From 40d06320e097434a924c0d57b26e5e1a7574625c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Sep 2016 16:11:25 +0200 Subject: Add staticdocs --- docs/chent.html | 180 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 180 insertions(+) create mode 100644 docs/chent.html (limited to 'docs/chent.html') diff --git a/docs/chent.html b/docs/chent.html new file mode 100644 index 0000000..0f4a43d --- /dev/null +++ b/docs/chent.html @@ -0,0 +1,180 @@ + + + + +chent. chents 0.2-3 + + + + + + + + + + + + + + + + + + +
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An R6 class for chemical entities with associated data

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+

Usage

+
chent
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+

Format

+ +

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

+ +

chyaml
List of information obtained from a YAML file

+ +

degradation
List of degradation endpoints

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Examples

+
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 + +Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) +[GCC 4.9.2] + +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 $mw: 130.2 +PubChem synonyms (up to 10): + [1] "957" "1-octanol" "Octan-1-ol" "octanol" + [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "n-Octyl alcohol" + [9] "caprylic alcohol" "111-87-5" +
+
plot(oct)
+
caffeine <- chent$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 +
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] "1,3,7-Trimethylxanthine" "Methyltheobromine" + [5] "Guaranine" "Cafeina" + [7] "Koffein" "Mateina" + [9] "Thein" "Theine" +
+
plot(caffeine)
+

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