From 525269a9f663d02546e2de22ddd79294cc246f57 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <johannes.ranke@jrwb.de>
Date: Thu, 5 Mar 2026 15:57:01 +0100
Subject: Rebuild docs

---
 docs/reference/chent.html        |  11 +-
 docs/reference/chent.md          | 802 +++++++++++++++++++++++++++++++++++++++
 docs/reference/draw_svg.chent.md |  37 ++
 docs/reference/index.html        |  26 +-
 docs/reference/index.md          |  20 +
 docs/reference/pai.html          |   7 +-
 docs/reference/pai.md            | 187 +++++++++
 docs/reference/plot.chent.html   |  15 +-
 docs/reference/plot.chent.md     |  51 +++
 docs/reference/ppp.md            | 102 +++++
 docs/reference/print.chent.md    |  20 +
 docs/reference/print.pai.md      |  20 +
 docs/reference/print.ppp.md      |  20 +
 13 files changed, 1296 insertions(+), 22 deletions(-)
 create mode 100644 docs/reference/chent.md
 create mode 100644 docs/reference/draw_svg.chent.md
 create mode 100644 docs/reference/index.md
 create mode 100644 docs/reference/pai.md
 create mode 100644 docs/reference/plot.chent.md
 create mode 100644 docs/reference/ppp.md
 create mode 100644 docs/reference/print.chent.md
 create mode 100644 docs/reference/print.pai.md
 create mode 100644 docs/reference/print.ppp.md

(limited to 'docs/reference')

diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index 131d548..e2f241d 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -11,7 +11,7 @@ generated using RDKit if RDKit and its python bindings are installed."></head><b
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -790,7 +790,9 @@ or according to Freundlich</p></dd>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Don't run examples per default, as PubChem may be unavailable</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</span> <span class="va">chent</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Querying PubChem for name caffeine ...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Get chemical information from RDKit using PubChem SMILES</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span>
@@ -807,7 +809,7 @@ or according to Freundlich</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Caffein"                 "Cafipel"                </span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
@@ -823,6 +825,7 @@ or according to Freundlich</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        user </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> "CCCCCCCCO" </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 130.2 </span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -834,7 +837,7 @@ or according to Freundlich</p></dd>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/chent.md b/docs/reference/chent.md
new file mode 100644
index 0000000..40716ce
--- /dev/null
+++ b/docs/reference/chent.md
@@ -0,0 +1,802 @@
+# An R6 class for chemical entities with associated data
+
+The class is initialised with an identifier. Chemical information is
+retrieved from the internet. Additionally, it can be generated using
+RDKit if RDKit and its python bindings are installed.
+
+## Format
+
+An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator
+object
+
+## Public fields
+
+- `identifier`:
+
+  (`character(1)`)  
+  The identifier that was used to initiate the object, with attribute
+  'source'
+
+- `inchikey`:
+
+  (`character(1)`)  
+  InChI Key, with attribute 'source'
+
+- `smiles`:
+
+  ([`character()`](https://rdrr.io/r/base/character.html))  
+  SMILES code(s), with attribute 'source'
+
+- `mw`:
+
+  (`numeric(1)`)  
+  Molecular weight, with attribute 'source'
+
+- `pubchem`:
+
+  ([`list()`](https://rdrr.io/r/base/list.html))  
+  List of information retrieved from PubChem
+
+- `rdkit`:
+
+  List of information obtained with RDKit
+
+- `mol`:
+
+  \<rdkit.Chem.rdchem.Mol\> object
+
+- `svg`:
+
+  SVG code
+
+- `Picture`:
+
+  Graph as a
+  [grImport::Picture](https://rdrr.io/pkg/grImport/man/Picture-class.html)
+  object obtained using the grImport package
+
+- `Pict_font_size`:
+
+  Font size as extracted from the intermediate PostScript file
+
+- `pdf_height`:
+
+  Height of the MediaBox in the pdf after cropping
+
+- `p0`:
+
+  Vapour pressure in Pa
+
+- `cwsat`:
+
+  Water solubility in mg/L
+
+- `PUF`:
+
+  Plant uptake factor
+
+- `chyaml`:
+
+  List of information obtained from a YAML file
+
+- `TPs`:
+
+  List of transformation products as chent objects
+
+- `transformations`:
+
+  Data frame of observed transformations
+
+- `soil_degradation`:
+
+  Dataframe of modelling DT50 values
+
+- `soil_ff`:
+
+  Dataframe of formation fractions
+
+- `soil_sorption`:
+
+  Dataframe of soil sorption data
+
+## Methods
+
+### Public methods
+
+- [`chent$new()`](#method-chent-new)
+
+- [`chent$try_pubchem()`](#method-chent-try_pubchem)
+
+- [`chent$get_pubchem()`](#method-chent-get_pubchem)
+
+- [`chent$get_rdkit()`](#method-chent-get_rdkit)
+
+- [`chent$get_chyaml()`](#method-chent-get_chyaml)
+
+- [`chent$add_p0()`](#method-chent-add_p0)
+
+- [`chent$add_cwsat()`](#method-chent-add_cwsat)
+
+- [`chent$add_PUF()`](#method-chent-add_PUF)
+
+- [`chent$add_TP()`](#method-chent-add_TP)
+
+- [`chent$add_transformation()`](#method-chent-add_transformation)
+
+- [`chent$add_soil_degradation()`](#method-chent-add_soil_degradation)
+
+- [`chent$add_soil_ff()`](#method-chent-add_soil_ff)
+
+- [`chent$add_soil_sorption()`](#method-chent-add_soil_sorption)
+
+- [`chent$pdf()`](#method-chent-pdf)
+
+- [`chent$png()`](#method-chent-png)
+
+- [`chent$emf()`](#method-chent-emf)
+
+- [`chent$clone()`](#method-chent-clone)
+
+------------------------------------------------------------------------
+
+### Method `new()`
+
+Creates a new instance of this
+[R6](https://r6.r-lib.org/reference/R6Class.html) class.
+
+#### Usage
+
+    chent$new(
+      identifier,
+      smiles = NULL,
+      inchikey = NULL,
+      pubchem = TRUE,
+      pubchem_from = c("name", "smiles", "inchikey"),
+      rdkit = TRUE,
+      template = NULL,
+      chyaml = FALSE
+    )
+
+#### Arguments
+
+- `identifier`:
+
+  Identifier to be stored in the object
+
+- `smiles`:
+
+  Optional user provided SMILES code
+
+- `inchikey`:
+
+  Optional user provided InChI Key
+
+- `pubchem`:
+
+  Should an attempt be made to retrieve chemical information from
+  PubChem via the webchem package?
+
+- `pubchem_from`:
+
+  Possibility to select the argument that is used to query pubchem
+
+- `rdkit`:
+
+  Should an attempt be made to retrieve chemical information from a
+  local rdkit installation via python and the reticulate package?
+
+- `template`:
+
+  An optional SMILES code to be used as template for RDKit
+
+- `chyaml`:
+
+  Should we look for a identifier.yaml file in the working directory?
+
+------------------------------------------------------------------------
+
+### Method `try_pubchem()`
+
+Try to get chemical information from PubChem
+
+#### Usage
+
+    chent$try_pubchem(query = self$identifier, from = "name")
+
+#### Arguments
+
+- `query`:
+
+  Query string to be passed to
+  [get_cid](https://docs.ropensci.org/webchem/reference/get_cid.html)
+
+- `from`:
+
+  Passed to
+  [get_cid](https://docs.ropensci.org/webchem/reference/get_cid.html)
+
+------------------------------------------------------------------------
+
+### Method `get_pubchem()`
+
+Get chemical information from PubChem for a known PubChem CID
+
+#### Usage
+
+    chent$get_pubchem(pubchem_cid)
+
+#### Arguments
+
+- `pubchem_cid`:
+
+  CID
+
+------------------------------------------------------------------------
+
+### Method `get_rdkit()`
+
+Get chemical information from RDKit if available
+
+#### Usage
+
+    chent$get_rdkit(template = NULL)
+
+#### Arguments
+
+- `template`:
+
+  An optional SMILES code to be used as template for RDKit
+
+------------------------------------------------------------------------
+
+### Method `get_chyaml()`
+
+Obtain information from a YAML file
+
+#### Usage
+
+    chent$get_chyaml(
+      repo = c("wd", "local", "web"),
+      chyaml = paste0(URLencode(self$identifier), ".yaml")
+    )
+
+#### Arguments
+
+- `repo`:
+
+  Should the file be looked for in the current working directory, a
+  local git repository under `~/git/chyaml`, or from the web (not
+  implemented).
+
+- `chyaml`:
+
+  The filename to be looked for
+
+------------------------------------------------------------------------
+
+### Method `add_p0()`
+
+Add a vapour pressure
+
+#### Usage
+
+    chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")
+
+#### Arguments
+
+- `p0`:
+
+  The vapour pressure in Pa
+
+- `T`:
+
+  Temperature
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `page`:
+
+  The page from which the information was taken
+
+- `remark`:
+
+  A remark
+
+------------------------------------------------------------------------
+
+### Method `add_cwsat()`
+
+Add a water solubility
+
+#### Usage
+
+    chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")
+
+#### Arguments
+
+- `cwsat`:
+
+  The water solubility in mg/L
+
+- `T`:
+
+  Temperature
+
+- `pH`:
+
+  pH value
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `page`:
+
+  The page from which the information was taken
+
+- `remark`:
+
+  A remark
+
+------------------------------------------------------------------------
+
+### Method `add_PUF()`
+
+Add a plant uptake factor
+
+#### Usage
+
+    chent$add_PUF(
+      PUF = 0,
+      source = "focus_generic_gw_2014",
+      page = 41,
+      remark = "Conservative default value"
+    )
+
+#### Arguments
+
+- `PUF`:
+
+  The plant uptake factor, a number between 0 and 1
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `page`:
+
+  The page from which the information was taken
+
+- `remark`:
+
+  A remark
+
+------------------------------------------------------------------------
+
+### Method `add_TP()`
+
+Add a transformation product to the internal list
+
+#### Usage
+
+    chent$add_TP(x, smiles = NULL, pubchem = FALSE)
+
+#### Arguments
+
+- `x`:
+
+  A chent object, or an identifier to generate a chent object
+
+- `smiles`:
+
+  Optional user provided SMILES code
+
+- `pubchem`:
+
+  Should chemical information be obtained from PubChem?
+
+------------------------------------------------------------------------
+
+### Method `add_transformation()`
+
+Add a line in the internal dataframe holding observed transformations
+
+#### Usage
+
+    chent$add_transformation(
+      study_type,
+      TP_identifier,
+      max_occurrence,
+      remark = "",
+      source = NA,
+      pages = NA
+    )
+
+#### Arguments
+
+- `study_type`:
+
+  A characterisation of the study type
+
+- `TP_identifier`:
+
+  An identifier of one of the transformation products in `self$TPs`
+
+- `max_occurrence`:
+
+  The maximum observed occurrence of the transformation product,
+  expressed as a fraction of the amount that would result from
+  stochiometric transformation
+
+- `remark`:
+
+  A remark
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `pages`:
+
+  The pages from which the information was taken
+
+------------------------------------------------------------------------
+
+### Method `add_soil_degradation()`
+
+Add a line in the internal dataframe holding modelling DT50 values
+
+#### Usage
+
+    chent$add_soil_degradation(
+      soils,
+      DT50_mod,
+      DT50_mod_ref,
+      type = NA,
+      country = NA,
+      pH_orig = NA,
+      pH_medium = NA,
+      pH_H2O = NA,
+      perc_OC = NA,
+      temperature = NA,
+      moisture = NA,
+      category = "lab",
+      formulation = NA,
+      model = NA,
+      chi2 = NA,
+      remark = "",
+      source,
+      page = NA
+    )
+
+#### Arguments
+
+- `soils`:
+
+  Names of the soils
+
+- `DT50_mod`:
+
+  The modelling DT50 in the sense of regulatory pesticide fate modelling
+
+- `DT50_mod_ref`:
+
+  The normalised modelling DT50 in the sense of regulatory pesticide
+  fate modelling
+
+- `type`:
+
+  The soil type
+
+- `country`:
+
+  The country (mainly for field studies)
+
+- `pH_orig`:
+
+  The pH stated in the study
+
+- `pH_medium`:
+
+  The medium in which this pH was measured
+
+- `pH_H2O`:
+
+  The pH extrapolated to pure water
+
+- `perc_OC`:
+
+  The percentage of organic carbon in the soil
+
+- `temperature`:
+
+  The temperature during the study in degrees Celsius
+
+- `moisture`:
+
+  The moisture during the study
+
+- `category`:
+
+  Is it a laboratory ('lab') or field study ('field')
+
+- `formulation`:
+
+  Name of the formulation applied, if it was not the technical active
+  ingredient
+
+- `model`:
+
+  The degradation model used for deriving `DT50_mod`
+
+- `chi2`:
+
+  The relative error as defined in FOCUS kinetics
+
+- `remark`:
+
+  A remark
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `page`:
+
+  The page from which the information was taken
+
+------------------------------------------------------------------------
+
+### Method `add_soil_ff()`
+
+Add one or more formation fractions for degradation in soil
+
+#### Usage
+
+    chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)
+
+#### Arguments
+
+- `target`:
+
+  The identifier(s) of the transformation product
+
+- `soils`:
+
+  The soil name(s) in which the transformation was observed
+
+- `ff`:
+
+  The formation fraction(s)
+
+- `remark`:
+
+  A remark
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `page`:
+
+  The page from which the information was taken
+
+------------------------------------------------------------------------
+
+### Method `add_soil_sorption()`
+
+Add soil sorption data
+
+#### Usage
+
+    chent$add_soil_sorption(
+      soils,
+      Kf,
+      Kfoc,
+      N,
+      type = NA,
+      pH_orig = NA,
+      pH_medium = NA,
+      pH_H2O = NA,
+      perc_OC = NA,
+      perc_clay = NA,
+      CEC = NA,
+      remark = "",
+      source,
+      page = NA
+    )
+
+#### Arguments
+
+- `soils`:
+
+  Names of the soils
+
+- `Kf`:
+
+  The sorption constant in L/kg, either linear (then `N` is 1) or
+  according to Freundlich
+
+- `Kfoc`:
+
+  The constant from above, normalised to soil organic carbon
+
+- `N`:
+
+  The Freundlich exponent
+
+- `type`:
+
+  The soil type
+
+- `pH_orig`:
+
+  The pH stated in the study
+
+- `pH_medium`:
+
+  The medium in which this pH was measured
+
+- `pH_H2O`:
+
+  The pH extrapolated to pure water
+
+- `perc_OC`:
+
+  The percentage of organic carbon in the soil
+
+- `perc_clay`:
+
+  The percentage of clay in the soil
+
+- `CEC`:
+
+  The cation exchange capacity
+
+- `remark`:
+
+  A remark
+
+- `source`:
+
+  An acronym specifying the source of the information
+
+- `page`:
+
+  The page from which the information was taken
+
+------------------------------------------------------------------------
+
+### Method [`pdf()`](https://rdrr.io/r/grDevices/pdf.html)
+
+Write a PDF image of the structure
+
+#### Usage
+
+    chent$pdf(
+      file = paste0(self$identifier, ".pdf"),
+      dir = "structures/pdf",
+      template = NULL
+    )
+
+#### Arguments
+
+- `file`:
+
+  The file to write to
+
+- `dir`:
+
+  The directory to write the file to
+
+- `template`:
+
+  An optional SMILES code to be used as template for RDKit
+
+------------------------------------------------------------------------
+
+### Method [`png()`](https://rdrr.io/r/grDevices/png.html)
+
+Write a PNG image of the structure
+
+#### Usage
+
+    chent$png(
+      file = paste0(self$identifier, ".png"),
+      dir = "structures/png",
+      antialias = "gray"
+    )
+
+#### Arguments
+
+- `file`:
+
+  The file to write to
+
+- `dir`:
+
+  The directory to write the file to
+
+- `antialias`:
+
+  Passed to [png](https://rdrr.io/r/grDevices/png.html)
+
+------------------------------------------------------------------------
+
+### Method `emf()`
+
+Write an EMF image of the structure using
+[emf](https://rdrr.io/pkg/devEMF/man/emf.html)
+
+#### Usage
+
+    chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")
+
+#### Arguments
+
+- `file`:
+
+  The file to write to
+
+- `dir`:
+
+  The directory to write the file to
+
+------------------------------------------------------------------------
+
+### Method `clone()`
+
+The objects of this class are cloneable with this method.
+
+#### Usage
+
+    chent$clone(deep = FALSE)
+
+#### Arguments
+
+- `deep`:
+
+  Whether to make a deep clone.
+
+## Examples
+
+``` r
+# Don't run examples per default, as PubChem may be unavailable
+# \dontrun{
+caffeine <- chent$new("caffeine")
+#> Querying PubChem for name caffeine ...
+#> Get chemical information from RDKit using PubChem 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 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Caffein"                 "Cafipel"                
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+
+oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
+#> 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 $mw: 130.2 
+# }
+```
diff --git a/docs/reference/draw_svg.chent.md b/docs/reference/draw_svg.chent.md
new file mode 100644
index 0000000..7b43988
--- /dev/null
+++ b/docs/reference/draw_svg.chent.md
@@ -0,0 +1,37 @@
+# Draw SVG graph from a chent object using RDKit
+
+Draw SVG graph from a chent object using RDKit
+
+## Usage
+
+``` r
+draw_svg.chent(
+  x,
+  width = 300,
+  height = 150,
+  filename = paste0(names(x$identifier), ".svg"),
+  subdir = "svg"
+)
+```
+
+## Arguments
+
+- x:
+
+  The chent object to be plotted
+
+- width:
+
+  The desired width in pixels
+
+- height:
+
+  The desired height in pixels
+
+- filename:
+
+  The filename
+
+- subdir:
+
+  The path to which the file should be written
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a8a9c05..52b7cfb 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -36,8 +36,7 @@
 
 
 
-
-    </div><div class="section level2">
+      <dl></dl></div><div class="section level2">
 
 
 
@@ -48,43 +47,50 @@
 
         </dt>
         <dd>An R6 class for chemical entities with associated data</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="pai.html">pai</a></code>
 
         </dt>
         <dd>An R6 class for pesticidal active ingredients and associated data</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="ppp.html">ppp</a></code>
 
         </dt>
         <dd>R6 class for a plant protection product with at least one active ingredient</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="draw_svg.chent.html">draw_svg.chent()</a></code>
 
         </dt>
         <dd>Draw SVG graph from a chent object using RDKit</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="plot.chent.html">plot(<i>&lt;chent&gt;</i>)</a></code>
 
         </dt>
         <dd>Plot method for chent objects</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="print.chent.html">print(<i>&lt;chent&gt;</i>)</a></code>
 
         </dt>
         <dd>Printing method for chent objects</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="print.pai.html">print(<i>&lt;pai&gt;</i>)</a></code>
 
         </dt>
         <dd>Printing method for pai objects (pesticidal active ingredients)</dd>
-      </dl><dl><dt>
+
+        <dt>
 
           <code><a href="print.ppp.html">print(<i>&lt;ppp&gt;</i>)</a></code>
 
@@ -99,7 +105,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/index.md b/docs/reference/index.md
new file mode 100644
index 0000000..c927189
--- /dev/null
+++ b/docs/reference/index.md
@@ -0,0 +1,20 @@
+# Package index
+
+## R6 Class definitions and methods
+
+- [`chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) : An R6
+  class for chemical entities with associated data
+- [`pai`](https://pkgdown.jrwb.de/chents/reference/pai.md) : An R6 class
+  for pesticidal active ingredients and associated data
+- [`ppp`](https://pkgdown.jrwb.de/chents/reference/ppp.md) : R6 class
+  for a plant protection product with at least one active ingredient
+- [`draw_svg.chent()`](https://pkgdown.jrwb.de/chents/reference/draw_svg.chent.md)
+  : Draw SVG graph from a chent object using RDKit
+- [`plot(`*`<chent>`*`)`](https://pkgdown.jrwb.de/chents/reference/plot.chent.md)
+  : Plot method for chent objects
+- [`print(`*`<chent>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.chent.md)
+  : Printing method for chent objects
+- [`print(`*`<pai>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.pai.md)
+  : Printing method for pai objects (pesticidal active ingredients)
+- [`print(`*`<ppp>`*`)`](https://pkgdown.jrwb.de/chents/reference/print.ppp.md)
+  : Printing method for ppp objects (plant protection products)
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 25ca564..29f9368 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -184,7 +184,9 @@ and the reticulate package?</p></dd>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">atr</span> <span class="op">&lt;-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Don't run examples per default, as PubChem may be unavailable</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">atr</span> <span class="op">&lt;-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Querying BCPC for atrazine ...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Querying PubChem for inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N ...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Get chemical information from RDKit using PubChem SMILES</span>
@@ -225,6 +227,7 @@ and the reticulate package?</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "1-DECANOL"       "Decan-1-ol"      "Decyl alcohol"   "112-30-1"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "n-Decyl alcohol" "n-Decanol"       "Capric alcohol"  "Nonylcarbinol"  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Antak"           "Royaltac"       </span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -236,7 +239,7 @@ and the reticulate package?</p></dd>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/pai.md b/docs/reference/pai.md
new file mode 100644
index 0000000..2291653
--- /dev/null
+++ b/docs/reference/pai.md
@@ -0,0 +1,187 @@
+# An R6 class for pesticidal active ingredients and associated data
+
+This class is derived from
+[chent](https://pkgdown.jrwb.de/chents/reference/chent.md). It makes it
+easy to create a
+[chent](https://pkgdown.jrwb.de/chents/reference/chent.md) from the ISO
+common name of a pesticide active ingredient, and additionally stores
+the ISO name as well as the complete result of querying the BCPC
+compendium using
+[bcpc_query](https://docs.ropensci.org/webchem/reference/bcpc_query.html).
+
+## Format
+
+An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator
+object
+
+## Super class
+
+[`chents::chent`](https://pkgdown.jrwb.de/chents/reference/chent.md) -\>
+`pai`
+
+## Public fields
+
+- `iso`:
+
+  ISO common name of the active ingredient according to ISO 1750
+
+- `bcpc`:
+
+  Information retrieved from the BCPC compendium available online at
+  \<pesticidecompendium.bcpc.org\>
+
+## Methods
+
+### Public methods
+
+- [`pai$new()`](#method-pai-new)
+
+- [`pai$clone()`](#method-pai-clone)
+
+Inherited methods
+
+- [`chents::chent$add_PUF()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_PUF)
+- [`chents::chent$add_TP()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_TP)
+- [`chents::chent$add_cwsat()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_cwsat)
+- [`chents::chent$add_p0()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_p0)
+- [`chents::chent$add_soil_degradation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_degradation)
+- [`chents::chent$add_soil_ff()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_ff)
+- [`chents::chent$add_soil_sorption()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_soil_sorption)
+- [`chents::chent$add_transformation()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-add_transformation)
+- [`chents::chent$emf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-emf)
+- [`chents::chent$get_chyaml()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_chyaml)
+- [`chents::chent$get_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_pubchem)
+- [`chents::chent$get_rdkit()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-get_rdkit)
+- [`chents::chent$pdf()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-pdf)
+- [`chents::chent$png()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-png)
+- [`chents::chent$try_pubchem()`](https://pkgdown.jrwb.de/chents/reference/chent.html#method-try_pubchem)
+
+------------------------------------------------------------------------
+
+### Method `new()`
+
+Create a new pai object
+
+#### Usage
+
+    pai$new(
+      iso,
+      identifier = iso,
+      smiles = NULL,
+      inchikey = NULL,
+      bcpc = TRUE,
+      pubchem = TRUE,
+      pubchem_from = "auto",
+      rdkit = TRUE,
+      template = NULL,
+      chyaml = FALSE
+    )
+
+#### Arguments
+
+- `iso`:
+
+  The ISO common name to be used in the query of the BCPC compendium
+
+- `identifier`:
+
+  Alternative identifier used for querying pubchem
+
+- `smiles`:
+
+  Optional user provided SMILES code
+
+- `inchikey`:
+
+  Optional user provided InChI Key
+
+- `bcpc`:
+
+  Should the BCPC compendium be queried?
+
+- `pubchem`:
+
+  Should an attempt be made to retrieve chemical information from
+  PubChem via the webchem package?
+
+- `pubchem_from`:
+
+  Possibility to select the argument that is used to query pubchem
+
+- `rdkit`:
+
+  Should an attempt be made to retrieve chemical information from a
+  local rdkit installation via python and the reticulate package?
+
+- `template`:
+
+  An optional SMILES code to be used as template for RDKit
+
+- `chyaml`:
+
+  Should we look for a identifier.yaml file in the working
+
+------------------------------------------------------------------------
+
+### Method `clone()`
+
+The objects of this class are cloneable with this method.
+
+#### Usage
+
+    pai$clone(deep = FALSE)
+
+#### Arguments
+
+- `deep`:
+
+  Whether to make a deep clone.
+
+## Examples
+
+``` r
+# Don't run examples per default, as PubChem may be unavailable
+# \dontrun{
+atr <- pai$new("atrazine")
+#> Querying BCPC for atrazine ...
+#> Querying PubChem for inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N ...
+#> Get chemical information from RDKit using PubChem SMILES
+#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
+print(atr)
+#> <pai> with ISO common name $iso atrazine 
+#> <chent>
+#> Identifier $identifier atrazine 
+#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>                      PubChem 
+#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
+#> Molecular weight $mw: 215.7 
+#> PubChem synonyms (up to 10):
+#>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Aatrex"       "Atranex"     
+#>  [6] "Atrazin"      "Oleogesaprim" "Atazinax"     "Atrasine"     "Chromozin"   
+if (!is.null(atr$Picture)) {
+  plot(atr)
+}
+
+# We can also define pais that are not found on the BCPC site
+decanol <- pai$new("1-Decanol")
+#> Querying BCPC for 1-Decanol ...
+#> Common name 1-Decanol is not known at the BCPC compendium, trying PubChem
+#> Querying PubChem for name 1-Decanol ...
+#> Get chemical information from RDKit using PubChem SMILES
+#> CCCCCCCCCCO
+print(decanol)
+#> <pai> without ISO common name
+#> <chent>
+#> Identifier $identifier 1-Decanol 
+#> InChI Key $inchikey MWKFXSUHUHTGQN-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>       PubChem 
+#> "CCCCCCCCCCO" 
+#> Molecular weight $mw: 158.3 
+#> PubChem synonyms (up to 10):
+#>  [1] "1-DECANOL"       "Decan-1-ol"      "Decyl alcohol"   "112-30-1"       
+#>  [5] "n-Decyl alcohol" "n-Decanol"       "Capric alcohol"  "Nonylcarbinol"  
+#>  [9] "Antak"           "Royaltac"       
+# }
+```
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index 49f54b2..c33b732 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">chents</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -58,9 +58,11 @@
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</span> <span class="va"><a href="chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> PubChem:</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem SMILES</span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Don't run examples per default, as PubChem may be unavailable</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">caffeine</span> <span class="op">&lt;-</span> <span class="va"><a href="chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"caffeine"</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Querying PubChem for name caffeine ...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Get chemical information from RDKit using PubChem SMILES</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
@@ -75,11 +77,12 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Caffein"                 "Cafipel"                </span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</span><span class="va">Picture</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-plt img"><img src="plot.chent-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -91,7 +94,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p>
 </div>
 
     </footer></div>
diff --git a/docs/reference/plot.chent.md b/docs/reference/plot.chent.md
new file mode 100644
index 0000000..eaa6817
--- /dev/null
+++ b/docs/reference/plot.chent.md
@@ -0,0 +1,51 @@
+# Plot method for chent objects
+
+Plot method for chent objects
+
+## Usage
+
+``` r
+# S3 method for class 'chent'
+plot(x, ...)
+```
+
+## Arguments
+
+- x:
+
+  The chent object to be plotted
+
+- ...:
+
+  Further arguments passed to
+  [grImport::grid.picture](https://rdrr.io/pkg/grImport/man/grid.picture.html)
+
+## Examples
+
+``` r
+# Don't run examples per default, as PubChem may be unavailable
+# \dontrun{
+caffeine <- chent$new("caffeine")
+#> Querying PubChem for name caffeine ...
+#> Get chemical information from RDKit using PubChem 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 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Caffein"                 "Cafipel"                
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+
+# }
+```
diff --git a/docs/reference/ppp.md b/docs/reference/ppp.md
new file mode 100644
index 0000000..77ff2b6
--- /dev/null
+++ b/docs/reference/ppp.md
@@ -0,0 +1,102 @@
+# R6 class for a plant protection product with at least one active ingredient
+
+Contains basic information about the active ingredients in the product
+
+## Format
+
+An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator
+object.
+
+## Public fields
+
+- `name`:
+
+  The name of the product
+
+- `ais`:
+
+  A list of active ingredients
+
+- `concentrations`:
+
+  The concentration of the ais
+
+- `concentration_units`:
+
+  Defaults to g/L
+
+- `density`:
+
+  The density of the product
+
+- `density_units`:
+
+  Defaults to g/L
+
+## Methods
+
+### Public methods
+
+- [`ppp$new()`](#method-ppp-new)
+
+- [`ppp$clone()`](#method-ppp-clone)
+
+------------------------------------------------------------------------
+
+### Method `new()`
+
+Creates a new instance of this
+[R6](https://r6.r-lib.org/reference/R6Class.html) class.
+
+#### Usage
+
+    ppp$new(
+      name,
+      ...,
+      concentrations,
+      concentration_units = "g/L",
+      density = 1000,
+      density_units = "g/L"
+    )
+
+#### Arguments
+
+- `name`:
+
+  The name of the product
+
+- `...`:
+
+  Identifiers of the active ingredients
+
+- `concentrations`:
+
+  Concentrations of the active ingredients
+
+- `concentration_units`:
+
+  Defaults to g/L
+
+- `density`:
+
+  The density
+
+- `density_units`:
+
+  Defaults to g/L
+
+------------------------------------------------------------------------
+
+### Method `clone()`
+
+The objects of this class are cloneable with this method.
+
+#### Usage
+
+    ppp$clone(deep = FALSE)
+
+#### Arguments
+
+- `deep`:
+
+  Whether to make a deep clone.
diff --git a/docs/reference/print.chent.md b/docs/reference/print.chent.md
new file mode 100644
index 0000000..f4d84bf
--- /dev/null
+++ b/docs/reference/print.chent.md
@@ -0,0 +1,20 @@
+# Printing method for chent objects
+
+Printing method for chent objects
+
+## Usage
+
+``` r
+# S3 method for class 'chent'
+print(x, ...)
+```
+
+## Arguments
+
+- x:
+
+  The chent object to be printed
+
+- ...:
+
+  Further arguments for compatibility with the S3 method
diff --git a/docs/reference/print.pai.md b/docs/reference/print.pai.md
new file mode 100644
index 0000000..86cad4b
--- /dev/null
+++ b/docs/reference/print.pai.md
@@ -0,0 +1,20 @@
+# Printing method for pai objects (pesticidal active ingredients)
+
+Printing method for pai objects (pesticidal active ingredients)
+
+## Usage
+
+``` r
+# S3 method for class 'pai'
+print(x, ...)
+```
+
+## Arguments
+
+- x:
+
+  The chent object to be printed
+
+- ...:
+
+  Further arguments for compatibility with the S3 method
diff --git a/docs/reference/print.ppp.md b/docs/reference/print.ppp.md
new file mode 100644
index 0000000..8387a54
--- /dev/null
+++ b/docs/reference/print.ppp.md
@@ -0,0 +1,20 @@
+# Printing method for ppp objects (plant protection products)
+
+Printing method for ppp objects (plant protection products)
+
+## Usage
+
+``` r
+# S3 method for class 'ppp'
+print(x, ...)
+```
+
+## Arguments
+
+- x:
+
+  The chent object to be printed
+
+- ...:
+
+  Further arguments for compatibility with the S3 method
-- 
cgit v1.2.3