diff options
| -rw-r--r-- | R/chent.R | 19 | ||||
| -rw-r--r-- | docs/pkgdown.yml | 2 | ||||
| -rw-r--r-- | docs/reference/chent.html | 69 | ||||
| -rw-r--r-- | docs/reference/pai.html | 3 | ||||
| -rw-r--r-- | docs/reference/ppp.html | 6 | ||||
| -rw-r--r-- | docs/search.json | 2 | ||||
| -rw-r--r-- | man/chent.Rd | 40 | ||||
| -rw-r--r-- | man/pai.Rd | 1 | ||||
| -rw-r--r-- | man/ppp.Rd | 4 |
9 files changed, 67 insertions, 79 deletions
@@ -102,7 +102,6 @@ chent <- R6Class("chent", #' @description #' Creates a new instance of this [R6][R6::R6Class] class. - #' initialize = function(identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'), rdkit = TRUE, template = NULL, @@ -166,6 +165,7 @@ chent <- R6Class("chent", invisible(self) }, + #' @description #' Try to get chemical information from PubChem #' @param query Query string to be passed to [get_cid][webchem::get_cid] #' @param from Passed to [get_cid][webchem::get_cid] @@ -181,6 +181,7 @@ chent <- R6Class("chent", } }, + #' @description #' Get chemical information from PubChem for a known PubChem CID #' @param pubchem_cid CID get_pubchem = function(pubchem_cid) { @@ -274,6 +275,7 @@ chent <- R6Class("chent", unlink(c(xmlfile, psfile, svgfile)) }, + #' @description #' Obtain information from a YAML file #' @param repo Should the file be looked for in the current working #' directory, a local git repository under `~/git/chyaml`, or from @@ -310,6 +312,7 @@ chent <- R6Class("chent", } }, + #' @description #' Add a vapour pressure #' @param p0 The vapour pressure in Pa add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") { @@ -320,6 +323,7 @@ chent <- R6Class("chent", attr(self$p0, "remark") <- remark }, + #' @description #' Add a water solubility #' @param cwsat The water solubility in mg/L add_cwsat = function(cwsat, T = NA, pH = NA, @@ -333,6 +337,7 @@ chent <- R6Class("chent", attr(self$cwsat, "remark") <- remark }, + #' @description #' Add a plant uptake factor #' @param PUF The plant uptake factor, a number between 0 and 1 add_PUF = function(PUF = 0, @@ -348,6 +353,7 @@ chent <- R6Class("chent", #' @field TPs List of transformation products as chent objects TPs = list(), + #' @description #' Add a transformation product to the internal list #' @param x A [chent] object, or an identifier to generate a [chent] object #' @param pubchem Should chemical information be obtained from PubChem? @@ -370,6 +376,7 @@ chent <- R6Class("chent", page = character(0), stringsAsFactors = FALSE), + #' @description #' Add a line in the internal dataframe holding observed transformations #' @param study_type A characterisation of the study type #' @param TP_identifier An identifier of one of the transformation products @@ -400,6 +407,7 @@ chent <- R6Class("chent", #' @field soil_degradation Dataframe of modelling DT50 values soil_degradation = NULL, + #' @description #' Add a line in the internal dataframe holding modelling DT50 values #' @param DT50_mod The modelling DT50 in the sense of regulatory pesticide #' fate modelling @@ -452,7 +460,8 @@ chent <- R6Class("chent", #' @field soil_ff Dataframe of formation fractions soil_ff = NULL, - # Add one or more formation fractions for degradation in soil + #' @description + #' Add one or more formation fractions for degradation in soil #' @param target The identifier(s) of the transformation product #' @param soils The soil name(s) in which the transformation was observed #' @param ff The formation fraction(s) @@ -478,6 +487,7 @@ chent <- R6Class("chent", #' @field soil_sorption Dataframe of soil sorption data soil_sorption = NULL, + #' @description #' Add soil sorption data #' @param Kf The sorption constant in L/kg, either linear (then `N` is 1) #' or according to Freundlich @@ -535,6 +545,7 @@ chent <- R6Class("chent", self$pdf_height <- as.numeric(gsub("/MediaBox \\[.* (.*)\\]", "\\1", m_line)) }, + #' @description #' Write a PNG image of the structure #' @param antialias Passed to [png][grDevices::png] png = function(file = paste0(self$identifier, ".png"), @@ -666,9 +677,10 @@ pai <- R6Class("pai", #' at <pesticidecompendium.bcpc.org> bcpc = NULL, + #' @description + #' Create a new pai object #' @param iso The ISO common name to be used in the query of the #' BCPC compendium - #' #' @param identifier Alternative identifier used for querying pubchem #' @param smiles Optional user provided SMILES code #' @param inchikey Optional user provided InChI Key @@ -786,6 +798,7 @@ ppp <- R6Class("ppp", #' @field density_units Defaults to g/L density_units = "g/L", + #' @description #' Creates a new instance of this [R6][R6::R6Class] class. #' @param name The name of the product #' @param ... Identifiers of the active ingredients diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 3194cc2..32462c1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.17.1.1 pkgdown: 2.1.0 pkgdown_sha: ~ articles: {} -last_built: 2024-11-28T15:57Z +last_built: 2024-12-02T08:20Z urls: reference: https://pkgdown.jrwb.de/chents/reference article: https://pkgdown.jrwb.de/chents/articles diff --git a/docs/reference/chent.html b/docs/reference/chent.html index cef2061..aed63b3 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -116,18 +116,15 @@ List of information retrieved from PubChem</p></dd> <dt><code>TPs</code></dt> -<dd><p>List of transformation products as chent objects -Add a transformation product to the internal list</p></dd> +<dd><p>List of transformation products as chent objects</p></dd> <dt><code>transformations</code></dt> -<dd><p>Data frame of observed transformations -Add a line in the internal dataframe holding observed transformations</p></dd> +<dd><p>Data frame of observed transformations</p></dd> <dt><code>soil_degradation</code></dt> -<dd><p>Dataframe of modelling DT50 values -Add a line in the internal dataframe holding modelling DT50 values</p></dd> +<dd><p>Dataframe of modelling DT50 values</p></dd> <dt><code>soil_ff</code></dt> @@ -135,8 +132,7 @@ Add a line in the internal dataframe holding modelling DT50 values</p></dd> <dt><code>soil_sorption</code></dt> -<dd><p>Dataframe of soil sorption data -Add soil sorption data</p></dd> +<dd><p>Dataframe of soil sorption data</p></dd> </dl><p></p></div> @@ -166,8 +162,7 @@ Add soil sorption data</p></dd> <li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li> </ul></div><p></p><hr><a id="method-chent-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> -<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p> -<p>Try to get chemical information from PubChem</p><div class="section"> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> <span> <span class="va">identifier</span>,</span> @@ -225,8 +220,7 @@ directory?</p></dd> </div><p></p><hr><a id="method-chent-try_pubchem"></a><div class="section"> <h3 id="method-try-pubchem-">Method <code>try_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-try-pubchem-"></a></h3> - -<div class="section"> +<p>Try to get chemical information from PubChem</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -238,8 +232,7 @@ directory?</p></dd> <dt><code>from</code></dt> -<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a> -Get chemical information from PubChem for a known PubChem CID</p></dd> +<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd> </dl><p></p></div> @@ -247,8 +240,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd> </div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section"> <h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3> - -<div class="section"> +<p>Get chemical information from PubChem for a known PubChem CID</p><div class="section"> <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_pubchem</span><span class="op">(</span><span class="va">pubchem_cid</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -264,8 +256,7 @@ Get chemical information from PubChem for a known PubChem CID</p></dd> </div><p></p><hr><a id="method-chent-get_rdkit"></a><div class="section"> <h3 id="method-get-rdkit-">Method <code>get_rdkit()</code><a class="anchor" aria-label="anchor" href="#method-get-rdkit-"></a></h3> -<p>Get chemical information from RDKit if available -Obtain information from a YAML file</p><div class="section"> +<p>Get chemical information from RDKit if available</p><div class="section"> <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -281,8 +272,7 @@ Obtain information from a YAML file</p><div class="section"> </div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section"> <h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3> - -<div class="section"> +<p>Obtain information from a YAML file</p><div class="section"> <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">get_chyaml</span><span class="op">(</span></span> <span> repo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wd"</span>, <span class="st">"local"</span>, <span class="st">"web"</span><span class="op">)</span>,</span> @@ -299,8 +289,7 @@ the web (not implemented).</p></dd> <dt><code>chyaml</code></dt> -<dd><p>The filename to be looked for -Add a vapour pressure</p></dd> +<dd><p>The filename to be looked for</p></dd> </dl><p></p></div> @@ -308,8 +297,7 @@ Add a vapour pressure</p></dd> </div><p></p><hr><a id="method-chent-add_p0"></a><div class="section"> <h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3> - -<div class="section"> +<p>Add a vapour pressure</p><div class="section"> <h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_p0</span><span class="op">(</span><span class="va">p0</span>, T <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -317,8 +305,7 @@ Add a vapour pressure</p></dd> <div class="section"> <h4 id="arguments-5">Arguments<a class="anchor" aria-label="anchor" href="#arguments-5"></a></h4> <p></p><div class="arguments"><dl><dt><code>p0</code></dt> -<dd><p>The vapour pressure in Pa -Add a water solubility</p></dd> +<dd><p>The vapour pressure in Pa</p></dd> <dt><code>T</code></dt> @@ -342,8 +329,7 @@ Add a water solubility</p></dd> </div><p></p><hr><a id="method-chent-add_cwsat"></a><div class="section"> <h3 id="method-add-cwsat-">Method <code>add_cwsat()</code><a class="anchor" aria-label="anchor" href="#method-add-cwsat-"></a></h3> - -<div class="section"> +<p>Add a water solubility</p><div class="section"> <h4 id="usage-6">Usage<a class="anchor" aria-label="anchor" href="#usage-6"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -351,8 +337,7 @@ Add a water solubility</p></dd> <div class="section"> <h4 id="arguments-6">Arguments<a class="anchor" aria-label="anchor" href="#arguments-6"></a></h4> <p></p><div class="arguments"><dl><dt><code>cwsat</code></dt> -<dd><p>The water solubility in mg/L -Add a plant uptake factor</p></dd> +<dd><p>The water solubility in mg/L</p></dd> <dt><code>T</code></dt> @@ -380,8 +365,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section"> <h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3> - -<div class="section"> +<p>Add a plant uptake factor</p><div class="section"> <h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span> <span> PUF <span class="op">=</span> <span class="fl">0</span>,</span> @@ -414,8 +398,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_TP"></a><div class="section"> <h3 id="method-add-tp-">Method <code>add_TP()</code><a class="anchor" aria-label="anchor" href="#method-add-tp-"></a></h3> - -<div class="section"> +<p>Add a transformation product to the internal list</p><div class="section"> <h4 id="usage-8">Usage<a class="anchor" aria-label="anchor" href="#usage-8"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -439,8 +422,7 @@ Add a plant uptake factor</p></dd> </div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section"> <h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3> - -<div class="section"> +<p>Add a line in the internal dataframe holding observed transformations</p><div class="section"> <h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span> <span> <span class="va">study_type</span>,</span> @@ -486,8 +468,7 @@ result from stochiometric transformation</p></dd> </div><p></p><hr><a id="method-chent-add_soil_degradation"></a><div class="section"> <h3 id="method-add-soil-degradation-">Method <code>add_soil_degradation()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-degradation-"></a></h3> - -<div class="section"> +<p>Add a line in the internal dataframe holding modelling DT50 values</p><div class="section"> <h4 id="usage-10">Usage<a class="anchor" aria-label="anchor" href="#usage-10"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span> <span> <span class="va">soils</span>,</span> @@ -593,8 +574,7 @@ the technical active ingredient</p></dd> </div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section"> <h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3> - -<div class="section"> +<p>Add one or more formation fractions for degradation in soil</p><div class="section"> <h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_ff</span><span class="op">(</span><span class="va">target</span>, <span class="va">soils</span>, ff <span class="op">=</span> <span class="fl">1</span>, remark <span class="op">=</span> <span class="st">""</span>, <span class="va">source</span>, page <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> @@ -630,8 +610,7 @@ the technical active ingredient</p></dd> </div><p></p><hr><a id="method-chent-add_soil_sorption"></a><div class="section"> <h3 id="method-add-soil-sorption-">Method <code>add_soil_sorption()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-sorption-"></a></h3> - -<div class="section"> +<p>Add soil sorption data</p><div class="section"> <h4 id="usage-12">Usage<a class="anchor" aria-label="anchor" href="#usage-12"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span> <span> <span class="va">soils</span>,</span> @@ -715,8 +694,7 @@ or according to Freundlich</p></dd> </div><p></p><hr><a id="method-chent-pdf"></a><div class="section"> <h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3> -<p>Write a PDF image of the structure -Write a PNG image of the structure</p><div class="section"> +<p>Write a PDF image of the structure</p><div class="section"> <h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">pdf</span><span class="op">(</span></span> <span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span> @@ -744,8 +722,7 @@ Write a PNG image of the structure</p><div class="section"> </div><p></p><hr><a id="method-chent-png"></a><div class="section"> <h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3> - -<div class="section"> +<p>Write a PNG image of the structure</p><div class="section"> <h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">png</span><span class="op">(</span></span> <span> file <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span> diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 30bbbac..b24c78e 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -96,8 +96,7 @@ at <pesticidecompendium.bcpc.org></p></dd> <li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li> </ul></details></p><hr><a id="method-pai-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> - -<div class="section"> +<p>Create a new pai object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> <span> <span class="va">iso</span>,</span> diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html index ef3933d..f7b7705 100644 --- a/docs/reference/ppp.html +++ b/docs/reference/ppp.html @@ -68,8 +68,7 @@ product</p> <dt><code>density_units</code></dt> -<dd><p>Defaults to g/L -Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p></dd> +<dd><p>Defaults to g/L</p></dd> </dl><p></p></div> @@ -84,8 +83,7 @@ Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.h <li><p><a href="#method-ppp-clone"><code>ppp$clone()</code></a></p></li> </ul></div><p></p><hr><a id="method-ppp-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> - -<div class="section"> +<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/ppp.html">ppp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> <span> <span class="va">name</span>,</span> diff --git a/docs/search.json b/docs/search.json index 118de07..f382756 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2024). chents: Chemical Entities R Objects. R package version 0.3.7, https://github.com/jranke/chents, https://pkgdown.jrwb.de/chents.","code":"@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2024}, note = {R package version 0.3.7, https://github.com/jranke/chents}, url = {https://pkgdown.jrwb.de/chents}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"R package chents provides utilities working chemical entities R.","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"Chemical Entities as R Objects","text":"chemical information retrieved PubChem website using webchem package Python RDKit (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions additional chemical information computed 2D graph can plotted Additional information can read local .yaml file","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Chemical Entities as R Objects","text":"can conveniently install chents repository kindly made available R-Universe project: order profit chemoinformatics, need install RDKit python bindings. Debian type Linux distribution, just use use package Windows MacOS, happy include installation instructions share , e.g. via Pull Request.","code":"install.packages(\"chents\", repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) sudo apt install python3-rdkit"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"configuration-of-the-python-version-to-use","dir":"","previous_headings":"","what":"Configuration of the Python version to use","title":"Chemical Entities as R Objects","text":"Debian type Linux distributions, can use following line global project specific .Rprofile file tell reticulate package use system Python version find RDKit installed system location.","code":"Sys.setenv(RETICULATE_PYTHON=\"/usr/bin/python3\")"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Chemical Entities as R Objects","text":"examples available reference jrwb.de. example, example code section chent object docs can see generate R object caffeine, show information retrieved PubChem plot virtue RDKit.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph picture object obtained using grImport Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects Add transformation product internal list transformations Data frame observed transformations Add line internal dataframe holding observed transformations soil_degradation Dataframe modelling DT50 values Add line internal dataframe holding modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data Add soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class. Try get chemical information PubChem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c(\"name\", \"smiles\", \"inchikey\"), rdkit = TRUE, template = NULL, chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory?","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid Get chemical information PubChem known PubChem CID","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-rdkit-","dir":"Reference","previous_headings":"","what":"Method get_rdkit()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information RDKit available Obtain information YAML file","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template optional SMILES code used template RDKit","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml( repo = c(\"wd\", \"local\", \"web\"), chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked Add vapour pressure","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa Add water solubility T Temperature source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L Add plant uptake factor T Temperature pH pH value source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF( PUF = 0, source = \"focus_generic_gw_2014\", page = 41, remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles Optional user provided SMILES code pubchem chemical information obtained PubChem?","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = \"\", source = NA, pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages pages information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$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 )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s) remark remark source acronym specifying source information page page information taken","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$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 )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent type soil type pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil perc_clay percentage clay soil CEC cation exchange capacity remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-pdf-","dir":"Reference","previous_headings":"","what":"Method pdf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PDF image structure Write PNG image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf( file = paste0(self$identifier, \".pdf\"), dir = \"structures/pdf\", template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template optional SMILES code used template RDKit","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png( file = paste0(self$identifier, \".png\"), dir = \"structures/png\", antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file antialias Passed png","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-emf-","dir":"Reference","previous_headings":"","what":"Method emf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write EMF image structure using emf","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) } oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Trying to get chemical information from RDKit using user SMILES #> CCCCCCCCO print(oct) #> <chent> #> Identifier $identifier 1-octanol #> InChI Key $inchikey NA #> SMILES string $smiles: #> user #> \"CCCCCCCCO\" #> Molecular weight $mw: 130.2"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent( x, width = 300, height = 150, filename = paste0(names(x$identifier), \".svg\"), subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org>","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new( iso, identifier = iso, smiles = NULL, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = \"auto\", rdkit = TRUE, template = NULL, chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem smiles Optional user provided SMILES code inchikey Optional user provided InChI Key bcpc BCPC compendium queried? pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# On Travis, we get a certificate validation error, # likely because the system (xenial) is so old, # therefore don't run this example on Travis if (Sys.getenv(\"TRAVIS\") == \"\") { atr <- pai$new(\"atrazine\") print(atr) if (!is.null(atr$Picture)) { plot(atr) } } #> BCPC: #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C #> <pai> with ISO common name $iso atrazine #> <chent> #> Identifier $identifier atrazine #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CCNC1=NC(=NC(=N1)Cl)NC(C)C\" #> Molecular weight $mw: 215.7 #> PubChem synonyms (up to 10): #> [1] \"atrazine\" \"1912-24-9\" \"Gesaprim\" \"Atranex\" \"Oleogesaprim\" #> [6] \"Atazinax\" \"Atrasine\" \"Chromozin\" \"Gesoprim\" \"Hungazin\""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for class 'chent' plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) }"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L Creates new instance R6 class.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$clone()","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new( name, ..., concentrations, concentration_units = \"g/L\", density = 1000, density_units = \"g/L\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for class 'chent' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for class 'pai' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for ppp objects (plant protection products) — print.ppp","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"Printing method ppp objects (plant protection products)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"","code":"# S3 method for class 'ppp' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-037","dir":"Changelog","previous_headings":"","what":"version 0.3.7","title":"version 0.3.7","text":"R/chent.R: attempt load chyaml file per default, format file resulting chyaml list object documented need inferred use pfm package.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-036","dir":"Changelog","previous_headings":"","what":"version 0.3.6","title":"version 0.3.6","text":"R/chent.R: Set fields smiles, inchikey mw NA fields still NULL end initialization, source attribute set “user”, assuming initialisation carefully done pubchem rdkit skipped structure well-defined. Please refer ChangeLog commit messages November 2021, changed GNUmakefile include commit messages file .","code":""}] +[{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder.","code":""},{"path":"https://pkgdown.jrwb.de/chents/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2024). chents: Chemical Entities R Objects. R package version 0.3.7, https://github.com/jranke/chents, https://pkgdown.jrwb.de/chents.","code":"@Manual{, title = {chents: Chemical Entities as R Objects}, author = {Johannes Ranke}, year = {2024}, note = {R package version 0.3.7, https://github.com/jranke/chents}, url = {https://pkgdown.jrwb.de/chents}, }"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"chents","dir":"","previous_headings":"","what":"Chemical Entities as R Objects","title":"Chemical Entities as R Objects","text":"R package chents provides utilities working chemical entities R.","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"Chemical Entities as R Objects","text":"chemical information retrieved PubChem website using webchem package Python RDKit (> 2015.03) installed configured use ‘reticulate’, basic chemoinformatics functions additional chemical information computed 2D graph can plotted Additional information can read local .yaml file","code":""},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Chemical Entities as R Objects","text":"can conveniently install chents repository kindly made available R-Universe project: order profit chemoinformatics, need install RDKit python bindings. Debian type Linux distribution, just use use package Windows MacOS, happy include installation instructions share , e.g. via Pull Request.","code":"install.packages(\"chents\", repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) sudo apt install python3-rdkit"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"configuration-of-the-python-version-to-use","dir":"","previous_headings":"","what":"Configuration of the Python version to use","title":"Chemical Entities as R Objects","text":"Debian type Linux distributions, can use following line global project specific .Rprofile file tell reticulate package use system Python version find RDKit installed system location.","code":"Sys.setenv(RETICULATE_PYTHON=\"/usr/bin/python3\")"},{"path":"https://pkgdown.jrwb.de/chents/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Chemical Entities as R Objects","text":"examples available reference jrwb.de. example, example code section chent object docs can see generate R object caffeine, show information retrieved PubChem plot virtue RDKit.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for chemical entities with associated data — chent","title":"An R6 class for chemical entities with associated data — chent","text":"class initialised identifier. Chemical information retrieved internet. Additionally, can generated using RDKit RDKit python bindings installed.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for chemical entities with associated data — chent","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for chemical entities with associated data — chent","text":"identifier (character(1)) identifier used initiate object, attribute 'source' inchikey (character(1)) InChI Key, attribute 'source' smiles (character()) SMILES code(s), attribute 'source' mw (numeric(1)) Molecular weight, attribute 'source' pubchem (list()) List information retrieved PubChem rdkit List information obtained RDKit mol <rdkit.Chem.rdchem.Mol> object svg SVG code Picture Graph picture object obtained using grImport Pict_font_size Font size extracted intermediate PostScript file pdf_height Height MediaBox pdf cropping p0 Vapour pressure Pa cwsat Water solubility mg/L PUF Plant uptake factor chyaml List information obtained YAML file TPs List transformation products chent objects transformations Data frame observed transformations soil_degradation Dataframe modelling DT50 values soil_ff Dataframe formation fractions soil_sorption Dataframe soil sorption data","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for chemical entities with associated data — chent","text":"chent$new() chent$try_pubchem() chent$get_pubchem() chent$get_rdkit() chent$get_chyaml() chent$add_p0() chent$add_cwsat() chent$add_PUF() chent$add_TP() chent$add_transformation() chent$add_soil_degradation() chent$add_soil_ff() chent$add_soil_sorption() chent$pdf() chent$png() chent$emf() chent$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for chemical entities with associated data — chent","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$new( identifier, smiles = NULL, inchikey = NULL, pubchem = TRUE, pubchem_from = c(\"name\", \"smiles\", \"inchikey\"), rdkit = TRUE, template = NULL, chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"identifier Identifier stored object smiles Optional user provided SMILES code inchikey Optional user provided InChI Key pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working directory?","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-try-pubchem-","dir":"Reference","previous_headings":"","what":"Method try_pubchem()","title":"An R6 class for chemical entities with associated data — chent","text":"Try get chemical information PubChem","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$try_pubchem(query, from = \"name\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"query Query string passed get_cid Passed get_cid","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-pubchem-","dir":"Reference","previous_headings":"","what":"Method get_pubchem()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information PubChem known PubChem CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_pubchem(pubchem_cid)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"pubchem_cid CID","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-rdkit-","dir":"Reference","previous_headings":"","what":"Method get_rdkit()","title":"An R6 class for chemical entities with associated data — chent","text":"Get chemical information RDKit available","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_rdkit(template = NULL)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"template optional SMILES code used template RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-get-chyaml-","dir":"Reference","previous_headings":"","what":"Method get_chyaml()","title":"An R6 class for chemical entities with associated data — chent","text":"Obtain information YAML file","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$get_chyaml( repo = c(\"wd\", \"local\", \"web\"), chyaml = paste0(URLencode(self$identifier), \".yaml\") )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"repo file looked current working directory, local git repository ~/git/chyaml, web (implemented). chyaml filename looked ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-p-","dir":"Reference","previous_headings":"","what":"Method add_p0()","title":"An R6 class for chemical entities with associated data — chent","text":"Add vapour pressure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_p0(p0, T = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"p0 vapour pressure Pa T Temperature source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-cwsat-","dir":"Reference","previous_headings":"","what":"Method add_cwsat()","title":"An R6 class for chemical entities with associated data — chent","text":"Add water solubility","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = \"\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"cwsat water solubility mg/L T Temperature pH pH value source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-puf-","dir":"Reference","previous_headings":"","what":"Method add_PUF()","title":"An R6 class for chemical entities with associated data — chent","text":"Add plant uptake factor","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_PUF( PUF = 0, source = \"focus_generic_gw_2014\", page = 41, remark = \"Conservative default value\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"PUF plant uptake factor, number 0 1 source acronym specifying source information page page information taken remark remark","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-tp-","dir":"Reference","previous_headings":"","what":"Method add_TP()","title":"An R6 class for chemical entities with associated data — chent","text":"Add transformation product internal list","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_TP(x, smiles = NULL, pubchem = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"x chent object, identifier generate chent object smiles Optional user provided SMILES code pubchem chemical information obtained PubChem?","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-transformation-","dir":"Reference","previous_headings":"","what":"Method add_transformation()","title":"An R6 class for chemical entities with associated data — chent","text":"Add line internal dataframe holding observed transformations","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_transformation( study_type, TP_identifier, max_occurrence, remark = \"\", source = NA, pages = NA )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"study_type characterisation study type TP_identifier identifier one transformation products self$TPs max_occurrence maximum observed occurrence transformation product, expressed fraction amount result stochiometric transformation remark remark source acronym specifying source information pages pages information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-soil-degradation-","dir":"Reference","previous_headings":"","what":"Method add_soil_degradation()","title":"An R6 class for chemical entities with associated data — chent","text":"Add line internal dataframe holding modelling DT50 values","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$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 )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils DT50_mod modelling DT50 sense regulatory pesticide fate modelling DT50_mod_ref normalised modelling DT50 sense regulatory pesticide fate modelling type soil type country country (mainly field studies) pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil temperature temperature study degrees Celsius moisture moisture study category laboratory ('lab') field study ('field') formulation Name formulation applied, technical active ingredient model degradation model used deriving DT50_mod chi2 relative error defined FOCUS kinetics remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-soil-ff-","dir":"Reference","previous_headings":"","what":"Method add_soil_ff()","title":"An R6 class for chemical entities with associated data — chent","text":"Add one formation fractions degradation soil","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$add_soil_ff(target, soils, ff = 1, remark = \"\", source, page = NA)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"target identifier(s) transformation product soils soil name(s) transformation observed ff formation fraction(s) remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-add-soil-sorption-","dir":"Reference","previous_headings":"","what":"Method add_soil_sorption()","title":"An R6 class for chemical entities with associated data — chent","text":"Add soil sorption data","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$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 )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"soils Names soils Kf sorption constant L/kg, either linear (N 1) according Freundlich Kfoc constant , normalised soil organic carbon N Freundlich exponent type soil type pH_orig pH stated study pH_medium medium pH measured pH_H2O pH extrapolated pure water perc_OC percentage organic carbon soil perc_clay percentage clay soil CEC cation exchange capacity remark remark source acronym specifying source information page page information taken","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-pdf-","dir":"Reference","previous_headings":"","what":"Method pdf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PDF image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$pdf( file = paste0(self$identifier, \".pdf\"), dir = \"structures/pdf\", template = NULL )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file template optional SMILES code used template RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-png-","dir":"Reference","previous_headings":"","what":"Method png()","title":"An R6 class for chemical entities with associated data — chent","text":"Write PNG image structure","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$png( file = paste0(self$identifier, \".png\"), dir = \"structures/png\", antialias = \"gray\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file antialias Passed png","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-emf-","dir":"Reference","previous_headings":"","what":"Method emf()","title":"An R6 class for chemical entities with associated data — chent","text":"Write EMF image structure using emf","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$emf(file = paste0(self$identifier, \".emf\"), dir = \"structures/emf\")"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"file file write dir directory write file ","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for chemical entities with associated data — chent","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"chent$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for chemical entities with associated data — chent","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for chemical entities with associated data — chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) } oct <- chent$new(\"1-octanol\", smiles = \"CCCCCCCCO\", pubchem = FALSE) #> Trying to get chemical information from RDKit using user SMILES #> CCCCCCCCO print(oct) #> <chent> #> Identifier $identifier 1-octanol #> InChI Key $inchikey NA #> SMILES string $smiles: #> user #> \"CCCCCCCCO\" #> Molecular weight $mw: 130.2"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"Draw SVG graph chent object using RDKit","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"","code":"draw_svg.chent( x, width = 300, height = 150, filename = paste0(names(x$identifier), \".svg\"), subdir = \"svg\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw SVG graph from a chent object using RDKit — draw_svg.chent","text":"x chent object plotted width desired width pixels height desired height pixels filename filename subdir path file written","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":null,"dir":"Reference","previous_headings":"","what":"An R6 class for pesticidal active ingredients and associated data — pai","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"class derived chent. makes easy create chent ISO common name pesticide active ingredient, additionally stores ISO name well complete result querying BCPC compendium using bcpc_query.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"R6Class generator object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"super-class","dir":"Reference","previous_headings":"","what":"Super class","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent -> pai","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name active ingredient according ISO 1750 bcpc Information retrieved BCPC compendium available online <pesticidecompendium.bcpc.org>","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"methods","dir":"Reference","previous_headings":"","what":"Methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"chents::chent$add_PUF() chents::chent$add_TP() chents::chent$add_cwsat() chents::chent$add_p0() chents::chent$add_soil_degradation() chents::chent$add_soil_ff() chents::chent$add_soil_sorption() chents::chent$add_transformation() chents::chent$emf() chents::chent$get_chyaml() chents::chent$get_pubchem() chents::chent$get_rdkit() chents::chent$pdf() chents::chent$png() chents::chent$try_pubchem()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"pai$new() pai$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"Create new pai object","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$new( iso, identifier = iso, smiles = NULL, inchikey = NULL, bcpc = TRUE, pubchem = TRUE, pubchem_from = \"auto\", rdkit = TRUE, template = NULL, chyaml = FALSE )"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"iso ISO common name used query BCPC compendium identifier Alternative identifier used querying pubchem smiles Optional user provided SMILES code inchikey Optional user provided InChI Key bcpc BCPC compendium queried? pubchem attempt made retrieve chemical information PubChem via webchem package? pubchem_from Possibility select argument used query pubchem rdkit attempt made retrieve chemical information local rdkit installation via python reticulate package? template optional SMILES code used template RDKit chyaml look identifier.yaml file working","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"pai$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/pai.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"An R6 class for pesticidal active ingredients and associated data — pai","text":"","code":"# On Travis, we get a certificate validation error, # likely because the system (xenial) is so old, # therefore don't run this example on Travis if (Sys.getenv(\"TRAVIS\") == \"\") { atr <- pai$new(\"atrazine\") print(atr) if (!is.null(atr$Picture)) { plot(atr) } } #> BCPC: #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CCNC1=NC(=NC(=N1)Cl)NC(C)C #> <pai> with ISO common name $iso atrazine #> <chent> #> Identifier $identifier atrazine #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CCNC1=NC(=NC(=N1)Cl)NC(C)C\" #> Molecular weight $mw: 215.7 #> PubChem synonyms (up to 10): #> [1] \"atrazine\" \"1912-24-9\" \"Gesaprim\" \"Atranex\" \"Oleogesaprim\" #> [6] \"Atazinax\" \"Atrasine\" \"Chromozin\" \"Gesoprim\" \"Hungazin\""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot method for chent objects — plot.chent","title":"Plot method for chent objects — plot.chent","text":"Plot method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot method for chent objects — plot.chent","text":"","code":"# S3 method for class 'chent' plot(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot method for chent objects — plot.chent","text":"x chent object plotted ... arguments passed grid.picture","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/plot.chent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot method for chent objects — plot.chent","text":"","code":"caffeine <- chent$new(\"caffeine\") #> PubChem: #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C print(caffeine) #> <chent> #> Identifier $identifier caffeine #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical #> \"CN1C=NC2=C1C(=O)N(C(=O)N2C)C\" #> Molecular weight $mw: 194.2 #> PubChem synonyms (up to 10): #> [1] \"caffeine\" \"58-08-2\" #> [3] \"Guaranine\" \"1,3,7-Trimethylxanthine\" #> [5] \"Methyltheobromine\" \"Theine\" #> [7] \"Thein\" \"Cafeina\" #> [9] \"Koffein\" \"Mateina\" if (!is.null(caffeine$Picture)) { plot(caffeine) }"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for a plant protection product with at least one active ingredient — ppp","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Contains basic information active ingredients product","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ais list active ingredients concentrations concentration ais concentration_units Defaults g/L density density product density_units Defaults g/L","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"ppp$new() ppp$clone()","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"Creates new instance R6 class.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$new( name, ..., concentrations, concentration_units = \"g/L\", density = 1000, density_units = \"g/L\" )"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"name name product ... Identifiers active ingredients concentrations Concentrations active ingredients concentration_units Defaults g/L density density density_units Defaults g/L","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"","code":"ppp$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/chents/reference/ppp.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for a plant protection product with at least one active ingredient — ppp","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for chent objects — print.chent","title":"Printing method for chent objects — print.chent","text":"Printing method chent objects","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for chent objects — print.chent","text":"","code":"# S3 method for class 'chent' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.chent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for chent objects — print.chent","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for pai objects (pesticidal active ingredients) — print.pai","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"Printing method pai objects (pesticidal active ingredients)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"","code":"# S3 method for class 'pai' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.pai.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for pai objects (pesticidal active ingredients) — print.pai","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":null,"dir":"Reference","previous_headings":"","what":"Printing method for ppp objects (plant protection products) — print.ppp","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"Printing method ppp objects (plant protection products)","code":""},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"","code":"# S3 method for class 'ppp' print(x, ...)"},{"path":"https://pkgdown.jrwb.de/chents/reference/print.ppp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Printing method for ppp objects (plant protection products) — print.ppp","text":"x chent object printed ... arguments compatibility S3 method","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-037","dir":"Changelog","previous_headings":"","what":"version 0.3.7","title":"version 0.3.7","text":"R/chent.R: attempt load chyaml file per default, format file resulting chyaml list object documented need inferred use pfm package.","code":""},{"path":"https://pkgdown.jrwb.de/chents/news/index.html","id":"version-036","dir":"Changelog","previous_headings":"","what":"version 0.3.6","title":"version 0.3.6","text":"R/chent.R: Set fields smiles, inchikey mw NA fields still NULL end initialization, source attribute set “user”, assuming initialisation carefully done pubchem rdkit skipped structure well-defined. Please refer ChangeLog commit messages November 2021, changed GNUmakefile include commit messages file .","code":""}] diff --git a/man/chent.Rd b/man/chent.Rd index 93c7a34..ba47feb 100644 --- a/man/chent.Rd +++ b/man/chent.Rd @@ -58,19 +58,15 @@ List of information retrieved from PubChem} \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{TPs}}{List of transformation products as chent objects} -\item{\code{transformations}}{Data frame of observed transformations -Add a line in the internal dataframe holding observed transformations} +\item{\code{transformations}}{Data frame of 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_degradation}}{Dataframe of modelling DT50 values} \item{\code{soil_ff}}{Dataframe of formation fractions} -\item{\code{soil_sorption}}{Dataframe of soil sorption data -Add soil sorption data} +\item{\code{soil_sorption}}{Dataframe of soil sorption data} } \if{html}{\out{</div>}} } @@ -101,8 +97,6 @@ Add soil sorption data} \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{<div class="r">}}\preformatted{chent$new( identifier, @@ -147,6 +141,7 @@ directory?} \if{html}{\out{<a id="method-chent-try_pubchem"></a>}} \if{latex}{\out{\hypertarget{method-chent-try_pubchem}{}}} \subsection{Method \code{try_pubchem()}}{ +Try to get chemical information from PubChem \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}} } @@ -156,8 +151,7 @@ directory?} \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} +\item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid}} } \if{html}{\out{</div>}} } @@ -166,6 +160,7 @@ Get chemical information from PubChem for a known PubChem CID} \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$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}} } @@ -183,7 +178,6 @@ Get chemical information from PubChem for a known PubChem CID} \if{latex}{\out{\hypertarget{method-chent-get_rdkit}{}}} \subsection{Method \code{get_rdkit()}}{ Get chemical information from RDKit if available -Obtain information from a YAML file \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}} } @@ -200,6 +194,7 @@ Obtain information from a YAML file \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$get_chyaml( repo = c("wd", "local", "web"), @@ -214,8 +209,7 @@ Obtain information from a YAML file directory, a local git repository under \verb{~/git/chyaml}, or from the web (not implemented).} -\item{\code{chyaml}}{The filename to be looked for -Add a vapour pressure} +\item{\code{chyaml}}{The filename to be looked for} } \if{html}{\out{</div>}} } @@ -224,6 +218,7 @@ Add a vapour pressure} \if{html}{\out{<a id="method-chent-add_p0"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_p0}{}}} \subsection{Method \code{add_p0()}}{ +Add a vapour pressure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } @@ -231,8 +226,7 @@ Add a vapour pressure} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{p0}}{The vapour pressure in Pa -Add a water solubility} +\item{\code{p0}}{The vapour pressure in Pa} \item{\code{T}}{Temperature} @@ -249,6 +243,7 @@ Add a water solubility} \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$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}} } @@ -256,8 +251,7 @@ Add a water solubility} \subsection{Arguments}{ \if{html}{\out{<div class="arguments">}} \describe{ -\item{\code{cwsat}}{The water solubility in mg/L -Add a plant uptake factor} +\item{\code{cwsat}}{The water solubility in mg/L} \item{\code{T}}{Temperature} @@ -276,6 +270,7 @@ Add a plant uptake factor} \if{html}{\out{<a id="method-chent-add_PUF"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_PUF}{}}} \subsection{Method \code{add_PUF()}}{ +Add a plant uptake factor \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_PUF( PUF = 0, @@ -303,6 +298,7 @@ Add a plant uptake factor} \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$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}} } @@ -323,6 +319,7 @@ Add a plant uptake factor} \if{html}{\out{<a id="method-chent-add_transformation"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_transformation}{}}} \subsection{Method \code{add_transformation()}}{ +Add a line in the internal dataframe holding observed transformations \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_transformation( study_type, @@ -359,6 +356,7 @@ result from stochiometric transformation} \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$add_soil_degradation( soils, @@ -431,6 +429,7 @@ the technical active ingredient} \if{html}{\out{<a id="method-chent-add_soil_ff"></a>}} \if{latex}{\out{\hypertarget{method-chent-add_soil_ff}{}}} \subsection{Method \code{add_soil_ff()}}{ +Add one or more formation fractions for degradation in soil \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)}\if{html}{\out{</div>}} } @@ -457,6 +456,7 @@ the technical active ingredient} \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$add_soil_sorption( soils, @@ -516,7 +516,6 @@ or according to Freundlich} \if{latex}{\out{\hypertarget{method-chent-pdf}{}}} \subsection{Method \code{pdf()}}{ Write a PDF image of the structure -Write a PNG image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$pdf( file = paste0(self$identifier, ".pdf"), @@ -541,6 +540,7 @@ Write a PNG image of the structure \if{html}{\out{<a id="method-chent-png"></a>}} \if{latex}{\out{\hypertarget{method-chent-png}{}}} \subsection{Method \code{png()}}{ +Write a PNG image of the structure \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{chent$png( file = paste0(self$identifier, ".png"), @@ -72,6 +72,7 @@ at <pesticidecompendium.bcpc.org>} \if{html}{\out{<a id="method-pai-new"></a>}} \if{latex}{\out{\hypertarget{method-pai-new}{}}} \subsection{Method \code{new()}}{ +Create a new pai object \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{pai$new( iso, @@ -23,8 +23,7 @@ product \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{density_units}}{Defaults to g/L} } \if{html}{\out{</div>}} } @@ -39,6 +38,7 @@ Creates a new instance of this \link[R6:R6Class]{R6} class.} \if{html}{\out{<a id="method-ppp-new"></a>}} \if{latex}{\out{\hypertarget{method-ppp-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{ppp$new( name, |