From f908377f1de2e04ca3720d10084169c46a477ce2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 28 Sep 2015 21:34:23 +0200 Subject: Several changes heading for a release to the public - Add tests - Add staticdocs - Documentation improvements - Several small code improvements --- inst/web/chent.html | 156 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 156 insertions(+) create mode 100644 inst/web/chent.html (limited to 'inst/web/chent.html') diff --git a/inst/web/chent.html b/inst/web/chent.html new file mode 100644 index 0000000..f2adb6b --- /dev/null +++ b/inst/web/chent.html @@ -0,0 +1,156 @@ + + + + +chent. chents 0.2-1 + + + + + + + + + + + + + + + +
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+ chents 0.2-1 +
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+ +

An R6 class for chemical entities with associated data

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+

Usage

+ 
chent
+ +
+

Format

+ +

An R6Class generator object

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+

Description

+ +

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.

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+

Fields

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identifier
The identifier that was used to initiate the object, with attribute 'source'

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inchikey
InChI Key, with attribute 'source'

+ +

smiles
SMILES code, with attribute 'source'

+ +

mw
Molecular weight, with attribute 'source'

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pubchem
List of information retreived from PubChem

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rdkit
List of information obtained with RDKit

+ +

Picture
Graph as a picture object obtained using grImport

+ +

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Examples

+ 
oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")
+oct$try_pubchem()
+

+http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&db=pccompound&term=1-octanol
+Found 1 entries in PubChem, using the first one.
+http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&db=pccompound&ID=957
+
print(oct)
+

+
<chent>
+Identifier $identifier 1-octanol 
+InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
+SMILES string $smiles CCCCCCCCO 
+Molecular weight $mw: 130.2 
+PubChem synonyms (first 10):
+ [1] "1-octanol"        "Octan-1-ol"       "octanol"          "N-octanol"        "Capryl alcohol"   "Octyl alcohol"   
+ [7] "n-Octyl alcohol"  "caprylic alcohol" "Heptyl carbinol"  "1-Hydroxyoctane" 
+

+
plot(oct)
+

+
caffeine <- chent$new("caffeine", source = "pubchem")
+

+http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&db=pccompound&term=caffeine
+Found 217 entries in PubChem, using the first one.
+http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&db=pccompound&ID=1188
+
print(caffeine)
+

+
<chent>
+Identifier $identifier caffeine 
+InChI Key $inchikey LRFVTYWOQMYALW-UHFFFAOYSA-N 
+SMILES string $smiles C1=NC2=C(N1)C(=O)NC(=O)N2 
+Molecular weight $mw: 152.1 
+PubChem synonyms (first 10):
+ [1] "xanthine"            "2,6-Dihydroxypurine" "69-89-6"             "Xanthin"             "2,6-dioxopurine"    
+ [6] "Pseudoxanthine"      "Isoxanthine"         "Xanthic oxide"       "1H-Purine-2,6-diol"  "Purine-2,6-diol"    
+

+
caffeine$get_rdkit()
+plot(caffeine)
+

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+ + \ No newline at end of file -- cgit v1.2.1