aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--.Rbuildignore2
-rw-r--r--.gitignore1
-rw-r--r--DESCRIPTION10
-rw-r--r--GNUmakefile2
-rw-r--r--R/chent.R201
-rw-r--r--chents.Rproj19
-rw-r--r--docs/404.html117
-rw-r--r--docs/authors.html139
-rw-r--r--docs/index.html73
-rw-r--r--docs/pkgdown.css83
-rw-r--r--docs/pkgdown.js4
-rw-r--r--docs/pkgdown.yml6
-rw-r--r--docs/reference/Rplot001.pngbin19923 -> 20712 bytes
-rw-r--r--docs/reference/chent-1.pngbin46431 -> 46730 bytes
-rw-r--r--docs/reference/chent.html807
-rw-r--r--docs/reference/draw_svg.chent.html173
-rw-r--r--docs/reference/index.html160
-rw-r--r--docs/reference/pai-1.pngbin33683 -> 34388 bytes
-rw-r--r--docs/reference/pai.html315
-rw-r--r--docs/reference/plot.chent-1.pngbin46149 -> 46142 bytes
-rw-r--r--docs/reference/plot.chent.html190
-rw-r--r--docs/reference/pp.html208
-rw-r--r--docs/reference/print.chent.html137
-rw-r--r--docs/reference/print.pai.html137
-rw-r--r--docs/sitemap.xml36
-rw-r--r--man/chent.Rd145
-rw-r--r--man/pai.Rd3
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
Binary files differ
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
Binary files differ
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>
-
-<!-- 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]>
+<!-- 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>
</div>
- </footer>
- </div>
+ </footer></div>
- </body>
-</html>
+
+ </body></html>
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>
-
-<!-- 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]>
+<!-- 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]>
<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-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
Binary files differ
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">
-<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]>
+<!-- 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>
- </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/plot.chent-1.png b/docs/reference/plot.chent-1.png
index 330f0a5..1e8885d 100644
--- a/docs/reference/plot.chent-1.png
+++ b/docs/reference/plot.chent-1.png
Binary files differ
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index 62bf38f..470ce79 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.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>Plot method for chent objects — plot.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="Plot method for chent objects — plot.chent" />
-<meta property="og:description" content="Plot 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]>
+<!-- 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>Plot method for chent objects — plot.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="Plot method for chent objects — plot.chent"><meta property="og:description" content="Plot 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>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>
<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/pp.html b/docs/reference/pp.html
index c4e4a01..2607035 100644
--- a/docs/reference/pp.html
+++ b/docs/reference/pp.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>R6 class for holding a product with at least one active ingredient — pp • 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="R6 class for holding a product with at least one active ingredient — pp" />
-<meta property="og:description" content="An R6 class for holding information about a product with at least one active ingredient" />
-
-
-
-
-<!-- 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>R6 class for holding a product with at least one active ingredient — pp • 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="R6 class for holding a product with at least one active ingredient — pp"><meta property="og:description" content="An R6 class for holding information about a product with at least one active ingredient"><!-- 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">
@@ -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>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>
-
-<!-- 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]>
+<!-- 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 -->
-<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]>
+<!-- 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",

Contact - Imprint