From 4bd4606c76dfc152547e0f5899a98494a4290d33 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 09:48:02 +0100 Subject: Rebuild static documentation with current pkdown --- docs/reference/chent-1.png | Bin 0 -> 34969 bytes docs/reference/chent.html | 81 ++++++++++++++---------- docs/reference/draw_svg.chent.html | 56 ++++++++++++----- docs/reference/index.html | 122 ++++++++++++++++++++++++------------- docs/reference/pai.html | 38 ++++++++---- docs/reference/plot.chent-1.png | Bin 0 -> 34969 bytes docs/reference/plot.chent.html | 50 ++++++++++----- docs/reference/pp.html | 35 ++++++++--- docs/reference/print.chent.html | 38 +++++++++--- docs/reference/print.pai.html | 38 +++++++++--- 10 files changed, 313 insertions(+), 145 deletions(-) create mode 100644 docs/reference/chent-1.png create mode 100644 docs/reference/plot.chent-1.png (limited to 'docs/reference') diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png new file mode 100644 index 0000000..8731cf1 Binary files /dev/null and b/docs/reference/chent-1.png differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html index 15c4d10..ef683ef 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -18,19 +18,30 @@ + + + + + + + - + + + @@ -49,6 +60,12 @@

@@ -75,7 +92,7 @@ the internet. Additionally, it can be generated using RDKit if RDKit and its python bindings are installed and configured for use with PythonInR.

-

chent

+

chent

Format

@@ -83,52 +100,52 @@ python bindings are installed and configured for use with PythonInR.

Fields

-

-

identifier: The identifier that was used to initiate the object, with attribute 'source'
inchikey: InChI Key, with attribute 'source'
smiles: SMILES code, with attribute 'source'
mw: Molecular weight, with attribute 'source'
pubchem: List of information retreived from PubChem
rdkit: List of information obtained with RDKit, if installed and -configured for use with PythonInR
svg: SVG code
Picture: Graph as a picture object obtained using grImport
Pict_font_size: Font size as extracted from the intermediate PostScript file
pdf_height: Height of the MediaBox in the pdf after cropping
chyaml: List of information obtained from a YAML file
degradation: List of degradation endpoints

+ +

identifier: The identifier that was used to initiate the object, with attribute 'source'
inchikey: InChI Key, with attribute 'source'
smiles: SMILES code, with attribute 'source'
mw: Molecular weight, with attribute 'source'
pubchem: List of information retreived from PubChem
rdkit: List of information obtained with RDKit, if installed and +configured for use with PythonInR
svg: SVG code
Picture: Graph as a picture object obtained using grImport
Pict_font_size: Font size as extracted from the intermediate PostScript file
pdf_height: Height of the MediaBox in the pdf after cropping
chyaml: List of information obtained from a YAML file
degradation: List of degradation endpoints

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 
-#> Initialize Python Version 3.4.2 (default, Oct  8 2014, 10:47:48) 
-#> [GCC 4.9.1]
#> Trying to get chemical information from RDKit using user SMILES
-#> CCCCCCCCO
#> Did not find chyaml file ./1-octanol.yaml
print(oct)
#> <chent>
+#> Initialize Python Version 2.7.13 (default, Nov 24 2017, 17:33:09) 
+#> [GCC 6.3.0 20170516]
#> Trying to get chemical information from RDKit using user SMILES
+#> CCCCCCCCO
#> Loading required namespace: grConvert
#> 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" 
+#>       "CCCCCCCCO"       "CCCCCCCCO" 
 #> Molecular weight $mw: 130.2 
 #> PubChem synonyms (up to 10):
-#>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
-#>  [5] "Octyl alcohol"    "N-octanol"        "Capryl alcohol"   "n-Octyl alcohol" 
-#>  [9] "111-87-5"         "caprylic alcohol"
plot(oct)
caffeine <- chent$new("caffeine")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> Trying to get chemical information from RDKit using PubChem_Canonical SMILES
+#>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
+#>  [5] "Octyl alcohol"    "N-octanol"        "111-87-5"         "Capryl alcohol"  
+#>  [9] "caprylic alcohol" "n-Octyl alcohol" 
plot(oct)
caffeine <- chent$new("caffeine")
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
#> 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" 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
 #> Molecular weight $mw: 194.2 
 #> PubChem synonyms (up to 10):
-#>  [1] "2519"                    "caffeine"               
-#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
-#>  [5] "Methyltheobromine"       "Cafeina"                
-#>  [7] "Thein"                   "Koffein"                
-#>  [9] "Mateina"                 "Theine"                 
plot(caffeine)

+#> [1] "2519" "caffeine" +#> [3] "1,3,7-Trimethylxanthine" "58-08-2" +#> [5] "Guaranine" "Thein" +#> [7] "Cafeina" "Methyltheobromine" +#> [9] "Koffein" "Mateina"

plot(caffeine)

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 2cc3804..5342eca 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -18,19 +18,28 @@ + + + + + + + - + + + @@ -49,6 +58,12 @@

@@ -73,22 +88,33 @@

Draw SVG graph from a chent object using RDKit

-

draw_svg.chent(x, width = 300, height = 150,
+    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
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    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

@@ -107,7 +133,7 @@

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 52967a5..29771c9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -18,19 +18,25 @@ + + - + + + - + + + @@ -49,6 +55,12 @@

@@ -66,50 +78,72 @@

-

R6 Class definitions and methods

-

- - -

An R6 class for chemical entities with associated data

-

chent

- -

Draw SVG graph from a chent object using RDKit

-

draw_svg.chent

- -

Plot method for chent objects

-

plot.chent

- -

Printing method for chent objects

-

print.chent

- -

An R6 class for pesticidal active ingredients and associated data

-

pai

- -

Printing method for pai objects (pesticidal active ingredients)

-

print.pai

- -

R6 class for holding a product with at least one active ingredient

-

pp

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

+ 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` +	Plot method for chent objects
+ `print` +	Printing method for chent objects
+ `pai` +	An R6 class for pesticidal active ingredients and associated data
+ `print` +	Printing method for pai objects (pesticidal active ingredients)
+ `pp` +	R6 class for holding a product with at least one active ingredient

@@ -127,7 +161,7 @@

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 4c143a1..30a5b77 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -18,19 +18,29 @@ + + + + + + + - + + + @@ -49,6 +59,12 @@

@@ -74,7 +90,7 @@ Additional chemical information is retrieved from the internet if available.

-

pai

+

pai

Format

@@ -82,11 +98,11 @@ Additional chemical information is retrieved from the internet if available.

Fields

-

-

iso: ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides
alanwood: List of information retreived from www.alanwood.net/pesticides

+ +

iso: ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides
alanwood: List of information retreived from www.alanwood.net/pesticides

Examples

@@ -97,11 +113,11 @@ Additional chemical information is retrieved from the internet if available.

#> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N #> SMILES string $smiles: #> PubChem_Canonical -#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" +#> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" #> Molecular weight $mw: 215.7 #> PubChem synonyms (up to 10): -#> [1] "2256" "atrazine" "1912-24-9" "Atranex" "Fenatrol" -#> [6] "Atred" "Oleogesaprim" "Atazinax" "Atrasine" "Chromozin"

+#> [1] "2256" "atrazine" "1912-24-9" "Gesaprim" "Chromozin" +#> [6] "Oleogesaprim" "Aktikon" "Argezin" "Atazinax" "Atranex"

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png new file mode 100644 index 0000000..8731cf1 Binary files /dev/null and b/docs/reference/plot.chent-1.png differ diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index 3cc23d9..cc3b96b 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -18,19 +18,28 @@ + + + + + + + - + + + @@ -49,6 +58,12 @@

@@ -73,16 +88,21 @@

Plot method for chent objects

-

# S3 method for chent
+    # S3 method for chent
 plot(x, ...)
     
      Arguments
-    
-      x
-      The chent object to be plotted
-      ...
-      Further arguments passed to grid.picture
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    x The chent object to be plotted
... Further arguments passed to grid.picture
     
 
     Examples
@@ -92,14 +112,14 @@
 #> InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
 #> SMILES string $smiles:
 #>              PubChem_Canonical 
-#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
+#> "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
 #> Molecular weight $mw: 194.2 
 #> PubChem synonyms (up to 10):
-#>  [1] "2519"                    "caffeine"               
-#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
-#>  [5] "Methyltheobromine"       "Cafeina"                
-#>  [7] "Thein"                   "Koffein"                
-#>  [9] "Mateina"                 "Theine"

plot(caffeine)

+#> [1] "2519" "caffeine" +#> [3] "1,3,7-Trimethylxanthine" "58-08-2" +#> [5] "Guaranine" "Thein" +#> [7] "Cafeina" "Methyltheobromine" +#> [9] "Koffein" "Mateina"

plot(caffeine)

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/pp.html b/docs/reference/pp.html index 4569a6f..538b885 100644 --- a/docs/reference/pp.html +++ b/docs/reference/pp.html @@ -18,19 +18,28 @@ + + + + + + + - + + + @@ -49,6 +58,12 @@

@@ -73,7 +88,7 @@

An R6 class for holding information about a product with at least one active ingredient

-

pp

+

pp

Format

@@ -81,13 +96,13 @@

Fields

-

-

name: The name of the product
ais: A list of active ingredients
concentrations: The concentration of the ais
concentration_units: Defaults to g/L

+ +

name: The name of the product
ais: A list of active ingredients
concentrations: The concentration of the ais
concentration_units: Defaults to g/L

@@ -109,7 +124,7 @@

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index 29b215a..81fde0d 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -18,19 +18,28 @@ + + + + + + + - + + + @@ -49,6 +58,12 @@

@@ -73,16 +88,21 @@

Printing method for chent objects

-

# S3 method for chent
+    # 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

@@ -101,7 +121,7 @@

-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index d2da6b8..08966de 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -18,19 +18,28 @@ + + + + + + + - + + + @@ -49,6 +58,12 @@

@@ -73,16 +88,21 @@

Printing method for pai objects (pesticidal active ingredients)

-

# S3 method for pai
+    # 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

@@ -101,7 +121,7 @@

-

Site built with pkgdown.

+

Site built with pkgdown.

-- cgit v1.2.1