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.html | 81 ++++++++++++++++++++++++++++++++--------------- 1 file changed, 55 insertions(+), 26 deletions(-) (limited to 'docs/reference/chent.html') 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.

-
+ + + -- cgit v1.2.1