Authors

+ + + +

+
Johannes Ranke. Author, maintainer, copyright holder. +
+

Citation

+ Source: DESCRIPTION +

-
Johannes Ranke. Author, maintainer, copyright holder. -
-

+ +

Ranke J (2023). +chents: Chemical Entities as R Objects. +R package version 0.3.1, https://github.com/jranke/chents. +

@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},
+}

@@ -123,22 +76,20 @@ -

- - + + 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 (> 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."> + +

- - +

+ +

The R package chents provides some utilities for working with chemical entities in R.

-Features

Features +

Some chemical information is retrieved from the PubChem website using the webchem package
If Python and RDKit (> 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
Additional information can be read from a local .yaml file

-Examples

Some examples are available from the reference on jrwb.de.

Examples +

Some examples are available from the reference on jrwb.de.

@@ -139,5 +140,7 @@ + + 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 = ""; - $(".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 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png index 7229a66..acab3e6 100644 Binary files a/docs/reference/chent-1.png and b/docs/reference/chent-1.png 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 @@ - - - - - - - -An R6 class for chemical entities with associated data — chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -An R6 class for chemical entities with associated data — chent • chents - - - - + + -

- -

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.

Format

An R6Class generator object

Public fields

identifier: (character(1))
+The identifier that was used to initiate the object, with attribute 'source'
inchikey: (character(1))
+InChI Key, with attribute 'source'
smiles: (character())
+SMILES code(s), with attribute 'source'
mw: (numeric(1))
+Molecular weight, with attribute 'source'
pubchem: (list())
+List of information retrieved from PubChem
chyaml: List of information obtained from a YAML file
TPs: List of transformation products as chent objects
transformations: Data frame of observed transformations
soil_degradation: Dataframe of modelling DT50 values
soil_ff: Dataframe of formation fractions
soil_sorption: Dataframe of soil sorption data

Methods

Public methods

- -

chent$new()
chent$try_pubchem()
chent$get_pubchem()
chent$get_rdkit()
chent$get_chyaml()
chent$add_p0()
chent$add_cwsat()
chent$add_PUF()
chent$add_TP()
chent$add_transformation()
chent$add_soil_degradation()
chent$add_soil_ff()
chent$add_soil_sorption()
chent$pdf()
chent$png()
chent$emf()
chent$clone()

Method `new()`

- -

Usage

chent$new(
-  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
-)

- -

Method `try_pubchem()`

- -

Usage

chent$try_pubchem(query, from = "name")

- -

Method `get_pubchem()`

- -

Usage

chent$get_pubchem(pubchem_cid)

- -

Method `get_rdkit()`

- -

Usage

chent$get_rdkit(template = NULL)

- -

Method `get_chyaml()`

- -

Usage

chent$get_chyaml(
-  repo = c("wd", "local", "web"),
-  chyaml = paste0(URLencode(self$identifier), ".yaml")
-)

- -

Method `add_p0()`

- -

Usage

chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")

- -

Method `add_cwsat()`

- -

Usage

chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")

- -

Method `add_PUF()`

- -

Usage

chent$add_PUF(
-  PUF = 0,
-  source = "focus_generic_gw_2014",
-  page = 41,
-  remark = "Conservative default value"
-)

- -

Method `add_TP()`

- -

Usage

chent$add_TP(x, smiles = NULL, pubchem = FALSE)

- -

Method `add_transformation()`

- -

Usage

chent$add_transformation(
-  study_type,
-  TP_identifier,
-  max_occurrence,
-  remark = "",
-  source = NA,
-  pages = NA
-)

- -

Method `add_soil_degradation()`

- -

Usage

chent$add_soil_degradation(
-  soils,
-  DT50_mod,
-  DT50_mod_ref,
-  type = NA,
-  country = NA,
-  pH_orig = NA,
-  pH_medium = NA,
-  pH_H2O = NA,
-  perc_OC = NA,
-  temperature = NA,
-  moisture = NA,
-  category = "lab",
-  formulation = NA,
-  model = NA,
-  chi2 = NA,
-  remark = "",
-  source,
-  page = NA
-)

- -

Method `add_soil_ff()`

- -

Usage

chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)

- -

Method `add_soil_sorption()`

- -

Usage

chent$add_soil_sorption(
-  soils,
-  Kf,
-  Kfoc,
-  N,
-  type = NA,
-  pH_orig = NA,
-  pH_medium = NA,
-  pH_H2O = NA,
-  perc_OC = NA,
-  perc_clay = NA,
-  CEC = NA,
-  remark = "",
-  source,
-  page = NA
-)

- -

Method `pdf()`

- -

Usage

chent$pdf(
-  file = paste0(self$identifier, ".pdf"),
-  dir = "structures/pdf",
-  template = NULL
-)

- -

Method `png()`

- -

Usage

chent$png(
-  file = paste0(self$identifier, ".png"),
-  dir = "structures/png",
-  antialias = "gray"
-)

- -

Method `emf()`

- -

Usage

chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")

- -

Method `clone()`

The objects of this class are cloneable with this method.

Usage

chent$clone(deep = FALSE)

- -

Arguments

deep: Whether to make a deep clone.

- - - -

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
-
#> PubChem:
#> Trying to get chemical information from RDKit using user SMILES
-#> CCCCCCCCO
#> Did not find chyaml file ./1-octanol.yaml
print(oct)
-
#> <chent>
-#> Identifier $identifier 1-octanol 
-#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
-#> SMILES string $smiles:
-#>              user PubChem_Canonical 
-#>       "CCCCCCCCO"       "CCCCCCCCO" 
-#> Molecular weight $mw: 130.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "1-octanol"        "Octan-1-ol"       "octanol"          "111-87-5"        
-#>  [5] "N-octanol"        "Octyl alcohol"    "Capryl alcohol"   "caprylic alcohol"
-#>  [9] "n-Octyl alcohol"  "Heptyl carbinol" 
if (!is.null(oct$Picture)) {
-  plot(oct)
-}
-

-caffeine <- chent$new("caffeine")
-
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
-#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
#> Did not find chyaml file ./caffeine.yaml
print(caffeine)
-
#> <chent>
-#> Identifier $identifier caffeine 
-#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#> SMILES string $smiles:
-#>              PubChem_Canonical 
-#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#> Molecular weight $mw: 194.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "caffeine"                "58-08-2"                
-#>  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#>  [5] "Thein"                   "Methyltheobromine"      
-#>  [7] "Cafeina"                 "Theine"                 
-#>  [9] "Koffein"                 "Mateina"                
if (!is.null(caffeine$Picture)) {
-  plot(caffeine)
-}
-

Public methods

+ +

chent$new()
chent$try_pubchem()
chent$get_pubchem()
chent$get_rdkit()
chent$get_chyaml()
chent$add_p0()
chent$add_cwsat()
chent$add_PUF()
chent$add_TP()
chent$add_transformation()
chent$add_soil_degradation()
chent$add_soil_ff()
chent$add_soil_sorption()
chent$pdf()
chent$png()
chent$emf()
chent$clone()

Method `new()`

Creates a new instance of this R6 class.

Usage

chent$new(
+  identifier,
+  smiles = NULL,
+  inchikey = NULL,
+  pubchem = TRUE,
+  pubchem_from = c("name", "smiles", "inchikey"),
+  rdkit = TRUE,
+  template = NULL,
+  chyaml = TRUE
+)

+ +

Arguments

identifier: Identifier to be stored in the object
smiles: Optional user provided SMILES code
inchikey: Optional user provided InChI Key
pubchem: Should an attempt be made to retrieve chemical +information from PubChem via the webchem package?
pubchem_from: Possibility to select the argument +that is used to query pubchem
rdkit: Should an attempt be made to retrieve chemical +information from a local rdkit installation via python +and the reticulate package?
template: An optional SMILES code to be used as template for RDKit
chyaml: Should we look for a identifier.yaml file in the working +directory? +Try to get chemical information from PubChem

+ +

Method `try_pubchem()`

+ +

Usage

chent$try_pubchem(query, from = "name")

+ +

Arguments

query: Query string to be passed to get_cid
from: Passed to get_cid +Get chemical information from PubChem for a known PubChem CID

+ +

Method `get_pubchem()`

+ +

Usage

chent$get_pubchem(pubchem_cid)

+ +

Arguments

pubchem_cid: CID

+ +

Method `get_rdkit()`

+ +

Usage

chent$get_rdkit(template = NULL)

+ + +

Method `get_chyaml()`

+ +

Usage

chent$get_chyaml(
+  repo = c("wd", "local", "web"),
+  chyaml = paste0(URLencode(self$identifier), ".yaml")
+)

+ + +

Method `add_p0()`

+ +

Usage

chent$add_p0(p0, T = NA, source = NA, page = NA, remark = "")

+ + +

Method `add_cwsat()`

+ +

Usage

chent$add_cwsat(cwsat, T = NA, pH = NA, source = NA, page = NA, remark = "")

+ + +

Method `add_PUF()`

+ +

Usage

chent$add_PUF(
+  PUF = 0,
+  source = "focus_generic_gw_2014",
+  page = 41,
+  remark = "Conservative default value"
+)

+ + +

Method `add_TP()`

+ +

Usage

chent$add_TP(x, smiles = NULL, pubchem = FALSE)

+ + +

Method `add_transformation()`

+ +

Usage

chent$add_transformation(
+  study_type,
+  TP_identifier,
+  max_occurrence,
+  remark = "",
+  source = NA,
+  pages = NA
+)

+ + +

Method `add_soil_degradation()`

+ +

Usage

chent$add_soil_degradation(
+  soils,
+  DT50_mod,
+  DT50_mod_ref,
+  type = NA,
+  country = NA,
+  pH_orig = NA,
+  pH_medium = NA,
+  pH_H2O = NA,
+  perc_OC = NA,
+  temperature = NA,
+  moisture = NA,
+  category = "lab",
+  formulation = NA,
+  model = NA,
+  chi2 = NA,
+  remark = "",
+  source,
+  page = NA
+)

+ + +

Method `add_soil_ff()`

+ +

Usage

chent$add_soil_ff(target, soils, ff = 1, remark = "", source, page = NA)

+ + +

Method `add_soil_sorption()`

+ +

Usage

chent$add_soil_sorption(
+  soils,
+  Kf,
+  Kfoc,
+  N,
+  type = NA,
+  pH_orig = NA,
+  pH_medium = NA,
+  pH_H2O = NA,
+  perc_OC = NA,
+  perc_clay = NA,
+  CEC = NA,
+  remark = "",
+  source,
+  page = NA
+)

+ + +

Method `pdf()`

+ +

Usage

chent$pdf(
+  file = paste0(self$identifier, ".pdf"),
+  dir = "structures/pdf",
+  template = NULL
+)

+ + +

Method `png()`

+ +

Usage

chent$png(
+  file = paste0(self$identifier, ".png"),
+  dir = "structures/png",
+  antialias = "gray"
+)

+ + +

Method `emf()`

+ +

Usage

chent$emf(file = paste0(self$identifier, ".emf"), dir = "structures/emf")

+ + +

Method `clone()`

The objects of this class are cloneable with this method.

Usage

chent$clone(deep = FALSE)

+ +

Arguments

deep: Whether to make a deep clone.

+ +

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO", pubchem = FALSE)
+#> Trying to get chemical information from RDKit using user SMILES
+#> CCCCCCCCO
+#> Did not find chyaml file ./1-octanol.yaml
+print(oct)
+#> <chent>
+#> Identifier $identifier 1-octanol 
+#> InChI Key $inchikey 
+#> SMILES string $smiles:
+#>        user 
+#> "CCCCCCCCO" 
+#> Molecular weight $mw: 130.2 
+if (!is.null(oct$Picture)) {
+  plot(oct)
+}
+
+caffeine <- chent$new("caffeine")
+#> PubChem:
+#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+#> Did not find chyaml file ./caffeine.yaml
+print(caffeine)
+#> <chent>
+#> Identifier $identifier caffeine 
+#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>              PubChem_Canonical 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Koffein"                 "Mateina"                
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+
+

- - + + 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 @@ - - - - - - - -Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents - + + - - - -

- -

@@ -117,65 +49,60 @@

Draw SVG graph from a chent object using RDKit

draw_svg.chent(
-  x,
-  width = 300,
-  height = 150,
-  filename = paste0(names(x$identifier), ".svg"),
-  subdir = "svg"
-)

- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - -

x	The chent object to be plotted
width	The desired width in pixels
height	The desired height in pixels
filename	The filename
subdir	The path to which the file should be written

draw_svg.chent(
+  x,
+  width = 300,
+  height = 150,
+  filename = paste0(names(x$identifier), ".svg"),
+  subdir = "svg"
+)

+ +

Arguments

x: The chent object to be plotted
width: The desired width in pixels
height: The desired height in pixels
filename: The filename
subdir: The path to which the file should be written

- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 9de4a87..d9eb797 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ - - - - - - - -Function reference • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Function reference • chents - - + + - - -

- -

- - - - - - - - - - -

R6 Class definitions and methods

+ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

+ R6 Class definitions and methods
+
`chent`	An R6 class for chemical entities with associated data
+
`draw_svg.chent()`	Draw SVG graph from a chent object using RDKit
+
`plot(<chent>)`	Plot method for chent objects
+
`print(<chent>)`	Printing method for chent objects
+
`pai`	An R6 class for pesticidal active ingredients and associated data
+
`print(<pai>)`	Printing method for pai objects (pesticidal active ingredients)
+
`pp`	R6 class for holding a product with at least one active ingredient

- +

- - + + diff --git a/docs/reference/pai-1.png b/docs/reference/pai-1.png index c235304..802fd50 100644 Binary files a/docs/reference/pai-1.png and b/docs/reference/pai-1.png 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 @@ - - - - - - - -An R6 class for pesticidal active ingredients and associated data — pai • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -An R6 class for pesticidal active ingredients and associated data — pai • chents - - - - + + -

- -

@@ -120,132 +52,143 @@ Additional chemical information is retrieved from the internet if available.

Format

An R6Class generator object

Super class

chents::chent -> pai

Public fields

iso: ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org
bcpc: List of information retrieved from pesticidecompendium.bcpc.org

Methods

+ +

Public methods

+ +

pai$new()
pai$clone()

Inherited methods

Method `new()`

+ +

Usage

pai$new(
+  iso,
+  identifier = iso,
+  smiles = NULL,
+  inchikey = NULL,
+  bcpc = TRUE,
+  pubchem = TRUE,
+  pubchem_from = "auto",
+  rdkit = TRUE,
+  template = NULL,
+  chyaml = TRUE
+)

chents::chent -> pai

Public fields

iso: ISO common name according to ISO 1750 as retreived from pesticidecompendium.bcpc.org

Method `clone()`

The objects of this class are cloneable with this method.

Usage

pai$clone(deep = FALSE)

bcpc

List of information retrieved from pesticidecompendium.bcpc.org

Arguments

deep: Whether to make a deep clone.

Methods

- -

Public methods

- -

pai$new()
pai$clone()

Inherited methods

- -

Method `new()`

- -

Usage

pai$new(
-  iso,
-  identifier = iso,
-  smiles = NULL,
-  smiles_source = "user",
-  inchikey = NULL,
-  inchikey_source = "user",
-  bcpc = TRUE,
-  pubchem = TRUE,
-  pubchem_from = "auto",
-  rdkit = TRUE,
-  template = NULL,
-  chyaml = TRUE
-)

- -

Method `clone()`

The objects of this class are cloneable with this method.

Usage

pai$clone(deep = FALSE)

- -

Arguments

deep: Whether to make a deep clone.

- - - -

Examples

# On Travis, we get a certificate validation error,
-# likely because the system (xenial) is so old,
-# therefore don't run this example on Travis
-if (Sys.getenv("TRAVIS") == "") {
-
-atr <- pai$new("atrazine")
-print(atr)
-if (!is.null(atr$Picture)) {
-  plot(atr)
-}
-
-}
-
#> BCPC:
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
-#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
#> Did not find chyaml file ./atrazine.yaml
#> <pai> with ISO common name $iso atrazine 
-#> <chent>
-#> Identifier $identifier atrazine 
-#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
-#> SMILES string $smiles:
-#>            PubChem_Canonical 
-#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
-#> Molecular weight $mw: 215.7 
-#> PubChem synonyms (up to 10):
-#>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Chromozin"   
-#>  [6] "Aktikon"      "Atrazin"      "Argezin"      "Atazinax"     "Atranex"

+ +

Examples

# On Travis, we get a certificate validation error,
+# likely because the system (xenial) is so old,
+# therefore don't run this example on Travis
+if (Sys.getenv("TRAVIS") == "") {
+
+atr <- pai$new("atrazine")
+print(atr)
+if (!is.null(atr$Picture)) {
+  plot(atr)
+}
+
+}
+#> BCPC:
+#> PubChem:
+#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
+#> Did not find chyaml file ./atrazine.yaml
+
+#> <pai> with ISO common name $iso atrazine 
+#> <chent>
+#> Identifier $identifier atrazine 
+#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>            PubChem_Canonical 
+#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
+#> Molecular weight $mw: 215.7 
+#> PubChem synonyms (up to 10):
+#>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Aktikon"     
+#>  [6] "Atranex"      "Chromozin"    "Atazinax"     "Atrasine"     "Gesoprim"    
+

- - + + diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png index 330f0a5..1e8885d 100644 Binary files a/docs/reference/plot.chent-1.png and b/docs/reference/plot.chent-1.png 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 @@ - - - - - - - -Plot method for chent objects — plot.chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Plot method for chent objects — plot.chent • chents - + + - - - -

- -

@@ -117,68 +49,70 @@

Plot method for chent objects

# S3 method for chent
-plot(x, ...)

- -

Arguments

- - - - - - - - - - -

x	The chent object to be plotted
...	Further arguments passed to `grid.picture`

- - -

Examples

caffeine <- chent$new("caffeine")
-
#> PubChem:
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
-#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
#> Did not find chyaml file ./caffeine.yaml
print(caffeine)
-
#> <chent>
-#> Identifier $identifier caffeine 
-#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
-#> SMILES string $smiles:
-#>              PubChem_Canonical 
-#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
-#> Molecular weight $mw: 194.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "caffeine"                "58-08-2"                
-#>  [3] "1,3,7-Trimethylxanthine" "Guaranine"              
-#>  [5] "Thein"                   "Methyltheobromine"      
-#>  [7] "Cafeina"                 "Theine"                 
-#>  [9] "Koffein"                 "Mateina"                
if (!is.null(caffeine$Picture)) {
-  plot(caffeine)
-}
-

# S3 method for chent
+plot(x, ...)

+ +

Arguments

x: The chent object to be plotted
...: Further arguments passed to grid.picture

+ +

Examples

caffeine <- chent$new("caffeine")
+#> PubChem:
+#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
+#> Did not find chyaml file ./caffeine.yaml
+print(caffeine)
+#> <chent>
+#> Identifier $identifier caffeine 
+#> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>              PubChem_Canonical 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> Molecular weight $mw: 194.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "caffeine"                "58-08-2"                
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Theine"                 
+#>  [7] "Thein"                   "Cafeina"                
+#>  [9] "Koffein"                 "Mateina"                
+if (!is.null(caffeine$Picture)) {
+  plot(caffeine)
+}
+
+

- - + + 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 @@ - - - - - - - -R6 class for holding a product with at least one active ingredient — pp • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -R6 class for holding a product with at least one active ingredient — pp • chents - - - - + + -

- -

@@ -118,89 +50,105 @@

Format

An R6Class generator object.

Public fields

name: The name of the product
ais: A list of active ingredients

Methods

Public methods

+ +

pp$new()
pp$print()
pp$clone()

Method `new()`

+ +

Usage

pp$new(
+  name,
+  ...,
+  concentrations,
+  concentration_units = "g/L",
+  density = 1000,
+  density_units = "g/L"
+)

pp$new()
pp$print()
pp$clone()

Method `new()`

Usage

pp$new(
-  name,
-  ...,
-  concentrations,
-  concentration_units = "g/L",
-  density = 1000,
-  density_units = "g/L"
-)

Method `print()`

Usage

pp$print()

Usage

pp$print()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

pp$clone(deep = FALSE)

Method `clone()`

The objects of this class are cloneable with this method.

Usage

pp$clone(deep = FALSE)

+ +

Arguments

deep: Whether to make a deep clone.

- - + + 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 @@ - - - - - - - -Printing method for chent objects — print.chent • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Printing method for chent objects — print.chent • chents - + + - - - -

- -

@@ -117,48 +49,43 @@

Printing method for chent objects

# S3 method for chent
-print(x, ...)

# S3 method for chent
+print(x, ...)

+ +

Arguments

x: The chent object to be printed
...: Further arguments for compatibility with the S3 method

x	The chent object to be printed
...	Further arguments for compatibility with the S3 method

- - + + 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 @@ - - - - - - - -Printing method for pai objects (pesticidal active ingredients) — print.pai • chents - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Printing method for pai objects (pesticidal active ingredients) — print.pai • chents - + + - - - -

- -

@@ -117,48 +49,43 @@

Printing method for pai objects (pesticidal active ingredients)

# S3 method for pai
-print(x, ...)

# S3 method for pai
+print(x, ...)

+ +

Arguments

x: The chent object to be printed
...: Further arguments for compatibility with the S3 method

x	The chent object to be printed
...	Further arguments for compatibility with the S3 method

- - + + 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 @@ + + + + /404.html + + + /authors.html + + + /index.html + + + /reference/chent.html + + + /reference/draw_svg.chent.html + + + /reference/index.html + + + /reference/pai.html + + + /reference/plot.chent.html + + + /reference/pp.html + + + /reference/print.chent.html + + + /reference/print.pai.html + + -- cgit v1.2.1

Page not found (404)

Authors

Authors

Citation

-chents

chents +

-Features

Features +

-Examples

Examples +

Links

Links

License

License

Developers

Citation

Dev status

Developers

An R6 class for chemical entities with associated data

Format

Public fields

Format

Public fields

Methods

Methods

Public methods

Method new()

Usage

Method try_pubchem()

Usage

Method get_pubchem()

Usage

Method get_rdkit()

Usage

Method get_chyaml()

Usage

Method add_p0()

Usage

Method add_cwsat()

Usage

Method add_PUF()

Usage

Method add_TP()

Usage

Method add_transformation()

Usage

Method add_soil_degradation()

Usage

Method add_soil_ff()

Usage

Method add_soil_sorption()

Usage

Method pdf()

Usage

Method png()

Usage

Method emf()

Usage

Method clone()

Usage

Arguments

Examples

Public methods

Method new()

Usage

Arguments

Method try_pubchem()

Usage

Arguments

Method get_pubchem()

Usage

Arguments

Method get_rdkit()

Usage

Method get_chyaml()

Usage

Method add_p0()

Usage

Method add_cwsat()

Usage

Method `new()`

Method `try_pubchem()`

Method `get_pubchem()`

Method `get_rdkit()`

Method `get_chyaml()`

Method `add_p0()`

Method `add_cwsat()`

Method `add_PUF()`

Method `add_TP()`

Method `add_transformation()`

Method `add_soil_degradation()`

Method `add_soil_ff()`

Method `add_soil_sorption()`

Method `pdf()`

Method `png()`

Method `emf()`

Method `clone()`

Method `new()`

Method `try_pubchem()`

Method `get_pubchem()`

Method `get_rdkit()`

Method `get_chyaml()`

Method `add_p0()`

Method `add_cwsat()`

Method `add_PUF()`

Method `add_TP()`

Method `add_transformation()`

Method `add_soil_degradation()`

Method `add_soil_ff()`

Method `add_soil_sorption()`

Method `pdf()`

Method `png()`

Method `emf()`

Method `clone()`

Method `new()`

Method `clone()`

Method `new()`

Method `clone()`