Make an RStudio project and improve the docs

27 files changed, 1364 insertions, 1604 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index e972bda..99eec76 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -5,3 +5,5 @@
 ^docs$
 ^_pkgdown\.yml$
 ^\.travis\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index 6865f3b..c1b5016 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 chents_*.tar.gz
 chents.Rcheck
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
index 815a9c0..e75912b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,15 +2,14 @@ Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
 Version: 0.3.1
-Date: 2023-06-08
+Date: 2023-11-10
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
-                    email = "jranke@uni-bremen.de"))
+                    email = "johannes.ranke@jrwb.de"))
 Description: Utilities for dealing with chemical entities and associated
     data as R objects. If Python and RDKit (> 2015.03) are installed and
     configured for use with 'reticulate', some basic chemoinformatics functions
     like the calculation of molecular weight and plotting of chemical
-    structures in R graphics are available. For plotting, you need
-    grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN.
+    structures in R graphics are available.
 Imports:
     webchem,
     R6,
@@ -28,4 +27,5 @@ LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
 URL: https://github.com/jranke/chents
-RoxygenNote: 7.2.1
+Roxygen: list(markdown = TRUE, r6 = TRUE)
+RoxygenNote: 7.2.3
diff --git a/GNUmakefile b/GNUmakefile
index c9975a9..8d2c094 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -27,11 +27,9 @@ pd: roxygen
 	@echo "DONE."
 
 $(TGZ): $(pkgfiles)
-	sed -i -e "s/Date:.*/Date: $(DATE)/" DESCRIPTION
 	@echo "Roxygenizing package..."
 	"$(R_HOME)/bin/Rscript" -e 'library(devtools); document()'
 	@echo "Building package..."
-	git log --no-merges -M --date=iso > ChangeLog
 	"$(R_HOME)/bin/R" CMD build .
 	@echo "DONE."
 
diff --git a/R/chent.R b/R/chent.R
index c89efec..dc9be6f 100644
--- a/R/chent.R
+++ b/R/chent.R
@@ -1,25 +1,8 @@
-# Copyright (C) 2016-2021  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package chents
-
-# This program is free software: you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
-
-#' An R6 class for chemical entities with associated data
+#' @title 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.
+#' @description The class is initialised with an identifier. Chemical 
+#' information is retrieved from the internet. Additionally, it can be 
+#' generated using RDKit if RDKit and its python bindings are installed.
 #'
 #' @export
 #' @format An \code{\link{R6Class}} generator object
@@ -28,27 +11,8 @@
 #' @importFrom grImport PostScriptTrace readPicture
 #' @importFrom yaml yaml.load_file
 #' @importFrom rsvg rsvg_ps
-#' @field identifier The identifier that was used to initiate the object, with attribute 'source'
-#' @field inchikey InChI Key, with attribute 'source'
-#' @field smiles SMILES code, with attribute 'source'
-#' @field mw Molecular weight, with attribute 'source'
-#' @field pubchem List of information retreived from PubChem
-#' @field rdkit List of information obtained with RDKit
-#' @field mol <rdkit.Chem.rdchem.Mol> object
-#' @field svg SVG code
-#' @field Picture Graph as a \code{\link{picture}} object obtained using grImport
-#' @field Pict_font_size Font size as extracted from the intermediate PostScript file
-#' @field pdf_height Height of the MediaBox in the pdf after cropping
-#' @field p0 Vapour pressure in Pa
-#' @field cwsat Water solubility in mg/L
-#' @field chyaml List of information obtained from a YAML file
-#' @field soil_degradation Dataframe of modelling DT50 values
-#' @field soil_ff Dataframe of formation fractions
-#' @field soil_sorption Dataframe of soil sorption data
-#' @field PUF Plant uptake factor
-#' @keywords data
 #' @examples
-#' oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
+#' oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
 #' print(oct)
 #' if (!is.null(oct$Picture)) {
 #'   plot(oct)
@@ -59,30 +23,80 @@
 #' if (!is.null(caffeine$Picture)) {
 #'   plot(caffeine)
 #' }
-
 chent <- R6Class("chent",
-  public <- list(
+  public = list(
+    #' @field identifier (`character(1)`)\cr
+    #' The identifier that was used to initiate the object, with attribute 'source'
     identifier = NULL,
+    
+    #' @field inchikey (`character(1)`)\cr
+    #' InChI Key, with attribute 'source'
     inchikey = NULL,
+    
+    #' @field smiles (`character()`)\cr
+    #' SMILES code(s), with attribute 'source'
     smiles = NULL,
+    
+    #' @field mw (`numeric(1)`)\cr
+    #' Molecular weight, with attribute 'source'
     mw = NULL,
+    
+    #' @field pubchem (`list()`)\cr
+    #' List of information retrieved from PubChem
     pubchem = NULL,
+    
+    #' @field rdkit
+    #' List of information obtained with RDKit
     rdkit = NULL,
+    
+    #' @field mol <rdkit.Chem.rdchem.Mol> object
     mol = NULL,
+    
+    #' @field svg SVG code
     svg = NULL,
+    
+    #' @field Picture Graph as a \code{\link{picture}} object obtained using grImport
     Picture = NULL,
+    
+    #' @field Pict_font_size Font size as extracted from the intermediate PostScript file
     Pict_font_size = NULL,
+    
+    #' @field pdf_height Height of the MediaBox in the pdf after cropping
     pdf_height = NULL,
+    
+    #' @field p0 Vapour pressure in Pa
     p0 = NULL,
+    
+    #' @field cwsat Water solubility in mg/L
     cwsat = NULL,
+
+    #' @field PUF Plant uptake factor
     PUF = NULL,
+    
+    #' @field chyaml List of information obtained from a YAML file
     chyaml = NULL,
-    initialize = function(identifier, smiles = NULL, smiles_source = 'user',
-                          inchikey = NULL, inchikey_source = 'user',
-                          pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'),
-                          rdkit = TRUE, template = NULL,
-                          chyaml = TRUE) {
-
+    
+    #' @description
+    #' Creates a new instance of this [R6][R6::R6Class] class.
+    #' 
+    #' @param identifier Identifier to be stored in the object 
+    #' @param smiles Optional user provided SMILES code
+    #' @param inchikey Optional user provided InChI Key
+    #' @param pubchem Should an attempt be made to retrieve chemical
+    #' information from PubChem via the webchem package?
+    #' @param pubchem_from Possibility to select the argument 
+    #' that is used to query pubchem
+    #' @param rdkit Should an attempt be made to retrieve chemical 
+    #' information from a local rdkit installation via python
+    #' and the reticulate package?
+    #' @param template An optional SMILES code to be used as template for RDKit
+    #' @param chyaml Should we look for a identifier.yaml file in the working
+    #' directory?
+    initialize = function(identifier, smiles = NULL, inchikey = NULL, 
+      pubchem = TRUE, pubchem_from = c('name', 'smiles', 'inchikey'),
+      rdkit = TRUE, template = NULL,
+      chyaml = TRUE) {
+      
       self$identifier <- identifier
       names(self$identifier) <- make.names(identifier)
       pubchem_from = match.arg(pubchem_from)
@@ -120,6 +134,10 @@ chent <- R6Class("chent",
       }
       invisible(self)
     },
+    
+    #' 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]
     try_pubchem = function(query, from = 'name') {
       message("PubChem:")
       if (missing(query)) query <- self$identifier
@@ -131,6 +149,9 @@ chent <- R6Class("chent",
         self$get_pubchem(pubchem_result[[1, "cid"]])
       }
     },
+    
+    #' Get chemical information from PubChem for a known PubChem CID
+    #' @param pubchem_cid CID
     get_pubchem = function(pubchem_cid) {
       self$pubchem = as.list(webchem::pc_prop(pubchem_cid, from = "cid",
         properties = c("MolecularFormula", "MolecularWeight",
@@ -170,6 +191,9 @@ chent <- R6Class("chent",
         }
       }
     },
+    
+    #' Get chemical information from RDKit if available
+    #' @param template Optional template specified as a SMILES code
     get_rdkit = function(template = NULL) {
       if(!rdkit_available) {
         stop("RDKit is not available")
@@ -212,11 +236,18 @@ chent <- R6Class("chent",
       self$Picture <- readPicture(xmlfile)
       unlink(c(xmlfile, psfile, svgfile))
     },
+    
+    #' 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
+    #' the web (not implemented).
     get_chyaml = function(repo = c("wd", "local", "web"),
-                          chyaml = paste0(URLencode(self$identifier), ".yaml")) {
+      chyaml = paste0(URLencode(self$identifier), ".yaml"))
+    {
       repo = match.arg(repo)
-      paths = c(wd = ".",
-                local = file.path("~", "git/chyaml"))
+      paths = c(
+        wd = ".",
+        local = file.path("~", "git/chyaml"))
 
       chyaml_handlers = list(
         expr = function(x) NULL, # To avoid security risks from reading chyaml files
@@ -240,6 +271,13 @@ chent <- R6Class("chent",
         message("web repositories not implemented")
       }
     },
+    
+    #' Add a vapour pressure
+    #' @param p0 The vapour pressure in Pa
+    #' @param T Temperature
+    #' @param source An acronym specifying the source of the information
+    #' @param page The page from which the information was taken
+    #' @param remark A remark
     add_p0 = function(p0, T = NA, source = NA, page = NA, remark = "") {
       self$p0 <- p0
       attr(self$p0, "T") <- T
@@ -247,6 +285,9 @@ chent <- R6Class("chent",
       attr(self$p0, "page") <- page
       attr(self$p0, "remark") <- remark
     },
+    
+    #' Add a water solubility
+    #' @param p0 The water solubility in mg/L
     add_cwsat = function(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "") {
       self$cwsat <- cwsat
       attr(self$cwsat, "T") <- T
@@ -255,13 +296,23 @@ chent <- R6Class("chent",
       attr(self$cwsat, "page") <- page
       attr(self$cwsat, "remark") <- remark
     },
+    
+    #' Add a plant uptake factor
+    #' @param PUF The plant uptake factor, a number between 0 and 1
     add_PUF = function(PUF = 0, source = "focus_generic_gw_2014", page = 41, remark = "Conservative default value") {
       self$PUF <- PUF
       attr(self$PUF, "source") <- source
       attr(self$PUF, "page") <- page
       attr(self$PUF, "remark") <- remark
     },
+    
+    #' @field TPs List of transformation products as chent objects
     TPs = list(),
+    
+    #' Add a transformation product to the internal list
+    #' @param x A [chent] object, or an identifier to generate a [chent] object
+    #' @param smiles A SMILES code for defining a [chent] object
+    #' @param pubchem Should chemical information be obtained from PubChem?
     add_TP = function(x, smiles = NULL, pubchem = FALSE) {
       if (inherits(x, "chent")) {
         id <- names(x$identifier)
@@ -272,14 +323,19 @@ chent <- R6Class("chent",
       }
       self$TPs[[id]] <- chent
     },
+    
+    #' @field transformations Data frame of observed transformations
     transformations = data.frame(study_type = character(0),
                                  TP_identifier = character(0),
                                  max_occurrence = numeric(0),
                                  source = character(0),
                                  pages = character(0),
                                  stringsAsFactors = FALSE),
+    
+    #' Add a line in the internal dataframe holding observed transformations
     add_transformation = function(study_type, TP_identifier, max_occurrence,
-                                  remark = "", source = NA, pages = NA) {
+      remark = "", source = NA, pages = NA)
+    {
       TP_name = make.names(TP_identifier)
       if (!inherits(self$TPs[[TP_name]], "chent")) {
         stop(paste("Please add the TP", TP_identifier, "first using chent$add_TP()"))
@@ -296,15 +352,20 @@ chent <- R6Class("chent",
                                                pages = pages,
                                                stringsAsFactors = FALSE))
     },
+    
+    #' @field soil_degradation Dataframe of modelling DT50 values
     soil_degradation = NULL,
+    
+    #' Add a line in the internal dataframe holding modelling DT50 values
     add_soil_degradation = function(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) {
+      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)
+    {
       new_soil_degradation = data.frame(
         soil = soils,
         DT50_mod = DT50_mod,
@@ -331,10 +392,14 @@ chent <- R6Class("chent",
         self$soil_degradation <- rbind(self$soil_degradation, new_soil_degradation)
       }
     },
+    
+    #' @field soil_ff Dataframe of formation fractions
     soil_ff = NULL,
+    
     add_soil_ff = function(target, soils, ff = 1, remark = "", source, page = NA) {
       new_soil_ff = data.frame(
         target = target,
+        target = target,
         soil = soils,
         ff = ff,
         remark = remark,
@@ -347,7 +412,10 @@ chent <- R6Class("chent",
         self$soil_ff <- rbind(self$soil_ff, new_soil_ff)
       }
     },
+    
+    #' @field soil_sorption Dataframe of soil sorption data
     soil_sorption = NULL,
+    
     add_soil_sorption = function(soils, Kf, Kfoc, N,
                                  type = NA,
                                  pH_orig = NA, pH_medium = NA,
@@ -372,8 +440,9 @@ chent <- R6Class("chent",
         self$soil_sorption <- rbind(self$soil_sorption, new_soil_sorption)
       }
     },
-    pdf = function(file = paste0(self$identifier, ".pdf"), dir = "structures/pdf",
-                   template = NULL) {
+    
+    pdf = function(file = paste0(self$identifier, ".pdf"),
+        dir = "structures/pdf", template = NULL) {
       if (!dir.exists(dir)) {
         message("Directory '", dir, "' does not exist")
         message("Trying to create directory '", dir, "'")
@@ -493,7 +562,6 @@ plot.chent = function(x, ...) {
 #' @format An \code{\link{R6Class}} generator object
 #' @field iso ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org
 #' @field bcpc List of information retrieved from pesticidecompendium.bcpc.org
-#' @keywords data
 #' @examples
 #' # On Travis, we get a certificate validation error,
 #' # likely because the system (xenial) is so old,
@@ -507,15 +575,14 @@ plot.chent = function(x, ...) {
 #' }
 #'
 #' }
-
 pai <- R6Class("pai",
   inherit = chent,
   public <- list(
     iso = NULL,
     bcpc = NULL,
     initialize = function(iso, identifier = iso,
-                          smiles = NULL, smiles_source = 'user',
-                          inchikey = NULL, inchikey_source = 'user',
+                          smiles = NULL,
+                          inchikey = NULL,
                           bcpc = TRUE,
                           pubchem = TRUE, pubchem_from = 'auto',
                           rdkit = TRUE, template = NULL,
@@ -564,7 +631,7 @@ pai <- R6Class("pai",
       }
 
       super$initialize(identifier = identifier,
-                       smiles = smiles, smiles_source = smiles_source,
+                       smiles = smiles, 
                        inchikey = self$inchikey,
                        pubchem = pubchem, pubchem_from = pubchem_from,
                        rdkit = rdkit, template = template, chyaml = chyaml)
diff --git a/chents.Rproj b/chents.Rproj
new file mode 100644
index 0000000..8de5cfd
--- /dev/null
+++ b/chents.Rproj
@@ -0,0 +1,19 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/docs/404.html b/docs/404.html
index 7bd3245..eb79a5d 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -1,66 +1,27 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
 <title>Page not found (404) • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="bootstrap-toc.css">
-<script src="bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="Page not found (404)" />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+</head>
+<body data-spy="scroll" data-target="#toc">
+    
 
-
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-title-body">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -71,40 +32,34 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
 <li>
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+<ul class="nav navbar-nav navbar-right">
+<li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
       </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
+</div>
+<!--/.nav-collapse -->
+  </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="contents col-md-9">
     <div class="page-header">
       <h1>Page not found (404)</h1>
@@ -115,31 +70,31 @@ Content not found. Please use links in the navbar.
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
     </nav>
-  </div>
+</div>
 
 </div>
 
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p>
+<p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer>
-   </div>
+</div>
 
   
 
 
+  
+
   </body>
 </html>
-
-
diff --git a/docs/authors.html b/docs/authors.html
index 327fe56..0c3b654 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,66 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="bootstrap-toc.css">
-<script src="bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Authors and Citation • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"><script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
-    <div class="container template-authors">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+    <div class="container template-citation-authors">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -71,51 +17,58 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
+    <div class="section level2 authors-section">
+      <div class="page-header">
+        <h1>Authors</h1>
+      </div>
+
+      
+      <ul class="list-unstyled"><li>
+          <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. 
+          </p>
+        </li>
+      </ul></div>
+    <div class="section level2 citation-section">
+    <div>
+      <h1 id="citation">Citation</h1>
+      <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small>
+    </div>
     </div>
 
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. 
-        </p>
-      </li>
-    </ul>
+
+    <p>Ranke J (2023).
+<em>chents: Chemical Entities as R Objects</em>.
+R package version 0.3.1, <a href="https://github.com/jranke/chents" class="external-link">https://github.com/jranke/chents</a>. 
+</p>
+    <pre>@Manual{,
+  title = {chents: Chemical Entities as R Objects},
+  author = {Johannes Ranke},
+  year = {2023},
+  note = {R package version 0.3.1},
+  url = {https://github.com/jranke/chents},
+}</pre>
 
   </div>
 
@@ -123,22 +76,20 @@
 
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/index.html b/docs/index.html
index c4ad646..f241bb6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -16,14 +16,15 @@
     data as R objects. If Python and RDKit (&gt; 2015.03) are installed and
     configured for use with reticulate, some basic chemoinformatics functions
     like the calculation of molecular weight and plotting of chemical
-    structures in R graphics are available. For plotting, you need
-    grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN.">
+    structures in R graphics are available.">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-home">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -36,25 +37,19 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
-  <a href="index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/jranke/chents/">
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
@@ -71,66 +66,72 @@
 
       </header><div class="row">
   <div class="contents col-md-9">
-<div id="chents" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#chents" class="anchor"></a>chents</h1></div>
-
+<div class="section level1">
+<div class="page-header"><h1 id="chents">chents<a class="anchor" aria-label="anchor" href="#chents"></a>
+</h1></div>
+<p><a href="https://app.travis-ci.com/github/jranke/chents" class="external-link"><img src="https://travis-ci.com/jranke/chents.svg?branch=main" alt="Build Status"></a> <a href="https://app.codecov.io/gh/jranke/chents" class="external-link"><img src="https://codecov.io/github/jranke/chents/branch/main/graphs/badge.svg" alt="codecov"></a></p>
 <p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R.</p>
-<div id="features" class="section level2">
-<h2 class="hasAnchor">
-<a href="#features" class="anchor"></a>Features</h2>
+<div class="section level2">
+<h2 id="features">Features<a class="anchor" aria-label="anchor" href="#features"></a>
+</h2>
 <ul>
 <li>Some chemical information is retrieved from the PubChem website using the webchem package</li>
 <li>If Python and RDKit (&gt; 2015.03) are installed and configured for use with ‘reticulate’, some basic chemoinformatics functions some additional chemical information is computed and a 2D graph can be plotted</li>
 <li>Additional information can be read from a local .yaml file</li>
 </ul>
 </div>
-<div id="examples" class="section level2">
-<h2 class="hasAnchor">
-<a href="#examples" class="anchor"></a>Examples</h2>
-<p>Some examples are available from the <a href="http://pkgdown.jrwb.de/chents/reference">reference on jrwb.de</a>.</p>
+<div class="section level2">
+<h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
+</h2>
+<p>Some examples are available from the <a href="https://pkgdown.jrwb.de/chents/reference" class="external-link">reference on jrwb.de</a>.</p>
 </div>
 </div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <div class="links">
-<h2>Links</h2>
+<h2 data-toc-skip>Links</h2>
 <ul class="list-unstyled">
-<li>Browse source code at <br><a href="https://github.com/jranke/chents/">https://​github.com/​jranke/​chents/​</a>
-</li>
+<li><a href="https://github.com/jranke/chents/" class="external-link">Browse source code</a></li>
 </ul>
 </div>
+
 <div class="license">
-<h2>License</h2>
+<h2 data-toc-skip>License</h2>
 <ul class="list-unstyled">
 <li>GPL</li>
 </ul>
 </div>
-<div class="developers">
-<h2>Developers</h2>
+
+
+<div class="citation">
+<h2 data-toc-skip>Citation</h2>
 <ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small>  </li>
+<li><a href="authors.html#citation">Citing chents</a></li>
 </ul>
 </div>
 
-  <div class="dev-status">
-<h2>Dev status</h2>
+<div class="developers">
+<h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
-<li><a href="https://travis-ci.com/jranke/chents"><img src="https://travis-ci.com/jranke/chents.svg?branch=main" alt="Build Status"></a></li>
-<li><a href="https://codecov.io/github/jranke/chents"><img src="https://codecov.io/github/jranke/chents/branch/main/graphs/badge.svg" alt="codecov"></a></li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small>  </li>
 </ul>
 </div>
-</div>
+
+
+
+  </div>
 </div>
 
 
       <footer><div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+  <p></p>
+<p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer>
@@ -139,5 +140,7 @@
   
 
 
+  
+
   </body>
 </html>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 1273238..80ea5b8 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -56,8 +56,10 @@ img.icon {
   float: right;
 }
 
-img {
+/* Ensure in-page images don't run outside their container */
+.contents img {
   max-width: 100%;
+  height: auto;
 }
 
 /* Fix bug in bootstrap (only seen in firefox) */
@@ -78,11 +80,10 @@ dd {
 /* Section anchors ---------------------------------*/
 
 a.anchor {
-  margin-left: -30px;
-  display:inline-block;
-  width: 30px;
-  height: 30px;
-  visibility: hidden;
+  display: none;
+  margin-left: 5px;
+  width: 20px;
+  height: 20px;
 
   background-image: url(./link.svg);
   background-repeat: no-repeat;
@@ -90,17 +91,15 @@ a.anchor {
   background-position: center center;
 }
 
-.hasAnchor:hover a.anchor {
-  visibility: visible;
-}
-
-@media (max-width: 767px) {
-  .hasAnchor:hover a.anchor {
-    visibility: hidden;
-  }
+h1:hover .anchor,
+h2:hover .anchor,
+h3:hover .anchor,
+h4:hover .anchor,
+h5:hover .anchor,
+h6:hover .anchor {
+  display: inline-block;
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
@@ -264,31 +263,26 @@ table {
 
 /* Syntax highlighting ---------------------------------------------------- */
 
-pre {
-  word-wrap: normal;
-  word-break: normal;
-  border: 1px solid #eee;
-}
-
-pre, code {
+pre, code, pre code {
   background-color: #f8f8f8;
   color: #333;
 }
+pre, pre code {
+  white-space: pre-wrap;
+  word-break: break-all;
+  overflow-wrap: break-word;
+}
 
-pre code {
-  overflow: auto;
-  word-wrap: normal;
-  white-space: pre;
+pre {
+  border: 1px solid #eee;
 }
 
-pre .img {
+pre .img, pre .r-plt {
   margin: 5px 0;
 }
 
-pre .img img {
+pre .img img, pre .r-plt img {
   background-color: #fff;
-  display: block;
-  height: auto;
 }
 
 code a, pre a {
@@ -305,9 +299,8 @@ a.sourceLine:hover {
 .kw      {color: #264D66;} /* keyword */
 .co      {color: #888888;} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.error   {font-weight: bolder;}
+.warning {font-weight: bolder;}
 
 /* Clipboard --------------------------*/
 
@@ -365,3 +358,27 @@ mark {
     content: "";
   }
 }
+
+/* Section anchors ---------------------------------
+   Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
+*/
+
+div.csl-bib-body { }
+div.csl-entry {
+  clear: both;
+}
+.hanging-indent div.csl-entry {
+  margin-left:2em;
+  text-indent:-2em;
+}
+div.csl-left-margin {
+  min-width:2em;
+  float:left;
+}
+div.csl-right-inline {
+  margin-left:2em;
+  padding-left:1em;
+}
+div.csl-indent {
+  margin-left: 2em;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index 7e7048f..6f0eee4 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -80,7 +80,7 @@
     $(document).ready(function() {
       var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
 
-      $(".examples, div.sourceCode").addClass("hasCopyButton");
+      $("div.sourceCode").addClass("hasCopyButton");
 
       // Insert copy buttons:
       $(copyButton).prependTo(".hasCopyButton");
@@ -91,7 +91,7 @@
       // Initialize clipboard:
       var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
         text: function(trigger) {
-          return trigger.parentNode.textContent;
+          return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, "");
         }
       });
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 098ab97..dd7c4f0 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,6 +1,6 @@
-pandoc: 2.9.2.1
-pkgdown: 1.6.1
+pandoc: 3.1.1
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2021-11-26T15:14Z
+last_built: 2023-11-10T17:41Z
 
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index 377b927..d92e93f 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png
index 7229a66..acab3e6 100644
--- a/docs/reference/chent-1.png
+++ b/docs/reference/chent-1.png
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index 941eabb..a6b8dde 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -1,69 +1,14 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>An R6 class for chemical entities with associated data — chent • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="../bootstrap-toc.css">
-<script src="../bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="An R6 class for chemical entities with associated data — chent" />
-<meta property="og:description" content="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." />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>An R6 class for chemical entities with associated data — chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for chemical entities with associated data — chent"><meta property="og:description" content="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."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
-
-  </head>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -74,361 +19,513 @@ python bindings are installed." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>An R6 class for chemical entities with associated data</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>chent.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>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.</p>
+    <p>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.</p>
     </div>
 
 
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object</p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>identifier</code></dt>
+<dd><p>(<code>character(1)</code>)<br>
+The identifier that was used to initiate the object, with attribute 'source'</p></dd>
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <code>R6Class</code> generator object</p>
-    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
+<dt><code>inchikey</code></dt>
+<dd><p>(<code>character(1)</code>)<br>
+InChI Key, with attribute 'source'</p></dd>
+
+
+<dt><code>smiles</code></dt>
+<dd><p>(<code><a href="https://rdrr.io/r/base/character.html" class="external-link">character()</a></code>)<br>
+SMILES code(s), with attribute 'source'</p></dd>
+
+
+<dt><code>mw</code></dt>
+<dd><p>(<code>numeric(1)</code>)<br>
+Molecular weight, with attribute 'source'</p></dd>
+
+
+<dt><code>pubchem</code></dt>
+<dd><p>(<code><a href="https://rdrr.io/r/base/list.html" class="external-link">list()</a></code>)<br>
+List of information retrieved from PubChem</p></dd>
+
 
-    <p><div class="r6-fields"></p><dl>
-<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd>
+<dt><code>rdkit</code></dt>
+<dd><p>List of information obtained with RDKit</p></dd>
 
-<dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd>
 
-<dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd>
+<dt><code>mol</code></dt>
+<dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</p></dd>
 
-<dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd>
 
-<dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd>
+<dt><code>svg</code></dt>
+<dd><p>SVG code</p></dd>
 
-<dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit</p></dd>
 
-<dt><code>mol</code></dt><dd><p>&lt;rdkit.Chem.rdchem.Mol&gt; object</p></dd>
+<dt><code>Picture</code></dt>
+<dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
 
-<dt><code>svg</code></dt><dd><p>SVG code</p></dd>
 
-<dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
+<dt><code>Pict_font_size</code></dt>
+<dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
 
-<dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
 
-<dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
+<dt><code>pdf_height</code></dt>
+<dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
 
-<dt><code>p0</code></dt><dd><p>Vapour pressure in Pa</p></dd>
 
-<dt><code>cwsat</code></dt><dd><p>Water solubility in mg/L</p></dd>
+<dt><code>p0</code></dt>
+<dd><p>Vapour pressure in Pa</p></dd>
 
-<dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
 
-<dt><code>soil_degradation</code></dt><dd><p>Dataframe of modelling DT50 values</p></dd>
+<dt><code>cwsat</code></dt>
+<dd><p>Water solubility in mg/L</p></dd>
 
-<dt><code>soil_ff</code></dt><dd><p>Dataframe of formation fractions</p></dd>
 
-<dt><code>soil_sorption</code></dt><dd><p>Dataframe of soil sorption data</p></dd>
+<dt><code>PUF</code></dt>
+<dd><p>Plant uptake factor</p></dd>
 
-<dt><code>PUF</code></dt><dd><p>Plant uptake factor</p></dd>
 
-</dl><p></div></p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
+<dt><code>chyaml</code></dt>
+<dd><p>List of information obtained from a YAML file</p></dd>
 
+
+<dt><code>TPs</code></dt>
+<dd><p>List of transformation products as chent objects</p></dd>
+
+
+<dt><code>transformations</code></dt>
+<dd><p>Data frame of observed transformations</p></dd>
+
+
+<dt><code>soil_degradation</code></dt>
+<dd><p>Dataframe of modelling DT50 values</p></dd>
+
+
+<dt><code>soil_ff</code></dt>
+<dd><p>Dataframe of formation fractions</p></dd>
+
+
+<dt><code>soil_sorption</code></dt>
+<dd><p>Dataframe of soil sorption data</p></dd>
+
+
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
     
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
-
-<ul>
-<li><p><a href='#method-new'><code>chent$new()</code></a></p></li>
-<li><p><a href='#method-try_pubchem'><code>chent$try_pubchem()</code></a></p></li>
-<li><p><a href='#method-get_pubchem'><code>chent$get_pubchem()</code></a></p></li>
-<li><p><a href='#method-get_rdkit'><code>chent$get_rdkit()</code></a></p></li>
-<li><p><a href='#method-get_chyaml'><code>chent$get_chyaml()</code></a></p></li>
-<li><p><a href='#method-add_p0'><code>chent$add_p0()</code></a></p></li>
-<li><p><a href='#method-add_cwsat'><code>chent$add_cwsat()</code></a></p></li>
-<li><p><a href='#method-add_PUF'><code>chent$add_PUF()</code></a></p></li>
-<li><p><a href='#method-add_TP'><code>chent$add_TP()</code></a></p></li>
-<li><p><a href='#method-add_transformation'><code>chent$add_transformation()</code></a></p></li>
-<li><p><a href='#method-add_soil_degradation'><code>chent$add_soil_degradation()</code></a></p></li>
-<li><p><a href='#method-add_soil_ff'><code>chent$add_soil_ff()</code></a></p></li>
-<li><p><a href='#method-add_soil_sorption'><code>chent$add_soil_sorption()</code></a></p></li>
-<li><p><a href='#method-pdf'><code>chent$pdf()</code></a></p></li>
-<li><p><a href='#method-png'><code>chent$png()</code></a></p></li>
-<li><p><a href='#method-emf'><code>chent$emf()</code></a></p></li>
-<li><p><a href='#method-clone'><code>chent$clone()</code></a></p></li>
-</ul>
-<p><hr>
-<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
-  <span class='va'>identifier</span>,
-  smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
-  smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
-  inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  pubchem_from <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"smiles"</span>, <span class='st'>"inchikey"</span><span class='op'>)</span>,
-  rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  template <span class='op'>=</span> <span class='cn'>NULL</span>,
-  chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-try_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>try_pubchem()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>try_pubchem</span><span class='op'>(</span><span class='va'>query</span>, from <span class='op'>=</span> <span class='st'>"name"</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-get_pubchem"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_pubchem()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_pubchem</span><span class='op'>(</span><span class='va'>pubchem_cid</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-get_rdkit"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_rdkit()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_rdkit</span><span class='op'>(</span>template <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-get_chyaml"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>get_chyaml()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>get_chyaml</span><span class='op'>(</span>
-  repo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
-  chyaml <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/utils/URLencode.html'>URLencode</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".yaml"</span><span class='op'>)</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_p0"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_p0()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_cwsat"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_cwsat()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_cwsat</span><span class='op'>(</span><span class='va'>cwsat</span>, T <span class='op'>=</span> <span class='cn'>NA</span>, pH <span class='op'>=</span> <span class='cn'>NA</span>, source <span class='op'>=</span> <span class='cn'>NA</span>, page <span class='op'>=</span> <span class='cn'>NA</span>, remark <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_PUF"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_PUF()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_PUF</span><span class='op'>(</span>
-  PUF <span class='op'>=</span> <span class='fl'>0</span>,
-  source <span class='op'>=</span> <span class='st'>"focus_generic_gw_2014"</span>,
-  page <span class='op'>=</span> <span class='fl'>41</span>,
-  remark <span class='op'>=</span> <span class='st'>"Conservative default value"</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_TP"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_TP()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_TP</span><span class='op'>(</span><span class='va'>x</span>, smiles <span class='op'>=</span> <span class='cn'>NULL</span>, pubchem <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_transformation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_transformation()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_transformation</span><span class='op'>(</span>
-  <span class='va'>study_type</span>,
-  <span class='va'>TP_identifier</span>,
-  <span class='va'>max_occurrence</span>,
-  remark <span class='op'>=</span> <span class='st'>""</span>,
-  source <span class='op'>=</span> <span class='cn'>NA</span>,
-  pages <span class='op'>=</span> <span class='cn'>NA</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_soil_degradation"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_degradation()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_degradation</span><span class='op'>(</span>
-  <span class='va'>soils</span>,
-  <span class='va'>DT50_mod</span>,
-  <span class='va'>DT50_mod_ref</span>,
-  type <span class='op'>=</span> <span class='cn'>NA</span>,
-  country <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
-  perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
-  temperature <span class='op'>=</span> <span class='cn'>NA</span>,
-  moisture <span class='op'>=</span> <span class='cn'>NA</span>,
-  category <span class='op'>=</span> <span class='st'>"lab"</span>,
-  formulation <span class='op'>=</span> <span class='cn'>NA</span>,
-  model <span class='op'>=</span> <span class='cn'>NA</span>,
-  chi2 <span class='op'>=</span> <span class='cn'>NA</span>,
-  remark <span class='op'>=</span> <span class='st'>""</span>,
-  <span class='va'>source</span>,
-  page <span class='op'>=</span> <span class='cn'>NA</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_soil_ff"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_ff()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</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></pre><p></div></p>
-
-<p><hr>
-<a id="method-add_soil_sorption"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>add_soil_sorption()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>add_soil_sorption</span><span class='op'>(</span>
-  <span class='va'>soils</span>,
-  <span class='va'>Kf</span>,
-  <span class='va'>Kfoc</span>,
-  <span class='va'>N</span>,
-  type <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_orig <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_medium <span class='op'>=</span> <span class='cn'>NA</span>,
-  pH_H2O <span class='op'>=</span> <span class='cn'>NA</span>,
-  perc_OC <span class='op'>=</span> <span class='cn'>NA</span>,
-  perc_clay <span class='op'>=</span> <span class='cn'>NA</span>,
-  CEC <span class='op'>=</span> <span class='cn'>NA</span>,
-  remark <span class='op'>=</span> <span class='st'>""</span>,
-  <span class='va'>source</span>,
-  page <span class='op'>=</span> <span class='cn'>NA</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-pdf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/pdf.html'>pdf()</a></code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>pdf</span><span class='op'>(</span>
-  file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".pdf"</span><span class='op'>)</span>,
-  dir <span class='op'>=</span> <span class='st'>"structures/pdf"</span>,
-  template <span class='op'>=</span> <span class='cn'>NULL</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-png"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/grDevices/png.html'>png()</a></code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>png</span><span class='op'>(</span>
-  file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".png"</span><span class='op'>)</span>,
-  dir <span class='op'>=</span> <span class='st'>"structures/png"</span>,
-  antialias <span class='op'>=</span> <span class='st'>"gray"</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-emf"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>emf()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>emf</span><span class='op'>(</span>file <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>self</span><span class='op'>$</span><span class='va'>identifier</span>, <span class='st'>".emf"</span><span class='op'>)</span>, dir <span class='op'>=</span> <span class='st'>"structures/emf"</span><span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>chent</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
-<p><div class="arguments"></p><dl>
-<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
-
-</dl><p></div></p>
-
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='va'>oct</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'>"1-octanol"</span>, smiles <span class='op'>=</span> <span class='st'>"CCCCCCCCO"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
-#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier 1-octanol 
-#&gt; InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;              user PubChem_Canonical 
-#&gt;       "CCCCCCCCO"       "CCCCCCCCO" 
-#&gt; Molecular weight $mw: 130.2 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "1-octanol"        "Octan-1-ol"       "octanol"          "111-87-5"        
-#&gt;  [5] "N-octanol"        "Octyl alcohol"    "Capryl alcohol"   "caprylic alcohol"
-#&gt;  [9] "n-Octyl alcohol"  "Heptyl carbinol" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>oct</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='input'>
-<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>
-</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier caffeine 
-#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;              PubChem_Canonical 
-#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#&gt; Molecular weight $mw: 194.2 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "caffeine"                "58-08-2"                
-#&gt;  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#&gt;  [5] "Thein"                   "Methyltheobromine"      
-#&gt;  [7] "Cafeina"                 "Theine"                 
-#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='img'><img src='chent-1.png' alt='' width='700' height='433' /></div></pre>
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-chent-new"><code>chent$new()</code></a></p></li>
+<li><p><a href="#method-chent-try_pubchem"><code>chent$try_pubchem()</code></a></p></li>
+<li><p><a href="#method-chent-get_pubchem"><code>chent$get_pubchem()</code></a></p></li>
+<li><p><a href="#method-chent-get_rdkit"><code>chent$get_rdkit()</code></a></p></li>
+<li><p><a href="#method-chent-get_chyaml"><code>chent$get_chyaml()</code></a></p></li>
+<li><p><a href="#method-chent-add_p0"><code>chent$add_p0()</code></a></p></li>
+<li><p><a href="#method-chent-add_cwsat"><code>chent$add_cwsat()</code></a></p></li>
+<li><p><a href="#method-chent-add_PUF"><code>chent$add_PUF()</code></a></p></li>
+<li><p><a href="#method-chent-add_TP"><code>chent$add_TP()</code></a></p></li>
+<li><p><a href="#method-chent-add_transformation"><code>chent$add_transformation()</code></a></p></li>
+<li><p><a href="#method-chent-add_soil_degradation"><code>chent$add_soil_degradation()</code></a></p></li>
+<li><p><a href="#method-chent-add_soil_ff"><code>chent$add_soil_ff()</code></a></p></li>
+<li><p><a href="#method-chent-add_soil_sorption"><code>chent$add_soil_sorption()</code></a></p></li>
+<li><p><a href="#method-chent-pdf"><code>chent$pdf()</code></a></p></li>
+<li><p><a href="#method-chent-png"><code>chent$png()</code></a></p></li>
+<li><p><a href="#method-chent-emf"><code>chent$emf()</code></a></p></li>
+<li><p><a href="#method-chent-clone"><code>chent$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-chent-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+<p>Creates a new instance of this <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6</a> class.</p><div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/chent.html">chent</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">identifier</span>,</span>
+<span>  smiles <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  pubchem_from <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">"name"</span>, <span class="st">"smiles"</span>, <span class="st">"inchikey"</span><span class="op">)</span>,</span>
+<span>  rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  chyaml <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>identifier</code></dt>
+<dd><p>Identifier to be stored in the object</p></dd>
+
+
+<dt><code>smiles</code></dt>
+<dd><p>Optional user provided SMILES code</p></dd>
+
+
+<dt><code>inchikey</code></dt>
+<dd><p>Optional user provided InChI Key</p></dd>
+
+
+<dt><code>pubchem</code></dt>
+<dd><p>Should an attempt be made to retrieve chemical
+information from PubChem via the webchem package?</p></dd>
+
+
+<dt><code>pubchem_from</code></dt>
+<dd><p>Possibility to select the argument
+that is used to query pubchem</p></dd>
+
+
+<dt><code>rdkit</code></dt>
+<dd><p>Should an attempt be made to retrieve chemical
+information from a local rdkit installation via python
+and the reticulate package?</p></dd>
+
+
+<dt><code>template</code></dt>
+<dd><p>An optional SMILES code to be used as template for RDKit</p></dd>
+
+
+<dt><code>chyaml</code></dt>
+<dd><p>Should we look for a identifier.yaml file in the working
+directory?
+Try to get chemical information from PubChem</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</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">
+<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">$</span><span class="fu">try_pubchem</span><span class="op">(</span><span class="va">query</span>, from <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>query</code></dt>
+<dd><p>Query string to be passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a></p></dd>
+
+
+<dt><code>from</code></dt>
+<dd><p>Passed to <a href="https://docs.ropensci.org/webchem/reference/get_cid.html" class="external-link">get_cid</a>
+Get chemical information from PubChem for a known PubChem CID</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div><p></p><hr><a id="method-chent-get_pubchem"></a><div class="section">
+<h3 id="method-get-pubchem-">Method <code>get_pubchem()</code><a class="anchor" aria-label="anchor" href="#method-get-pubchem-"></a></h3>
+
+<div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+
+<div class="section">
+<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>pubchem_cid</code></dt>
+<dd><p>CID</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</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>
+
+<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">$</span><span class="fu">get_rdkit</span><span class="op">(</span>template <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-get_chyaml"></a><div class="section">
+<h3 id="method-get-chyaml-">Method <code>get_chyaml()</code><a class="anchor" aria-label="anchor" href="#method-get-chyaml-"></a></h3>
+
+<div class="section">
+<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+<span>  chyaml <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="fu"><a href="https://rdrr.io/r/utils/URLencode.html" class="external-link">URLencode</a></span><span class="op">(</span><span class="va">self</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".yaml"</span><span class="op">)</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_p0"></a><div class="section">
+<h3 id="method-add-p-">Method <code>add_p0()</code><a class="anchor" aria-label="anchor" href="#method-add-p-"></a></h3>
+
+<div class="section">
+<h4 id="usage-5">Usage<a class="anchor" aria-label="anchor" href="#usage-5"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+
+
+</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">
+<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">$</span><span class="fu">add_cwsat</span><span class="op">(</span><span class="va">cwsat</span>, T <span class="op">=</span> <span class="cn">NA</span>, pH <span class="op">=</span> <span class="cn">NA</span>, source <span class="op">=</span> <span class="cn">NA</span>, page <span class="op">=</span> <span class="cn">NA</span>, remark <span class="op">=</span> <span class="st">""</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_PUF"></a><div class="section">
+<h3 id="method-add-puf-">Method <code>add_PUF()</code><a class="anchor" aria-label="anchor" href="#method-add-puf-"></a></h3>
+
+<div class="section">
+<h4 id="usage-7">Usage<a class="anchor" aria-label="anchor" href="#usage-7"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_PUF</span><span class="op">(</span></span>
+<span>  PUF <span class="op">=</span> <span class="fl">0</span>,</span>
+<span>  source <span class="op">=</span> <span class="st">"focus_generic_gw_2014"</span>,</span>
+<span>  page <span class="op">=</span> <span class="fl">41</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">"Conservative default value"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</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">
+<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">$</span><span class="fu">add_TP</span><span class="op">(</span><span class="va">x</span>, smiles <span class="op">=</span> <span class="cn">NULL</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_transformation"></a><div class="section">
+<h3 id="method-add-transformation-">Method <code>add_transformation()</code><a class="anchor" aria-label="anchor" href="#method-add-transformation-"></a></h3>
+
+<div class="section">
+<h4 id="usage-9">Usage<a class="anchor" aria-label="anchor" href="#usage-9"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">add_transformation</span><span class="op">(</span></span>
+<span>  <span class="va">study_type</span>,</span>
+<span>  <span class="va">TP_identifier</span>,</span>
+<span>  <span class="va">max_occurrence</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">""</span>,</span>
+<span>  source <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pages <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</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">
+<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">$</span><span class="fu">add_soil_degradation</span><span class="op">(</span></span>
+<span>  <span class="va">soils</span>,</span>
+<span>  <span class="va">DT50_mod</span>,</span>
+<span>  <span class="va">DT50_mod_ref</span>,</span>
+<span>  type <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  country <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  temperature <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  moisture <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  category <span class="op">=</span> <span class="st">"lab"</span>,</span>
+<span>  formulation <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  model <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  chi2 <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">""</span>,</span>
+<span>  <span class="va">source</span>,</span>
+<span>  page <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-add_soil_ff"></a><div class="section">
+<h3 id="method-add-soil-ff-">Method <code>add_soil_ff()</code><a class="anchor" aria-label="anchor" href="#method-add-soil-ff-"></a></h3>
+
+<div class="section">
+<h4 id="usage-11">Usage<a class="anchor" aria-label="anchor" href="#usage-11"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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>
+
+
+</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">
+<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">$</span><span class="fu">add_soil_sorption</span><span class="op">(</span></span>
+<span>  <span class="va">soils</span>,</span>
+<span>  <span class="va">Kf</span>,</span>
+<span>  <span class="va">Kfoc</span>,</span>
+<span>  <span class="va">N</span>,</span>
+<span>  type <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_orig <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_medium <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  pH_H2O <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  perc_OC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  perc_clay <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  CEC <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  remark <span class="op">=</span> <span class="st">""</span>,</span>
+<span>  <span class="va">source</span>,</span>
+<span>  page <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-pdf"></a><div class="section">
+<h3 id="method-pdf-">Method <code><a href="https://rdrr.io/r/grDevices/pdf.html" class="external-link">pdf()</a></code><a class="anchor" aria-label="anchor" href="#method-pdf-"></a></h3>
+
+<div class="section">
+<h4 id="usage-13">Usage<a class="anchor" aria-label="anchor" href="#usage-13"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">$</span><span class="va">identifier</span>, <span class="st">".pdf"</span><span class="op">)</span>,</span>
+<span>  dir <span class="op">=</span> <span class="st">"structures/pdf"</span>,</span>
+<span>  template <span class="op">=</span> <span class="cn">NULL</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-png"></a><div class="section">
+<h3 id="method-png-">Method <code><a href="https://rdrr.io/r/grDevices/png.html" class="external-link">png()</a></code><a class="anchor" aria-label="anchor" href="#method-png-"></a></h3>
+
+<div class="section">
+<h4 id="usage-14">Usage<a class="anchor" aria-label="anchor" href="#usage-14"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</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">$</span><span class="va">identifier</span>, <span class="st">".png"</span><span class="op">)</span>,</span>
+<span>  dir <span class="op">=</span> <span class="st">"structures/png"</span>,</span>
+<span>  antialias <span class="op">=</span> <span class="st">"gray"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-emf"></a><div class="section">
+<h3 id="method-emf-">Method <code>emf()</code><a class="anchor" aria-label="anchor" href="#method-emf-"></a></h3>
+
+<div class="section">
+<h4 id="usage-15">Usage<a class="anchor" aria-label="anchor" href="#usage-15"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">emf</span><span class="op">(</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">$</span><span class="va">identifier</span>, <span class="st">".emf"</span><span class="op">)</span>, dir <span class="op">=</span> <span class="st">"structures/emf"</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+
+</div><p></p><hr><a id="method-chent-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-16">Usage<a class="anchor" aria-label="anchor" href="#usage-16"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">chent</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
+
+
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">oct</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">"1-octanol"</span>, smiles <span class="op">=</span> <span class="st">"CCCCCCCCO"</span>, pubchem <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using user SMILES</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> CCCCCCCCO</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./1-octanol.yaml</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">oct</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier 1-octanol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
+<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 $mw: 130.2 </span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">oct</span><span class="op">$</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">oct</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><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> PubChem:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Trying to get chemical information from RDKit using PubChem_Canonical 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-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./caffeine.yaml</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>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier caffeine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>              PubChem_Canonical </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 194.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "caffeine"                "58-08-2"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</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="chent-1.png" alt="" width="700" height="433"></span>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index 1805ff1..cae8c0b 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -1,67 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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-<script src="../bootstrap-toc.js"></script>
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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-<meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent" />
-<meta property="og:description" content="Draw SVG graph from a chent object using RDKit" />
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-
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-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Draw SVG graph from a chent object using RDKit — draw_svg.chent"><meta property="og:description" content="Draw SVG graph from a chent object using RDKit"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Draw SVG graph from a chent object using RDKit</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>draw_svg.chent.Rd</code></div>
     </div>
 
@@ -117,65 +49,60 @@
     <p>Draw SVG graph from a chent object using RDKit</p>
     </div>
 
-    <pre class="usage"><span class='fu'>draw_svg.chent</span><span class='op'>(</span>
-  <span class='va'>x</span>,
-  width <span class='op'>=</span> <span class='fl'>300</span>,
-  height <span class='op'>=</span> <span class='fl'>150</span>,
-  filename <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>identifier</span><span class='op'>)</span>, <span class='st'>".svg"</span><span class='op'>)</span>,
-  subdir <span class='op'>=</span> <span class='st'>"svg"</span>
-<span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be plotted</p></td>
-    </tr>
-    <tr>
-      <th>width</th>
-      <td><p>The desired width in pixels</p></td>
-    </tr>
-    <tr>
-      <th>height</th>
-      <td><p>The desired height in pixels</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>The filename</p></td>
-    </tr>
-    <tr>
-      <th>subdir</th>
-      <td><p>The path to which the file should be written</p></td>
-    </tr>
-    </table>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">draw_svg.chent</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  width <span class="op">=</span> <span class="fl">300</span>,</span>
+<span>  height <span class="op">=</span> <span class="fl">150</span>,</span>
+<span>  filename <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">identifier</span><span class="op">)</span>, <span class="st">".svg"</span><span class="op">)</span>,</span>
+<span>  subdir <span class="op">=</span> <span class="st">"svg"</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be plotted</p></dd>
+
 
+<dt>width</dt>
+<dd><p>The desired width in pixels</p></dd>
+
+
+<dt>height</dt>
+<dd><p>The desired height in pixels</p></dd>
+
+
+<dt>filename</dt>
+<dd><p>The filename</p></dd>
+
+
+<dt>subdir</dt>
+<dd><p>The path to which the file should be written</p></dd>
+
+</dl></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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+  
 
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 9de4a87..d9eb797 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,66 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="../bootstrap-toc.css">
-<script src="../bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Function reference" />
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-
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-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Function reference • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-index">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -71,136 +17,86 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="contents col-md-9">
     <div class="page-header">
       <h1>Reference</h1>
     </div>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2>
+    <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
+          <h2 id="r-class-definitions-and-methods">R6 Class definitions and methods <a href="#r-class-definitions-and-methods" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p>
         </th>
-      </tr>
-      
-      
-    </tbody><tbody>
-      
-      
-      <tr>
-        
-        <td>
+      </tr></tbody><tbody><tr><td>
           <p><code><a href="chent.html">chent</a></code> </p>
         </td>
         <td><p>An R6 class for chemical entities with associated data</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="draw_svg.chent.html">draw_svg.chent()</a></code> </p>
         </td>
         <td><p>Draw SVG graph from a chent object using RDKit</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="plot.chent.html">plot(<i>&lt;chent&gt;</i>)</a></code> </p>
         </td>
         <td><p>Plot method for chent objects</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="print.chent.html">print(<i>&lt;chent&gt;</i>)</a></code> </p>
         </td>
         <td><p>Printing method for chent objects</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="pai.html">pai</a></code> </p>
         </td>
         <td><p>An R6 class for pesticidal active ingredients and associated data</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="print.pai.html">print(<i>&lt;pai&gt;</i>)</a></code> </p>
         </td>
         <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td>
-      </tr><tr>
-        
-        <td>
+      </tr><tr><td>
           <p><code><a href="pp.html">pp</a></code> </p>
         </td>
         <td><p>R6 class for holding a product with at least one active ingredient</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+      </tr></tbody></table></div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png
index c235304..802fd50 100644
--- a/docs/reference/pai-1.png
+++ b/docs/reference/pai-1.png
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 0bb3399..636007f 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -1,68 +1,13 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
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-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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-<meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai" />
-<meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name.
-Additional chemical information is retrieved from the internet if available." />
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-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai"><meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name.
+Additional chemical information is retrieved from the internet if available."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
-
-  </head>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -73,44 +18,31 @@ Additional chemical information is retrieved from the internet if available." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>An R6 class for pesticidal active ingredients and associated data</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>pai.Rd</code></div>
     </div>
 
@@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.</p>
     </div>
 
 
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object</p>
+    </div>
+    <div id="super-class">
+    <h2>Super class</h2>
+    <p><code><a href="chent.html">chents::chent</a></code> -&gt; <code>pai</code></p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>iso</code></dt>
+<dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+
+
+<dt><code>bcpc</code></dt>
+<dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <code>R6Class</code> generator object</p>
-    <h2 class="hasAnchor" id="super-class"><a class="anchor" href="#super-class"></a>Super class</h2>
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
+    
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-pai-new"><code>pai$new()</code></a></p></li>
+<li><p><a href="#method-pai-clone"><code>pai$clone()</code></a></p></li>
+</ul></div><p><details><summary>Inherited methods</summary><ul><li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href="chent.html#method-add_PUF"><code>chents::chent$add_PUF()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href="chent.html#method-add_TP"><code>chents::chent$add_TP()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href="chent.html#method-add_cwsat"><code>chents::chent$add_cwsat()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href="chent.html#method-add_p0"><code>chents::chent$add_p0()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href="chent.html#method-add_soil_degradation"><code>chents::chent$add_soil_degradation()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href="chent.html#method-add_soil_ff"><code>chents::chent$add_soil_ff()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href="chent.html#method-add_soil_sorption"><code>chents::chent$add_soil_sorption()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href="chent.html#method-add_transformation"><code>chents::chent$add_transformation()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href="chent.html#method-emf"><code>chents::chent$emf()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href="chent.html#method-get_chyaml"><code>chents::chent$get_chyaml()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href="chent.html#method-get_pubchem"><code>chents::chent$get_pubchem()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href="chent.html#method-get_rdkit"><code>chents::chent$get_rdkit()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href="chent.html#method-pdf"><code>chents::chent$pdf()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href="chent.html#method-png"><code>chents::chent$png()</code></a></span></li>
+<li><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href="chent.html#method-try_pubchem"><code>chents::chent$try_pubchem()</code></a></span></li>
+</ul></details></p><hr><a id="method-pai-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pai.html">pai</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">iso</span>,</span>
+<span>  identifier <span class="op">=</span> <span class="va">iso</span>,</span>
+<span>  smiles <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  inchikey <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  bcpc <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  pubchem <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  pubchem_from <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  rdkit <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  template <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  chyaml <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-    <p><code><a href='chent.html'>chents::chent</a></code> -&gt; <code>pai</code></p>
-    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    <p><div class="r6-fields"></p><dl>
-<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org</p></dd>
+</div><p></p><hr><a id="method-pai-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</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">pai</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
 
-</dl><p></div></p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
-    
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
-
-<ul>
-<li><p><a href='#method-new'><code>pai$new()</code></a></p></li>
-<li><p><a href='#method-clone'><code>pai$clone()</code></a></p></li>
-</ul>
-<p><details ><summary>Inherited methods</summary>
-<ul>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_PUF"><a href='../../chents/html/chent.html#method-add_PUF'><code>chents::chent$add_PUF()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_TP"><a href='../../chents/html/chent.html#method-add_TP'><code>chents::chent$add_TP()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_cwsat"><a href='../../chents/html/chent.html#method-add_cwsat'><code>chents::chent$add_cwsat()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_p0"><a href='../../chents/html/chent.html#method-add_p0'><code>chents::chent$add_p0()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_degradation"><a href='../../chents/html/chent.html#method-add_soil_degradation'><code>chents::chent$add_soil_degradation()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_ff"><a href='../../chents/html/chent.html#method-add_soil_ff'><code>chents::chent$add_soil_ff()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_soil_sorption"><a href='../../chents/html/chent.html#method-add_soil_sorption'><code>chents::chent$add_soil_sorption()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="add_transformation"><a href='../../chents/html/chent.html#method-add_transformation'><code>chents::chent$add_transformation()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="emf"><a href='../../chents/html/chent.html#method-emf'><code>chents::chent$emf()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_chyaml"><a href='../../chents/html/chent.html#method-get_chyaml'><code>chents::chent$get_chyaml()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_pubchem"><a href='../../chents/html/chent.html#method-get_pubchem'><code>chents::chent$get_pubchem()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="get_rdkit"><a href='../../chents/html/chent.html#method-get_rdkit'><code>chents::chent$get_rdkit()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="pdf"><a href='../../chents/html/chent.html#method-pdf'><code>chents::chent$pdf()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="png"><a href='../../chents/html/chent.html#method-png'><code>chents::chent$png()</code></a></span></p></li>
-<li><p><span class="pkg-link" data-pkg="chents" data-topic="chent" data-id="try_pubchem"><a href='../../chents/html/chent.html#method-try_pubchem'><code>chents::chent$try_pubchem()</code></a></span></p></li>
-</ul>
-</details>
-
-<hr>
-<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
-  <span class='va'>iso</span>,
-  identifier <span class='op'>=</span> <span class='va'>iso</span>,
-  smiles <span class='op'>=</span> <span class='cn'>NULL</span>,
-  smiles_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  inchikey <span class='op'>=</span> <span class='cn'>NULL</span>,
-  inchikey_source <span class='op'>=</span> <span class='st'>"user"</span>,
-  bcpc <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  pubchem <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  pubchem_from <span class='op'>=</span> <span class='st'>"auto"</span>,
-  rdkit <span class='op'>=</span> <span class='cn'>TRUE</span>,
-  template <span class='op'>=</span> <span class='cn'>NULL</span>,
-  chyaml <span class='op'>=</span> <span class='cn'>TRUE</span>
-<span class='op'>)</span></pre><p></div></p>
-
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pai</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
-
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
-<p><div class="arguments"></p><dl>
-<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
-
-</dl><p></div></p>
-
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='co'># On Travis, we get a certificate validation error,</span>
-<span class='co'># likely because the system (xenial) is so old,</span>
-<span class='co'># therefore don't run this example on Travis</span>
-<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>==</span> <span class='st'>""</span><span class='op'>)</span> <span class='op'>{</span>
-
-<span class='va'>atr</span> <span class='op'>&lt;-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</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'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>)</span>
-<span class='op'>}</span>
-
-<span class='op'>}</span>
-</div><div class='output co'>#&gt; <span class='message'>BCPC:</span></div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CCNC1=NC(=NC(=N1)Cl)NC(C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./atrazine.yaml</span></div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; &lt;pai&gt; with ISO common name $iso atrazine 
-#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier atrazine 
-#&gt; InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;            PubChem_Canonical 
-#&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
-#&gt; Molecular weight $mw: 215.7 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Chromozin"   
-#&gt;  [6] "Aktikon"      "Atrazin"      "Argezin"      "Atazinax"     "Atranex"     </div></pre>
+</dl><p></p></div>
+</div>
+
+</div>
+
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># On Travis, we get a certificate validation error,</span></span></span>
+<span class="r-in"><span><span class="co"># likely because the system (xenial) is so old,</span></span></span>
+<span class="r-in"><span><span class="co"># therefore don't run this example on Travis</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">==</span> <span class="st">""</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">atr</span> <span class="op">&lt;-</span> <span class="va">pai</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"atrazine"</span><span class="op">)</span></span></span>
+<span class="r-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">atr</span><span class="op">)</span></span></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">atr</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">atr</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> BCPC:</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_Canonical SMILES</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> CCNC1=NC(=NC(=N1)Cl)NC(C)C</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./atrazine.yaml</span>
+<span class="r-plt img"><img src="pai-1.png" alt="" width="700" height="433"></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;pai&gt; with ISO common name $iso atrazine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;chent&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier atrazine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>            PubChem_Canonical </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 215.7 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Aktikon"     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6] "Atranex"      "Chromozin"    "Atazinax"     "Atrasine"     "Gesoprim"    </span>
+</code></pre></div>
+    </div>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
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+    </nav></div>
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+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
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         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
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   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Plot method for chent objects</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>plot.chent.Rd</code></div>
     </div>
 
@@ -117,68 +49,70 @@
     <p>Plot method for chent objects</p>
     </div>
 
-    <pre class="usage"><span class='co'># S3 method for chent</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
-
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be plotted</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments passed to <code>grid.picture</code></p></td>
-    </tr>
-    </table>
-
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><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>
-</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
-#&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; &lt;chent&gt;
-#&gt; Identifier $identifier caffeine 
-#&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#&gt; SMILES string $smiles:
-#&gt;              PubChem_Canonical 
-#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#&gt; Molecular weight $mw: 194.2 
-#&gt; PubChem synonyms (up to 10):
-#&gt;  [1] "caffeine"                "58-08-2"                
-#&gt;  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#&gt;  [5] "Thein"                   "Methyltheobromine"      
-#&gt;  [7] "Cafeina"                 "Theine"                 
-#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>$</span><span class='va'>Picture</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>caffeine</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='433' /></div></pre>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for chent</span></span>
+<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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be plotted</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Further arguments passed to <code>grid.picture</code></p></dd>
+
+</dl></div>
+
+    <div id="ref-examples">
+    <h2>Examples</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_Canonical 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-msg co"><span class="r-pr">#&gt;</span> Did not find chyaml file ./caffeine.yaml</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>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Identifier $identifier caffeine </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SMILES string $smiles:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>              PubChem_Canonical </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Molecular weight $mw: 194.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> PubChem synonyms (up to 10):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "caffeine"                "58-08-2"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Methyltheobromine"       "Theine"                 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Thein"                   "Cafeina"                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Koffein"                 "Mateina"                </span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NULL.html" class="external-link">is.null</a></span><span class="op">(</span><span class="va">caffeine</span><span class="op">$</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>
+</code></pre></div>
+    </div>
   </div>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
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-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>R6 class for holding a product with at least one active ingredient</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>pp.Rd</code></div>
     </div>
 
@@ -118,89 +50,105 @@
     </div>
 
 
+    <div id="format">
+    <h2>Format</h2>
+    <p>An <code>R6Class</code> generator object.</p>
+    </div>
+    <div id="public-fields">
+    <h2>Public fields</h2>
+    <p></p><div class="r6-fields"><dl><dt><code>name</code></dt>
+<dd><p>The name of the product</p></dd>
 
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>An <code>R6Class</code> generator object.</p>
-    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
+<dt><code>ais</code></dt>
+<dd><p>A list of active ingredients</p></dd>
 
-    <p><div class="r6-fields"></p><dl>
-<dt><code>name</code></dt><dd><p>The name of the product</p></dd>
 
-<dt><code>ais</code></dt><dd><p>A list of active ingredients</p></dd>
+<dt><code>concentrations</code></dt>
+<dd><p>The concentration of the ais</p></dd>
 
-<dt><code>concentrations</code></dt><dd><p>The concentration of the ais</p></dd>
 
-<dt><code>concentration_units</code></dt><dd><p>Defaults to g/L</p></dd>
+<dt><code>concentration_units</code></dt>
+<dd><p>Defaults to g/L</p></dd>
 
-</dl><p></div></p>
-    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
+</dl><p></p></div>
+    </div>
+    <div id="methods">
+    <h2>Methods</h2>
     
-<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>
+<div class="section">
+<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
+
+<ul><li><p><a href="#method-pp-new"><code>pp$new()</code></a></p></li>
+<li><p><a href="#method-pp-print"><code>pp$print()</code></a></p></li>
+<li><p><a href="#method-pp-clone"><code>pp$clone()</code></a></p></li>
+</ul></div><p></p><hr><a id="method-pp-new"></a><div class="section">
+<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
+
+<div class="section">
+<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/pp.html">pp</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
+<span>  <span class="va">name</span>,</span>
+<span>  <span class="va">...</span>,</span>
+<span>  <span class="va">concentrations</span>,</span>
+<span>  concentration_units <span class="op">=</span> <span class="st">"g/L"</span>,</span>
+<span>  density <span class="op">=</span> <span class="fl">1000</span>,</span>
+<span>  density_units <span class="op">=</span> <span class="st">"g/L"</span></span>
+<span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-<ul>
-<li><p><a href='#method-new'><code>pp$new()</code></a></p></li>
-<li><p><a href='#method-print'><code>pp$print()</code></a></p></li>
-<li><p><a href='#method-clone'><code>pp$clone()</code></a></p></li>
-</ul>
-<p><hr>
-<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
 
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>
-  <span class='va'>name</span>,
-  <span class='va'>...</span>,
-  <span class='va'>concentrations</span>,
-  concentration_units <span class='op'>=</span> <span class='st'>"g/L"</span>,
-  density <span class='op'>=</span> <span class='fl'>1000</span>,
-  density_units <span class='op'>=</span> <span class='st'>"g/L"</span>
-<span class='op'>)</span></pre><p></div></p>
+</div><p></p><hr><a id="method-pp-print"></a><div class="section">
+<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
 
-<p><hr>
-<a id="method-print"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>
+<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">pp</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
 
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>print</span><span class='op'>(</span><span class='op'>)</span></pre><p></div></p>
 
-<p><hr>
-<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
-<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
-<p><div class="r"></p><pre><span class='va'>pp</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
+</div><p></p><hr><a id="method-pp-clone"></a><div class="section">
+<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
+<p>The objects of this class are cloneable with this method.</p><div class="section">
+<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
+<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">pp</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
+</div>
+
+<div class="section">
+<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
+<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
+<dd><p>Whether to make a deep clone.</p></dd>
 
-<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
-<p><div class="arguments"></p><dl>
-<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
 
-</dl><p></div></p>
+</dl><p></p></div>
+</div>
 
+</div>
 
+    </div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index b188ed9..08497dd 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -1,67 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Printing method for chent objects — print.chent • chents</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="../bootstrap-toc.css">
-<script src="../bootstrap-toc.js"></script>
-
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-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Printing method for chent objects — print.chent • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for chent objects — print.chent"><meta property="og:description" content="Printing method for chent objects"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Printing method for chent objects</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>print.chent.Rd</code></div>
     </div>
 
@@ -117,48 +49,43 @@
     <p>Printing method for chent objects</p>
     </div>
 
-    <pre class="usage"><span class='co'># S3 method for chent</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for chent</span></span>
+<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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be printed</p></dd>
+
 
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be printed</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments for compatibility with the S3 method</p></td>
-    </tr>
-    </table>
+<dt>...</dt>
+<dd><p>Further arguments for compatibility with the S3 method</p></dd>
 
+</dl></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index 284792f..3faa5f7 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -1,67 +1,12 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Printing method for pai objects (pesticidal active ingredients) — print.pai • chents</title>
-
-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-
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-<script src="../bootstrap-toc.js"></script>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Printing method for pai objects (pesticidal active ingredients) — print.pai • chents</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Printing method for pai objects (pesticidal active ingredients) — print.pai"><meta property="og:description" content="Printing method for pai objects (pesticidal active ingredients)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -72,44 +17,31 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chents</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.3.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <ul class="nav navbar-nav"><li>
   <a href="../reference/index.html">Reference</a>
 </li>
-      </ul>
-      <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/chents/">
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/chents/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
-      </ul>
-      
-    </div><!--/.nav-collapse -->
+      </ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Printing method for pai objects (pesticidal active ingredients)</h1>
-    <small class="dont-index">Source: <a href='https://github.com/jranke/chents/blob/master/R/chent.R'><code>R/chent.R</code></a></small>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/chents/blob/HEAD/R/chent.R" class="external-link"><code>R/chent.R</code></a></small>
     <div class="hidden name"><code>print.pai.Rd</code></div>
     </div>
 
@@ -117,48 +49,43 @@
     <p>Printing method for pai objects (pesticidal active ingredients)</p>
     </div>
 
-    <pre class="usage"><span class='co'># S3 method for pai</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for pai</span></span>
+<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">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>The chent object to be printed</p></dd>
+
 
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>The chent object to be printed</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Further arguments for compatibility with the S3 method</p></td>
-    </tr>
-    </table>
+<dt>...</dt>
+<dd><p>Further arguments for compatibility with the S3 method</p></dd>
 
+</dl></div>
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
-    </nav>
-  </div>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
new file mode 100644
index 0000000..986ccf3
--- /dev/null
+++ b/docs/sitemap.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+  <url>
+    <loc>/404.html</loc>
+  </url>
+  <url>
+    <loc>/authors.html</loc>
+  </url>
+  <url>
+    <loc>/index.html</loc>
+  </url>
+  <url>
+    <loc>/reference/chent.html</loc>
+  </url>
+  <url>
+    <loc>/reference/draw_svg.chent.html</loc>
+  </url>
+  <url>
+    <loc>/reference/index.html</loc>
+  </url>
+  <url>
+    <loc>/reference/pai.html</loc>
+  </url>
+  <url>
+    <loc>/reference/plot.chent.html</loc>
+  </url>
+  <url>
+    <loc>/reference/pp.html</loc>
+  </url>
+  <url>
+    <loc>/reference/print.chent.html</loc>
+  </url>
+  <url>
+    <loc>/reference/print.pai.html</loc>
+  </url>
+</urlset>
diff --git a/man/chent.Rd b/man/chent.Rd
index 15fbc54..e069938 100644
--- a/man/chent.Rd
+++ b/man/chent.Rd
@@ -7,12 +7,12 @@
 An \code{\link{R6Class}} generator object
 }
 \description{
-The class is initialised with an identifier. Chemical information is retrieved from
-the internet. Additionally, it can be generated using RDKit if RDKit and its
-python bindings are installed.
+The class is initialised with an identifier. Chemical
+information is retrieved from the internet. Additionally, it can be
+generated using RDKit if RDKit and its python bindings are installed.
 }
 \examples{
-oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
+oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
 print(oct)
 if (!is.null(oct$Picture)) {
   plot(oct)
@@ -24,19 +24,23 @@ if (!is.null(caffeine$Picture)) {
   plot(caffeine)
 }
 }
-\keyword{data}
 \section{Public fields}{
 \if{html}{\out{<div class="r6-fields">}}
 \describe{
-\item{\code{identifier}}{The identifier that was used to initiate the object, with attribute 'source'}
+\item{\code{identifier}}{(\code{character(1)})\cr
+The identifier that was used to initiate the object, with attribute 'source'}
 
-\item{\code{inchikey}}{InChI Key, with attribute 'source'}
+\item{\code{inchikey}}{(\code{character(1)})\cr
+InChI Key, with attribute 'source'}
 
-\item{\code{smiles}}{SMILES code, with attribute 'source'}
+\item{\code{smiles}}{(\code{character()})\cr
+SMILES code(s), with attribute 'source'}
 
-\item{\code{mw}}{Molecular weight, with attribute 'source'}
+\item{\code{mw}}{(\code{numeric(1)})\cr
+Molecular weight, with attribute 'source'}
 
-\item{\code{pubchem}}{List of information retreived from PubChem}
+\item{\code{pubchem}}{(\code{list()})\cr
+List of information retrieved from PubChem}
 
 \item{\code{rdkit}}{List of information obtained with RDKit}
 
@@ -54,15 +58,22 @@ if (!is.null(caffeine$Picture)) {
 
 \item{\code{cwsat}}{Water solubility in mg/L}
 
+\item{\code{PUF}}{Plant uptake factor}
+
 \item{\code{chyaml}}{List of information obtained from a YAML file}
 
-\item{\code{soil_degradation}}{Dataframe of modelling DT50 values}
+\item{\code{TPs}}{List of transformation products as chent objects
+Add a transformation product to the internal list}
+
+\item{\code{transformations}}{Data frame of observed transformations
+Add a line in the internal dataframe holding 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_ff}}{Dataframe of formation fractions}
 
 \item{\code{soil_sorption}}{Dataframe of soil sorption data}
-
-\item{\code{PUF}}{Plant uptake factor}
 }
 \if{html}{\out{</div>}}
 }
@@ -92,13 +103,12 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<a id="method-chent-new"></a>}}
 \if{latex}{\out{\hypertarget{method-chent-new}{}}}
 \subsection{Method \code{new()}}{
+Creates a new instance of this \link[R6:R6Class]{R6} class.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{chent$new(
   identifier,
   smiles = NULL,
-  smiles_source = "user",
   inchikey = NULL,
-  inchikey_source = "user",
   pubchem = TRUE,
   pubchem_from = c("name", "smiles", "inchikey"),
   rdkit = TRUE,
@@ -107,6 +117,33 @@ if (!is.null(caffeine$Picture)) {
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{identifier}}{Identifier to be stored in the object}
+
+\item{\code{smiles}}{Optional user provided SMILES code}
+
+\item{\code{inchikey}}{Optional user provided InChI Key}
+
+\item{\code{pubchem}}{Should an attempt be made to retrieve chemical
+information from PubChem via the webchem package?}
+
+\item{\code{pubchem_from}}{Possibility to select the argument
+that is used to query pubchem}
+
+\item{\code{rdkit}}{Should an attempt be made to retrieve chemical
+information from a local rdkit installation via python
+and the reticulate package?}
+
+\item{\code{template}}{An optional SMILES code to be used as template for RDKit}
+
+\item{\code{chyaml}}{Should we look for a identifier.yaml file in the working
+directory?
+Try to get chemical information from PubChem}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-try_pubchem"></a>}}
@@ -116,6 +153,16 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<div class="r">}}\preformatted{chent$try_pubchem(query, from = "name")}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{query}}{Query string to be passed to \link[webchem:get_cid]{get_cid}}
+
+\item{\code{from}}{Passed to \link[webchem:get_cid]{get_cid}
+Get chemical information from PubChem for a known PubChem CID}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-get_pubchem"></a>}}
@@ -125,6 +172,14 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<div class="r">}}\preformatted{chent$get_pubchem(pubchem_cid)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{pubchem_cid}}{CID
+Get chemical information from RDKit if available}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-get_rdkit"></a>}}
@@ -134,6 +189,14 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<div class="r">}}\preformatted{chent$get_rdkit(template = NULL)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{template}}{Optional template specified as a SMILES code
+Obtain information from a YAML file}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-get_chyaml"></a>}}
@@ -146,6 +209,16 @@ if (!is.null(caffeine$Picture)) {
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{repo}}{Should the file be looked for in the current working
+directory, a local git repository under \verb{~/git/chyaml}, or from
+the web (not implemented).
+Add a vapour pressure}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_p0"></a>}}
@@ -155,6 +228,22 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{p0}}{The vapour pressure in Pa}
+
+\item{\code{T}}{Temperature}
+
+\item{\code{source}}{An acronym specifying the source of the information}
+
+\item{\code{page}}{The page from which the information was taken}
+
+\item{\code{remark}}{A remark
+Add a water solubility}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_cwsat"></a>}}
@@ -164,6 +253,14 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{p0}}{The water solubility in mg/L
+Add a plant uptake factor}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_PUF"></a>}}
@@ -178,6 +275,13 @@ if (!is.null(caffeine$Picture)) {
 )}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{PUF}}{The plant uptake factor, a number between 0 and 1}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_TP"></a>}}
@@ -187,6 +291,17 @@ if (!is.null(caffeine$Picture)) {
 \if{html}{\out{<div class="r">}}\preformatted{chent$add_TP(x, smiles = NULL, pubchem = FALSE)}\if{html}{\out{</div>}}
 }
 
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{x}}{A \link{chent} object, or an identifier to generate a \link{chent} object}
+
+\item{\code{smiles}}{A SMILES code for defining a \link{chent} object}
+
+\item{\code{pubchem}}{Should chemical information be obtained from PubChem?}
+}
+\if{html}{\out{</div>}}
+}
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-chent-add_transformation"></a>}}
diff --git a/man/pai.Rd b/man/pai.Rd
index 088f5b9..d966a9e 100644
--- a/man/pai.Rd
+++ b/man/pai.Rd
@@ -25,7 +25,6 @@ if (!is.null(atr$Picture)) {
 
 }
 }
-\keyword{data}
 \section{Super class}{
 \code{\link[chents:chent]{chents::chent}} -> \code{pai}
 }
@@ -75,9 +74,7 @@ if (!is.null(atr$Picture)) {
   iso,
   identifier = iso,
   smiles = NULL,
-  smiles_source = "user",
   inchikey = NULL,
-  inchikey_source = "user",
   bcpc = TRUE,
   pubchem = TRUE,
   pubchem_from = "auto",