diff options
Diffstat (limited to 'man/pai.Rd')
| -rw-r--r-- | man/pai.Rd | 125 |
1 files changed, 85 insertions, 40 deletions
@@ -1,82 +1,127 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/chent.R -\docType{class} \name{pai} \alias{pai} \title{An R6 class for pesticidal active ingredients and associated data} \format{ -An \code{\link{R6Class}} generator object +An \link[R6:R6Class]{R6::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. +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}. +} +\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>} } \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()}}{ +Create a new pai object \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, template = NULL, - chyaml = TRUE + chyaml = FALSE )}\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} + +\item{\code{smiles}}{Optional user provided SMILES code} + +\item{\code{inchikey}}{Optional user provided InChI Key} + +\item{\code{bcpc}}{Should the BCPC compendium be queried?} + +\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} +} +\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}{ |