From 62c0a43b968ff36786c73396e030a1de4ad4f326 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 6 Mar 2017 14:58:00 +0100 Subject: Delete leftovers from staticdocs, rerun pkgdown --- docs/chent.html | 180 -------------------------------------------------------- 1 file changed, 180 deletions(-) delete mode 100644 docs/chent.html (limited to 'docs/chent.html') diff --git a/docs/chent.html b/docs/chent.html deleted file mode 100644 index 0f4a43d..0000000 --- a/docs/chent.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - -chent. chents 0.2-3 - - - - - - - - - - - - - - - -
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An R6 class for chemical entities with associated data

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Usage

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chent
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Format

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An R6Class generator object

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Description

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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.

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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'

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smiles
SMILES code, with attribute 'source'

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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, if installed and -configured for use with PythonInR

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Picture
Graph as a picture object obtained using grImport

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chyaml
List of information obtained from a YAML file

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degradation
List of degradation endpoints

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Examples

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

-PubChem:
-http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
-Found 1 entries in PubChem, using the first one.
-http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON
-http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
-Loading required namespace: PythonInR
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-Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) 
-[GCC 4.9.2]
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-Trying to get chemical information from RDKit using user SMILES
-CCCCCCCCO
-Did not find chyaml file ./1-octanol.yaml
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print(oct)

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<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] "N-octanol"        "Octyl alcohol"    "Capryl alcohol"   "n-Octyl alcohol" 
- [9] "caprylic alcohol" "111-87-5"        
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plot(oct)

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caffeine <- chent$new("caffeine")

-PubChem:
-http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
-Found 1 entries in PubChem, using the first one.
-http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON
-http://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
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print(caffeine)

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<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] "1,3,7-Trimethylxanthine" "Methyltheobromine"      
- [5] "Guaranine"               "Cafeina"                
- [7] "Koffein"                 "Mateina"                
- [9] "Thein"                   "Theine"                 
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plot(caffeine)

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