From 79123acfdd9a9b905a5b177e2b7aa0d604e52267 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 Nov 2021 00:22:03 +0100 Subject: Add plot example, update static docs --- docs/reference/pai.html | 155 +++++++++++++++++++++++++++++++++++------------- 1 file changed, 113 insertions(+), 42 deletions(-) (limited to 'docs/reference/pai.html') diff --git a/docs/reference/pai.html b/docs/reference/pai.html index e240e11..e5ecb99 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -8,21 +8,29 @@ An R6 class for pesticidal active ingredients and associated data — pai • chents + - + - - + + + + + + + - + + - + - - + + + @@ -30,11 +38,11 @@ - + - + @@ -48,9 +56,10 @@ Additional chemical information is retrieved from the internet if available." /> + - +
@@ -72,7 +81,7 @@ Additional chemical information is retrieved from the internet if available." />
  • - +
    • @@ -80,11 +89,10 @@ Additional chemical information is retrieved from the internet if available." /> Reference
-
  • - - + +
    • @@ -95,6 +103,7 @@ Additional chemical information is retrieved from the internet if available." />
+
@@ -106,30 +115,92 @@ Additional chemical information is retrieved from the internet if available." />
-

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

-
- 
pai
- + +

Format

An R6Class generator object

- -

Fields

+

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

-
-
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

-
- +

Public methods

+ + +

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

- 
atr <- pai$new("atrazine")
#> alanwood.net:
#> Querying atrazine.html
#> PubChem:
#> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/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
-#> CCNC1=NC(=NC(=N1)Cl)NC(C)C
#> Did not find chyaml file ./atrazine.yaml
print(atr)
#> <pai> with ISO common name $iso atrazine 
+    
atr <- pai$new("atrazine")
+
#> 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
print(atr)
+
#> <pai> with ISO common name $iso atrazine 
 #> <chent>
 #> Identifier $identifier atrazine 
 #> InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
@@ -138,36 +209,36 @@ Additional chemical information is retrieved from the internet if available.

 #> "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
 #> Molecular weight $mw: 215.7 
 #> PubChem synonyms (up to 10):
-#>  [1] "2256"         "atrazine"     "1912-24-9"    "Gesaprim"     "Chromozin"   
-#>  [6] "Oleogesaprim" "Aktikon"      "Argezin"      "Atazinax"     "Atranex"     

+#>  [1] "atrazine"     "1912-24-9"    "Gesaprim"     "Oleogesaprim" "Chromozin"   
+#>  [6] "Aktikon"      "Atrazin"      "Argezin"      "Atazinax"     "Atranex"     
if (!is.null(atr$Picture)) {
+  plot(atr)
+}
+
- + + + -- cgit v1.2.3