From aac6606d2aee79e547f725353a42266c00ed2299 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 6 Mar 2017 14:52:04 +0100 Subject: Switch to pkgdown and link to pkgdown.jrwb.de --- docs/reference/chent-22.png | Bin 0 -> 12574 bytes docs/reference/chent.html | 160 +++++++++++++++++++++++++++++++++++++ docs/reference/draw_svg.chent.html | 117 +++++++++++++++++++++++++++ docs/reference/index.html | 137 +++++++++++++++++++++++++++++++ docs/reference/pai.html | 133 ++++++++++++++++++++++++++++++ docs/reference/plot.chent-11.png | Bin 0 -> 12574 bytes docs/reference/plot.chent.html | 128 +++++++++++++++++++++++++++++ docs/reference/pp.html | 119 +++++++++++++++++++++++++++ docs/reference/print.chent.html | 111 +++++++++++++++++++++++++ docs/reference/print.pai.html | 111 +++++++++++++++++++++++++ 10 files changed, 1016 insertions(+) create mode 100644 docs/reference/chent-22.png create mode 100644 docs/reference/chent.html create mode 100644 docs/reference/draw_svg.chent.html create mode 100644 docs/reference/index.html create mode 100644 docs/reference/pai.html create mode 100644 docs/reference/plot.chent-11.png create mode 100644 docs/reference/plot.chent.html create mode 100644 docs/reference/pp.html create mode 100644 docs/reference/print.chent.html create mode 100644 docs/reference/print.pai.html (limited to 'docs/reference') diff --git a/docs/reference/chent-22.png b/docs/reference/chent-22.png new file mode 100644 index 0000000..69b3b08 Binary files /dev/null and b/docs/reference/chent-22.png differ diff --git a/docs/reference/chent.html b/docs/reference/chent.html new file mode 100644 index 0000000..15c4d10 --- /dev/null +++ b/docs/reference/chent.html @@ -0,0 +1,160 @@ + + + + + + + + +An R6 class for chemical entities with associated data — chent • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

An R6 class for chemical entities with associated data

+
+ + +

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
+ +

Format

+ +

An R6Class generator object

+ +

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
+

+ + +

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>
+#> Identifier $identifier 1-octanol 
+#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
+#> SMILES string $smiles:
+#>              user PubChem_Canonical 
+#>       "CCCCCCCCO"       "CCCCCCCCO" 
+#> Molecular weight $mw: 130.2 
+#> PubChem synonyms (up to 10):
+#>  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
+#>  [5] "Octyl alcohol"    "N-octanol"        "Capryl alcohol"   "n-Octyl alcohol" 
+#>  [9] "111-87-5"         "caprylic alcohol"
plot(oct)
caffeine <- chent$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
+#> 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] "2519"                    "caffeine"               
+#>  [3] "Guaranine"               "1,3,7-Trimethylxanthine"
+#>  [5] "Methyltheobromine"       "Cafeina"                
+#>  [7] "Thein"                   "Koffein"                
+#>  [9] "Mateina"                 "Theine"                 
plot(caffeine)
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html new file mode 100644 index 0000000..2cc3804 --- /dev/null +++ b/docs/reference/draw_svg.chent.html @@ -0,0 +1,117 @@ + + + + + + + + +Draw SVG graph from a chent object using RDKit — draw_svg.chent • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Draw SVG graph from a chent object using RDKit

+
+ + +

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
+
+ + +
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/index.html b/docs/reference/index.html new file mode 100644 index 0000000..e9dc7a8 --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,137 @@ + + + + + + + + +Function reference • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Function reference

+

version 0.2-5

+
+ +
+

Class definitions

+

R6 classes and their methods

+ + +

An R6 class for chemical entities with associated data

+ + +

Draw SVG graph from a chent object using RDKit

+ + +

Plot method for chent objects

+ + +

Printing method for chent objects

+ + +

An R6 class for pesticidal active ingredients and associated data

+ + +

Printing method for pai objects (pesticidal active ingredients)

+ + +

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

+ + +
+
+ + +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/pai.html b/docs/reference/pai.html new file mode 100644 index 0000000..4c143a1 --- /dev/null +++ b/docs/reference/pai.html @@ -0,0 +1,133 @@ + + + + + + + + +An R6 class for pesticidal active ingredients and associated data — pai • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

An R6 class for pesticidal active ingredients and associated data

+
+ + +

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

+ +

+

+
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

+ 
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 
+#> <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] "2256"         "atrazine"     "1912-24-9"    "Atranex"      "Fenatrol"    
+#>  [6] "Atred"        "Oleogesaprim" "Atazinax"     "Atrasine"     "Chromozin"
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/plot.chent-11.png b/docs/reference/plot.chent-11.png new file mode 100644 index 0000000..69b3b08 Binary files /dev/null and b/docs/reference/plot.chent-11.png differ diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html new file mode 100644 index 0000000..3cc23d9 --- /dev/null +++ b/docs/reference/plot.chent.html @@ -0,0 +1,128 @@ + + + + + + + + +Plot method for chent objects — plot.chent • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Plot method for chent objects

+
+ + +

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:
#> 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" 
+#> 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)
+
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/pp.html b/docs/reference/pp.html new file mode 100644 index 0000000..4569a6f --- /dev/null +++ b/docs/reference/pp.html @@ -0,0 +1,119 @@ + + + + + + + + +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

+
+ + +

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

+ + + 
pp
+ +

Format

+ +

An R6Class generator object.

+ +

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
+

+ + +
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html new file mode 100644 index 0000000..29b215a --- /dev/null +++ b/docs/reference/print.chent.html @@ -0,0 +1,111 @@ + + + + + + + + +Printing method for chent objects — print.chent • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Printing method for chent objects

+
+ + +

Printing method for chent objects

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

Arguments

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

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html new file mode 100644 index 0000000..d2da6b8 --- /dev/null +++ b/docs/reference/print.pai.html @@ -0,0 +1,111 @@ + + + + + + + + +Printing method for pai objects (pesticidal active ingredients) — print.pai • chents + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Printing method for pai objects (pesticidal active ingredients)

+
+ + +

Printing method for pai objects (pesticidal active ingredients)

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

Arguments

+
+
x
+
The chent object to be printed
+
...
+
Further arguments for compatibility with the S3 method
+
+ + +
+ +
+ + +
+ + + -- cgit v1.2.1