values +Add a line in the internal dataframe holding modelling DT50 values} -\item{\code{PUF}}{Plant uptake factor} +\item{\code{soil_ff}}{Dataframe of formation fractions} + +\item{\code{soil_sorption}}{Dataframe of soil sorption data +Add soil sorption data} } \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$new( identifier, smiles = NULL, - smiles_source = "user", inchikey = NULL, - inchikey_source = "user", pubchem = TRUE, pubchem_from = c("name", "smiles", "inchikey"), rdkit = TRUE, @@ -93,37 +118,90 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{identifier}}{Identifier to be stored in the object} + +\item{\code{smiles}}{Optional user provided SMILES code} + +\item{\code{inchikey}}{Optional user provided InChI Key} + +\item{\code{pubchem}}{Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?} + +\item{\code{pubchem_from}}{Possibility to select the argument +that is used to query pubchem} + +\item{\code{rdkit}}{Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?} + +\item{\code{template}}{An optional SMILES code to be used as template for RDKit} + +\item{\code{chyaml}}{Should we look for a identifier.yaml file in the working +directory? +Try to get chemical information from PubChem} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-try_pubchem"></a>}} -\if{latex}{\out{\hypertarget{method-try_pubchem}{}}} +\if{html}{\out{<a id="method-chent-try_pubchem"></a>}} +\if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} \subsection{Method \code{try_pubchem()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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} +Get chemical information from PubChem for a known PubChem 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()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{pubchem_cid}}{CID +Get chemical information from RDKit if available} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-get_rdkit"></a>}} -\if{latex}{\out{\hypertarget{method-get_rdkit}{}}} +\if{html}{\out{<a id="method-chent-get_rdkit"></a>}} +\if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} \subsection{Method \code{get_rdkit()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{template}}{Optional template specified as a SMILES code +Obtain information from a YAML file} +} +\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()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_chyaml( @@ -132,28 +210,74 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{repo}}{Should the file be looked for in the current working +directory, a local git repository under \verb{~/git/chyaml}, or from +the web (not implemented).} + +\item{\code{chyaml}}{The filename to be looked for +Add a vapour pressure} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_p0"></a>}} -\if{latex}{\out{\hypertarget{method-add_p0}{}}} +\if{html}{\out{<a id="method-chent-add_p0"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} \subsection{Method \code{add_p0()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$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 +Add a water solubility} +} +\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()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{cwsat}}{The water solubility in mg/L} + +\item{\code{T}}{Temperature} + +\item{\code{pH}}{The pH value} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{page}}{The page from which the information was taken} + +\item{\code{remark}}{A remark +Add a plant uptake factor} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_PUF"></a>}} -\if{latex}{\out{\hypertarget{method-add_PUF}{}}} +\if{html}{\out{<a id="method-chent-add_PUF"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} \subsection{Method \code{add_PUF()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF( @@ -164,19 +288,43 @@ 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()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object} + +\item{\code{smiles}}{A SMILES code for defining a \link{chent} object} + +\item{\code{pubchem}}{Should chemical information be obtained from PubChem?} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_transformation"></a>}} -\if{latex}{\out{\hypertarget{method-add_transformation}{}}} +\if{html}{\out{<a id="method-chent-add_transformation"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} \subsection{Method \code{add_transformation()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_transformation( @@ -189,10 +337,30 @@ 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$TPs}} + +\item{\code{max_occurrence}}{The maximum observed occurrence of the +transformation product, expressed as a fraction of the amount that would +result from stochiometric transformation} + +\item{\code{remark}}{A remark} + +\item{\code{source}}{An acronym specifying the source of the information} + +\item{\code{pages}}{The page from which the information was taken} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_soil_degradation"></a>}} -\if{latex}{\out{\hypertarget{method-add_soil_degradation}{}}} +\if{html}{\out{<a id="method-chent-add_soil_degradation"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_degradation}{}}} \subsection{Method \code{add_soil_degradation()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_degradation( @@ -217,19 +385,74 @@ 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()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{target}}{The identifier(s) of the transformation product} + +\item{\code{soils}}{The soil name(s) in which the transformation was observed} + +\item{\code{ff}}{The formation fraction(s)} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-add_soil_sorption"></a>}} -\if{latex}{\out{\hypertarget{method-add_soil_sorption}{}}} +\if{html}{\out{<a id="method-chent-add_soil_sorption"></a>}} +\if{latex}{\out{\hypertarget{method-chent-add_soil_sorption}{}}} \subsection{Method \code{add_soil_sorption()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_sorption( @@ -250,10 +473,27 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\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{perc_clay}}{The percentage of clay in the soil} + +\item{\code{CEC}}{The cation exchange capacity +Write a PDF image of the structure} +} +\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()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$pdf( @@ -263,10 +503,22 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{file}}{The file to write to} + +\item{\code{dir}}{The directory to write the file to} + +\item{\code{template}}{A template expressed as SMILES to use in RDKit +Write a PNG image of the structure} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-png"></a>}} -\if{latex}{\out{\hypertarget{method-png}{}}} +\if{html}{\out{<a id="method-chent-png"></a>}} +\if{latex}{\out{\hypertarget{method-chent-png}{}}} \subsection{Method \code{png()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$png( @@ -276,19 +528,34 @@ configured for use with PythonInR} )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{antialias}}{Passed to \link[grDevices:png]{png} +Write an EMF image of the structure using \link[devEMF:emf]{emf}} +} +\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()}}{ \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} +} +\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}{ @@ -8,63 +8,82 @@ An \code{\link{R6Class}} generator object } \description{ -The class is initialised with an identifier which is generally an ISO common name. -Additional chemical information is retrieved from the internet if available. +The class is initialised with an identifier which is generally +an ISO common name. Additional chemical information is retrieved from the +internet if available. +} +\examples{ +# On Travis, we get a certificate validation error, +# likely because the system (xenial) is so old, +# therefore don't run this example on Travis +if (Sys.getenv("TRAVIS") == "") { + +atr <- pai$new("atrazine") +print(atr) +if (!is.null(atr$Picture)) { + plot(atr) +} + +} } -\keyword{data} \section{Super class}{ \code{\link[chents:chent]{chents::chent}} -> \code{pai} } \section{Public fields}{ \if{html}{\out{<div class="r6-fields">}} \describe{ -\item{\code{iso}}{ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides} +\item{\code{iso}}{ISO common name of the active ingredient according to ISO 1750} -\item{\code{alanwood}}{List of information retreived from www.alanwood.net/pesticides} +\item{\code{bcpc}}{Information retrieved from the BCPC compendium available online +at <pesticidecompendium.bcpc.org> +Creates a new instance of this \link[R6:R6Class]{R6} class.} } \if{html}{\out{</div>}} } \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{pai$new()}} -\item \href{#method-clone}{\code{pai$clone()}} -} -} -\if{html}{ -\out{<details ><summary>Inherited methods</summary>} -\itemize{ -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF">}\href{../../chents/html/chent.html#method-add_PUF}{\code{chents::chent$add_PUF()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP">}\href{../../chents/html/chent.html#method-add_TP}{\code{chents::chent$add_TP()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat">}\href{../../chents/html/chent.html#method-add_cwsat}{\code{chents::chent$add_cwsat()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0">}\href{../../chents/html/chent.html#method-add_p0}{\code{chents::chent$add_p0()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation">}\href{../../chents/html/chent.html#method-add_soil_degradation}{\code{chents::chent$add_soil_degradation()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff">}\href{../../chents/html/chent.html#method-add_soil_ff}{\code{chents::chent$add_soil_ff()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption">}\href{../../chents/html/chent.html#method-add_soil_sorption}{\code{chents::chent$add_soil_sorption()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation">}\href{../../chents/html/chent.html#method-add_transformation}{\code{chents::chent$add_transformation()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf">}\href{../../chents/html/chent.html#method-emf}{\code{chents::chent$emf()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml">}\href{../../chents/html/chent.html#method-get_chyaml}{\code{chents::chent$get_chyaml()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem">}\href{../../chents/html/chent.html#method-get_pubchem}{\code{chents::chent$get_pubchem()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit">}\href{../../chents/html/chent.html#method-get_rdkit}{\code{chents::chent$get_rdkit()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf">}\href{../../chents/html/chent.html#method-pdf}{\code{chents::chent$pdf()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png">}\href{../../chents/html/chent.html#method-png}{\code{chents::chent$png()}}\out{</span>} -\item \out{<span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem">}\href{../../chents/html/chent.html#method-try_pubchem}{\code{chents::chent$try_pubchem()}}\out{</span>} -} -\out{</details>} -} +\item \href{#method-pai-new}{\code{pai$new()}} +\item \href{#method-pai-clone}{\code{pai$clone()}} +} +} +\if{html}{\out{ +<details><summary>Inherited methods</summary> +<ul> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-chent-add_PUF'><code>chents::chent$add_PUF()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-chent-add_TP'><code>chents::chent$add_TP()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-chent-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-chent-add_p0'><code>chents::chent$add_p0()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-chent-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-chent-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-chent-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-chent-add_transformation'><code>chents::chent$add_transformation()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-chent-emf'><code>chents::chent$emf()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-chent-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-chent-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-chent-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-chent-pdf'><code>chents::chent$pdf()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-chent-png'><code>chents::chent$png()</code></a></span></li> +<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-chent-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></li> +</ul> +</details> +}} \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-new"></a>}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{<a id="method-pai-new"></a>}} +\if{latex}{\out{\hypertarget{method-pai-new}{}}} \subsection{Method \code{new()}}{ +This class is derived from \link{chent}. It makes it easy +to create a \link{chent} from the ISO common name of a pesticide active +ingredient, and additionally stores the ISO name as well as +the complete result of querying the BCPC compendium using +\link[webchem:bcpc_query]{bcpc_query}. \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{pai$new( iso, identifier = iso, smiles = NULL, - smiles_source = "user", inchikey = NULL, - inchikey_source = "user", - alanwood = TRUE, + bcpc = TRUE, pubchem = TRUE, pubchem_from = "auto", rdkit = TRUE, @@ -73,10 +92,20 @@ Additional chemical information is retrieved from the internet if available. )}\if{html}{\out{</div>}} } +\subsection{Arguments}{ +\if{html}{\out{<div class="arguments">}} +\describe{ +\item{\code{iso}}{The ISO common name to be used in the query of the +BCPC compendium} + +\item{\code{identifier}}{Alternative identifier used for querying pubchem} +} +\if{html}{\out{</div>}} +} } \if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-clone"></a>}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{<a id="method-pai-clone"></a>}} +\if{latex}{\out{\hypertarget{method-pai-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/plot.chent.Rd b/man/plot.chent.Rd index e5a8770..f2850fa 100644 --- a/man/plot.chent.Rd +++ b/man/plot.chent.Rd @@ -14,3 +14,10 @@ \description{ Plot method for chent objects } +\examples{ +caffeine <- chent$new("caffeine") +print(caffeine) +if (!is.null(caffeine$Picture)) { + plot(caffeine) +} +} diff --git a/man/pp.Rd b/man/pp.Rd deleted file mode 100644 index cd950df..0000000 --- a/man/pp.Rd +++ /dev/null @@ -1,77 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/chent.R -\docType{class} -\name{pp} -\alias{pp} -\title{R6 class for holding a product with at least one active ingredient} -\format{ -An \code{\link{R6Class}} generator object. -} -\description{ -An R6 class for holding information about a product with at least one active ingredient -} -\keyword{data} -\section{Public fields}{ -\if{html}{\out{<div class="r6-fields">}} -\describe{ -\item{\code{name}}{The name of the product} - -\item{\code{ais}}{A list of active ingredients} - -\item{\code{concentrations}}{The concentration of the ais} - -\item{\code{concentration_units}}{Defaults to g/L} -} -\if{html}{\out{</div>}} -} -\section{Methods}{ -\subsection{Public methods}{ -\itemize{ -\item \href{#method-new}{\code{pp$new()}} -\item \href{#method-print}{\code{pp$print()}} -\item \href{#method-clone}{\code{pp$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{pp$new( - name, - ..., - concentrations, - concentration_units = "g/L", - density = 1000, - density_units = "g/L" -)}\if{html}{\out{</div>}} -} - -} -\if{html}{\out{<hr>}} -\if{html}{\out{<a id="method-print"></a>}} -\if{latex}{\out{\hypertarget{method-print}{}}} -\subsection{Method \code{print()}}{ -\subsection{Usage}{ -\if{html}{\out{<div class="r">}}\preformatted{pp$print()}\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{pp$clone(deep = FALSE)}\if{html}{\out{</div>}} -} - -\subsection{Arguments}{ -\if{html}{\out{<div class="arguments">}} -\describe{ -\item{\code{deep}}{Whether to make a deep clone.} -} -\if{html}{\out{</div>}} -} -} -} diff --git a/man/ppp.Rd b/man/ppp.Rd new file mode 100644 index 0000000..c0d35f1 --- /dev/null +++ b/man/ppp.Rd @@ -0,0 +1,100 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/chent.R +\docType{class} +\name{ppp} +\alias{ppp} +\title{R6 class for a plant protection product with at least one active ingredient} +\format{ +An \code{\link{R6Class}} generator object. +} +\description{ +Contains basic information about the active ingredients in the +product +} +\section{Public fields}{ +\if{html}{\out{<div class="r6-fields">}} +\describe{ +\item{\code{name}}{The name of the product} + +\item{\code{ais}}{A list of active ingredients} + +\item{\code{concentrations}}{The concentration of the ais} + +\item{\code{concentration_units}}{Defaults to g/L} + +\item{\code{density}}{The density of the product} + +\item{\code{density_units}}{Defaults to g/L +Creates a new instance of this \link[R6:R6Class]{R6} class.} + +\item{\code{...}}{Identifiers of the active ingredients} + +\item{\code{concentrations}}{Concentrations of the active ingredients} + +\item{\code{concentration_units}}{Defaults to g/L} + +\item{\code{density}}{The density} + +\item{\code{density_units}}{Defaults to g/L +Printing method} +} +\if{html}{\out{</div>}} +} +\section{Active bindings}{ +\if{html}{\out{<div class="r6-active-bindings">}} +\describe{ +\item{\code{...}}{Identifiers of the active ingredients} +} +\if{html}{\out{</div>}} +} +\section{Methods}{ +\subsection{Public methods}{ +\itemize{ +\item \href{#method-ppp-new}{\code{ppp$new()}} +\item \href{#method-ppp-print}{\code{ppp$print()}} +\item \href{#method-ppp-clone}{\code{ppp$clone()}} +} +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-ppp-new"></a>}} +\if{latex}{\out{\hypertarget{method-ppp-new}{}}} +\subsection{Method \code{new()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{ppp$new( + name, + ..., + concentrations, + concentration_units = "g/L", + density = 1000, + density_units = "g/L" +)}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-ppp-print"></a>}} +\if{latex}{\out{\hypertarget{method-ppp-print}{}}} +\subsection{Method \code{print()}}{ +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{ppp$print()}\if{html}{\out{</div>}} +} + +} +\if{html}{\out{<hr>}} +\if{html}{\out{<a id="method-ppp-clone"></a>}} +\if{latex}{\out{\hypertarget{method-ppp-clone}{}}} +\subsection{Method \code{clone()}}{ +The objects of this class are cloneable with this method. +\subsection{Usage}{ +\if{html}{\out{<div class="r">}}\preformatted{ppp$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>}} +} +} +} |