From e4be5e83c8c525b3745d2d7813336319d10f8855 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 22:07:06 +0100 Subject: Update to bootstrap 5 --- docs/reference/Rplot001.png | Bin 20412 -> 1011 bytes docs/reference/chent.html | 130 +++++++++++++------------------ docs/reference/draw_svg.chent.html | 90 ++++++++++------------ docs/reference/index.html | 152 +++++++++++++++++++------------------ docs/reference/pai.html | 119 +++++++++++++---------------- docs/reference/plot.chent.html | 112 ++++++++++++--------------- docs/reference/ppp.html | 100 ++++++++++++------------ docs/reference/print.chent.html | 90 ++++++++++------------ docs/reference/print.pai.html | 90 ++++++++++------------ 9 files changed, 404 insertions(+), 479 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 0e4970e..17a3580 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html index 48ccf3f..cb0b1eb 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,65 +1,64 @@ -An R6 class for chemical entities with associated data — chent • chentsAn R6 class for chemical entities with associated data — chent • chents + + Skip to contents -
-
-
-
-

An R6 class for chemical entities with associated data

- Source: R/chent.R - +
+ + +
+
+
+
+

An R6 class for chemical entities with associated data

+ Source: R/chent.R +
chent.Rd
-
+

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

+
+

Format

An R6Class generator object

-
-

Public fields

+
+

Public fields

identifier

(character(1))
The identifier that was used to initiate the object, with attribute 'source'

@@ -151,8 +150,8 @@ Add soil sorption data

-
-

Methods

+
+

Methods

Public methods

@@ -767,69 +766,48 @@ Write an EMF image of the structure using -

Examples

+
+

Examples

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

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index a95748e..4272133 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -1,55 +1,53 @@ -Draw SVG graph from a chent object using RDKit — draw_svg.chent • chentsDraw SVG graph from a chent object using RDKit — draw_svg.chent • chents + + Skip to contents -
-
-
-
-

Draw SVG graph from a chent object using RDKit

- Source: R/chent.R - +
+ + +
+
+
+
+

Draw SVG graph from a chent object using RDKit

+ Source: R/chent.R +
draw_svg.chent.Rd
-
+

Draw SVG graph from a chent object using RDKit

-
+
+

Usage

draw_svg.chent(
   x,
   width = 300,
@@ -59,8 +57,8 @@
 )
-
-

Arguments

+
+

Arguments

x

The chent object to be plotted

@@ -82,26 +80,22 @@
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/index.html b/docs/reference/index.html index 6bc6df8..eac8cbf 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,101 +1,107 @@ -Function reference • chentsFunction reference • chents + + Skip to contents -
-
+
+
+
+

Function reference

+
+
+

R6 Class definitions and methods

+ -
-
-
-

Reference

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

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)

-

ppp

-

R6 class for a plant protection product with at least one active ingredient

- - -
+
+ + 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)
+
+ + ppp +
+
R6 class for a plant protection product with at least one active ingredient
+
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 2448b60..e3170af 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -1,69 +1,68 @@ -An R6 class for pesticidal active ingredients and associated data — pai • chentsAn R6 class for pesticidal active ingredients and associated data — pai • chents + + Skip to contents -
-
-
-
-

An R6 class for pesticidal active ingredients and associated data

- Source: R/chent.R - +
+ + +
+
+
+
+

An R6 class for pesticidal active ingredients and associated data

+ Source: R/chent.R +
pai.Rd
-
+

The class is initialised with an identifier which is generally an ISO common name. Additional chemical information is retrieved from the internet if available.

-
-

Format

+
+

Format

An R6Class generator object

-
-

Super class

+
+

Super class

chents::chent -> pai

-
-

Public fields

+
+

Public fields

iso

ISO common name of the active ingredient according to ISO 1750

@@ -76,8 +75,8 @@ Creates a new instance of this -

Methods

+
+

Methods

Public methods

@@ -155,8 +154,8 @@ BCPC compendium

-
-

Examples

+
+

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
@@ -173,41 +172,25 @@ BCPC compendium

 #> 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 $mw: 215.7 
-#> PubChem synonyms (up to 10):
-#>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Aktikon"     
-#>  [6] "Atranex"      "Chromozin"    "Atazinax"     "Atrasine"     "Gesoprim"    
+#> Error in URLencode(self$identifier): could not find function "URLencode"
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index 26d8445..1a07967 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -1,61 +1,59 @@ -Plot method for chent objects — plot.chent • chentsPlot method for chent objects — plot.chent • chents + + Skip to contents -
-
-
-
-

Plot method for chent objects

- Source: R/chent.R - +
+ + +
+
+
+
+

Plot method for chent objects

+ Source: R/chent.R +
plot.chent.Rd
-
+

Plot method for chent objects

-
+
+

Usage

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

Arguments

+
+

Arguments

x

The chent object to be plotted

@@ -65,53 +63,37 @@
-
-

Examples

+
+

Examples

caffeine <- chent$new("caffeine")
 #> PubChem:
 #> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
 #> CN1C=NC2=C1C(=O)N(C(=O)N2C)C
-#> Did not find chyaml file ./caffeine.yaml
+#> Error in URLencode(self$identifier): could not find function "URLencode"
 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 $mw: 194.2 
-#> PubChem synonyms (up to 10):
-#>  [1] "caffeine"                "58-08-2"                
-#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
-#>  [5] "Methyltheobromine"       "Theine"                 
-#>  [7] "Thein"                   "Cafeina"                
-#>  [9] "Koffein"                 "Mateina"                
+#> Error in eval(expr, envir, enclos): object 'caffeine' not found
 if (!is.null(caffeine$Picture)) {
   plot(caffeine)
 }
-
+#> Error in eval(expr, envir, enclos): object 'caffeine' not found
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/ppp.html b/docs/reference/ppp.html index 7a9b861..4f12543 100644 --- a/docs/reference/ppp.html +++ b/docs/reference/ppp.html @@ -1,63 +1,61 @@ -R6 class for a plant protection product with at least one active ingredient — ppp • chentsR6 class for a plant protection product with at least one active ingredient — ppp • chents + + Skip to contents -
-
-
-
-

R6 class for a plant protection product with at least one active ingredient

- Source: R/chent.R - +
+ + +
+
+
+
+

R6 class for a plant protection product with at least one active ingredient

+ Source: R/chent.R +
ppp.Rd
-
+

Contains basic information about the active ingredients in the product

-
-

Format

+
+

Format

An R6Class generator object.

-
-

Public fields

+
+

Public fields

name

The name of the product

@@ -106,16 +104,16 @@ Printing method

-
-

Active bindings

+
+

Active bindings

...

Identifiers of the active ingredients

-
-

Methods

+
+

Methods

Public methods

@@ -168,26 +166,22 @@ Printing method

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index da3ba4f..4e7bb98 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -1,61 +1,59 @@ -Printing method for chent objects — print.chent • chentsPrinting method for chent objects — print.chent • chents + + Skip to contents -
-
-
-
-

Printing method for chent objects

- Source: R/chent.R - +
+ + +
+
+
+
+

Printing method for chent objects

+ Source: R/chent.R +
print.chent.Rd
-
+

Printing method for chent objects

-
+
+

Usage

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

Arguments

+
+

Arguments

x

The chent object to be printed

@@ -65,26 +63,22 @@
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index 5a08066..9ebefa6 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -1,61 +1,59 @@ -Printing method for pai objects (pesticidal active ingredients) — print.pai • chentsPrinting method for pai objects (pesticidal active ingredients) — print.pai • chents + + Skip to contents -
-
-
-
-

Printing method for pai objects (pesticidal active ingredients)

- Source: R/chent.R - +
+ + +
+
+
+
+

Printing method for pai objects (pesticidal active ingredients)

+ Source: R/chent.R +
print.pai.Rd
-
+

Printing method for pai objects (pesticidal active ingredients)

-
+
+

Usage

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

Arguments

+
+

Arguments

x

The chent object to be printed

@@ -65,26 +63,22 @@
-
- -
+
-
- -- cgit v1.2.1