From aa80ce4f46f9ff1a2851ba9ba873a55a8f6ebc6d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 19 Feb 2019 17:17:48 +0100 Subject: Change package URL to github to get source code links --- docs/reference/chent-1.png | Bin 34969 -> 34374 bytes docs/reference/chent-22.png | Bin 12574 -> 0 bytes docs/reference/chent.html | 81 +++++++++++------ docs/reference/draw_svg.chent.html | 60 +++++++++---- docs/reference/index.html | 180 ++++++++++++++++++++----------------- docs/reference/pai.html | 58 ++++++++---- docs/reference/plot.chent-1.png | Bin 34969 -> 34374 bytes docs/reference/plot.chent-11.png | Bin 12574 -> 0 bytes docs/reference/plot.chent.html | 68 +++++++++----- docs/reference/pp.html | 56 ++++++++---- docs/reference/print.chent.html | 60 +++++++++---- docs/reference/print.pai.html | 60 +++++++++---- 12 files changed, 406 insertions(+), 217 deletions(-) delete mode 100644 docs/reference/chent-22.png delete mode 100644 docs/reference/plot.chent-11.png (limited to 'docs/reference') diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png index 8731cf1..a1798d9 100644 Binary files a/docs/reference/chent-1.png and b/docs/reference/chent-1.png differ diff --git a/docs/reference/chent-22.png b/docs/reference/chent-22.png deleted file mode 100644 index 69b3b08..0000000 Binary files a/docs/reference/chent-22.png and /dev/null differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html index ef683ef..aa367f6 100644 --- a/docs/reference/chent.html +++ b/docs/reference/chent.html @@ -1,6 +1,6 @@ - + @@ -9,32 +9,39 @@ An R6 class for chemical entities with associated data — chent • chents - + - - + + - + - + + + + - - - + + + + + + - + + @@ -80,17 +98,21 @@ python bindings are installed and configured for use with PythonInR." /> -
+

An R6 class for chemical entities with associated data

+ Source: R/chent.R +
+

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 and configured for use with PythonInR.

+ 
chent
@@ -113,16 +135,21 @@ configured for use with PythonInR

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

+
p0

Vapour pressure in Pa

+
cwsat

Water solubility in mg/L

chyaml

List of information obtained from a YAML file

-
degradation

List of degradation endpoints

+
soil_degradation

Dataframe of modelling DT50 values

+
soil_ff

Dataframe of formation fractions

+
soil_sorption

Dataframe of soil sorption data

+
PUF

Plant uptake factor

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 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>
+#> Initialize Python Version 2.7.13 (default, Sep 26 2018, 18:42:22) 
+#> [GCC 6.3.0 20170516]
#> Trying to get chemical information from RDKit using User SMILES
+#> CCCCCCCCO
#> Lade nötigen Namensraum: 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:
@@ -131,9 +158,9 @@ configured for use with PythonInR

 #> Molecular weight $mw: 130.2 
 #> PubChem synonyms (up to 10):
 #>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
-#>  [5] "Octyl alcohol"    "N-octanol"        "111-87-5"         "Capryl alcohol"  
-#>  [9] "caprylic alcohol" "n-Octyl alcohol" 
plot(oct)
caffeine <- chent$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>
+#>  [5] "111-87-5"         "N-octanol"        "Capryl alcohol"   "Octyl 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:
@@ -142,10 +169,10 @@ configured for use with PythonInR

 #> Molecular weight $mw: 194.2 
 #> PubChem synonyms (up to 10):
 #>  [1] "2519"                    "caffeine"               
-#>  [3] "1,3,7-Trimethylxanthine" "58-08-2"                
-#>  [5] "Guaranine"               "Thein"                  
+#>  [3] "58-08-2"                 "Guaranine"              
+#>  [5] "1,3,7-Trimethylxanthine" "Thein"                  
 #>  [7] "Cafeina"                 "Methyltheobromine"      
-#>  [9] "Koffein"                 "Mateina"                
plot(caffeine)
+#> [9] "Koffein" "Mateina"
plot(caffeine)
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

-
+ + + diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html index 5342eca..54fec7c 100644 --- a/docs/reference/draw_svg.chent.html +++ b/docs/reference/draw_svg.chent.html @@ -1,6 +1,6 @@ - + @@ -9,30 +9,37 @@ Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents - + - - + + - + - + + + + - - - + + + + + + - + + @@ -78,20 +96,24 @@ -
+

Draw SVG graph from a chent object using RDKit

+ Source: R/chent.R +
+

Draw SVG graph from a chent object using RDKit

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

Arguments

+

Arguments

@@ -133,11 +155,13 @@
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

- + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 29771c9..e05a1c4 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,6 +1,6 @@ - + @@ -9,27 +9,34 @@ Function reference • chents - + - - + + - + - + + + + - - - + + + + + + - + + @@ -75,76 +93,72 @@ -
-
+
+
-

- Reference - version 0.2-6 -

+

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

-

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

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

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

-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

-
+ + + diff --git a/docs/reference/pai.html b/docs/reference/pai.html index 30a5b77..d90bcc9 100644 --- a/docs/reference/pai.html +++ b/docs/reference/pai.html @@ -1,6 +1,6 @@ - + @@ -9,31 +9,38 @@ An R6 class for pesticidal active ingredients and associated data — pai • chents - + - - + + - + - + + + + - - - + + + + + + - + + @@ -79,16 +97,20 @@ Additional chemical information is retrieved from the internet if available." /> -
+

An R6 class for pesticidal active ingredients and associated data

+ Source: R/chent.R +
+

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
@@ -107,7 +129,7 @@ Additional chemical information is retrieved from the internet if available.

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 
+#> 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 
@@ -139,11 +161,13 @@ Additional chemical information is retrieved from the internet if available.

 

 
 

-  
Site built with pkgdown.

+  
Site built with pkgdown 1.3.0.

 

-
+ + + diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png index 8731cf1..a1798d9 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-11.png b/docs/reference/plot.chent-11.png deleted file mode 100644 index 69b3b08..0000000 Binary files a/docs/reference/plot.chent-11.png and /dev/null differ diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html index cc3b96b..cde7a87 100644 --- a/docs/reference/plot.chent.html +++ b/docs/reference/plot.chent.html @@ -1,6 +1,6 @@ - + @@ -9,30 +9,37 @@ Plot method for chent objects — plot.chent • chents - + - - + + - + - + + + + - - - + + + + + + - + +
@@ -78,20 +96,24 @@ -
+

Plot method for chent objects

+ Source: R/chent.R +
+

Plot method for chent objects

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

Arguments

+

Arguments

@@ -107,7 +129,7 @@

Examples

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>
+#> 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:
@@ -116,10 +138,10 @@
 #> Molecular weight $mw: 194.2 
 #> PubChem synonyms (up to 10):
 #>  [1] "2519"                    "caffeine"               
-#>  [3] "1,3,7-Trimethylxanthine" "58-08-2"                
-#>  [5] "Guaranine"               "Thein"                  
+#>  [3] "58-08-2"                 "Guaranine"              
+#>  [5] "1,3,7-Trimethylxanthine" "Thein"                  
 #>  [7] "Cafeina"                 "Methyltheobromine"      
-#>  [9] "Koffein"                 "Mateina"                
plot(caffeine)
+#> [9] "Koffein" "Mateina"
plot(caffeine)
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

- + + + diff --git a/docs/reference/pp.html b/docs/reference/pp.html index 538b885..8dbed29 100644 --- a/docs/reference/pp.html +++ b/docs/reference/pp.html @@ -1,6 +1,6 @@ - + @@ -9,30 +9,37 @@ R6 class for holding a product with at least one active ingredient — pp • chents - + - - + + - + - + + + + - - - + + + + + + - + + @@ -78,15 +96,19 @@ -
+

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

+ Source: R/chent.R +
+

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

+ 
pp
@@ -124,11 +146,13 @@
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

-
+ + + diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html index 81fde0d..8ab91bc 100644 --- a/docs/reference/print.chent.html +++ b/docs/reference/print.chent.html @@ -1,6 +1,6 @@ - + @@ -9,30 +9,37 @@ Printing method for chent objects — print.chent • chents - + - - + + - + - + + + + - - - + + + + + + - + +
@@ -78,20 +96,24 @@ -
+

Printing method for chent objects

+ Source: R/chent.R +
+

Printing method for chent objects

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

Arguments

+

Arguments

@@ -121,11 +143,13 @@
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

- + + + diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html index 08966de..7f8c6f3 100644 --- a/docs/reference/print.pai.html +++ b/docs/reference/print.pai.html @@ -1,6 +1,6 @@ - + @@ -9,30 +9,37 @@ Printing method for pai objects (pesticidal active ingredients) — print.pai • chents - + - - + + - + - + + + + - - - + + + + + + - + + @@ -78,20 +96,24 @@ -
+

Printing method for pai objects (pesticidal active ingredients)

+ Source: R/chent.R +
+

Printing method for pai objects (pesticidal active ingredients)

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

Arguments

+

Arguments

@@ -121,11 +143,13 @@
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

- + + + -- cgit v1.2.1