ChemmineOB: R interface to a subset of OpenBabel functionalities

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

AuthorKevin Horan, Thomas Girke
Date of publicationNone
MaintainerThomas Girke <thomas.girke@ucr.edu>
Licensefile LICENSE
Version1.12.0
https://github.com/girke-lab/ChemmineOB

View on Bioconductor

Functions

canonicalNumbering_OB Man page
convertFormat Man page
convertFormatFile Man page
exactMass_OB Man page
[<-,ExternalReference-method Man page
[,ExternalReference-method Man page
fingerprint_OB Man page
forEachMol Man page
length,SWIGArray-method Man page
$,_p_OpenBabel__AliasData-method Man page
$,_p_OpenBabel__AliasData-method Man page
[[<-,_p_OpenBabel__DoubleType,character-method Man page
$<-,_p_OpenBabel__DoubleType-method Man page
$,_p_OpenBabel__DoubleType-method Man page
$,_p_OpenBabel__FastSearchIndexer-method Man page
$,_p_OpenBabel__FastSearch-method Man page
[[<-,_p_OpenBabel__FptIndexHeader,character-method Man page
$<-,_p_OpenBabel__FptIndexHeader-method Man page
$,_p_OpenBabel__FptIndexHeader-method Man page
$,_p_OpenBabel__matrix3x3-method Man page
$,_p_OpenBabel__OBAngleData-method Man page
$,_p_OpenBabel__OBAngle-method Man page
$,_p_OpenBabel__OBAromaticTyper-method Man page
[[<-,_p_OpenBabel__OBAtomAtomIter,character-method Man page
$<-,_p_OpenBabel__OBAtomAtomIter-method Man page
$,_p_OpenBabel__OBAtomAtomIter-method Man page
[[<-,_p_OpenBabel__OBAtomBondIter,character-method Man page
$<-,_p_OpenBabel__OBAtomBondIter-method Man page
$,_p_OpenBabel__OBAtomBondIter-method Man page
[[<-,_p_OpenBabel__OBAtom,character-method Man page
$,_p_OpenBabel__OBAtomClassData-method Man page
$<-,_p_OpenBabel__OBAtom-method Man page
$,_p_OpenBabel__OBAtom-method Man page
$,_p_OpenBabel__OBAtomTyper-method Man page
$,_p_OpenBabel__OBBase-method Man page
$,_p_OpenBabel__OBBitVec-method Man page
[[<-,_p_OpenBabel__OBBond,character-method Man page
$<-,_p_OpenBabel__OBBond-method Man page
$,_p_OpenBabel__OBBond-method Man page
$,_p_OpenBabel__OBBuilder-method Man page
$,_p_OpenBabel__OBChainsParser-method Man page
$,_p_OpenBabel__OBChiralData-method Man page
$,_p_OpenBabel__OBCommentData-method Man page
$,_p_OpenBabel__OBConformerData-method Man page
$,_p_OpenBabel__OBConversion-method Man page
$,_p_OpenBabel__OBDescriptor-method Man page
$,_p_OpenBabel__OBDOSData-method Man page
$,_p_OpenBabel__OBElectronicTransitionData-method Man page
$,_p_OpenBabel__OBElement-method Man page
$,_p_OpenBabel__OBElementTable-method Man page
$,_p_OpenBabel__OBError-method Man page
$,_p_OpenBabel__OBExternalBondData-method Man page
$,_p_OpenBabel__OBExternalBond-method Man page
[[<-,_p_OpenBabel__OBFFCalculation2,character-method Man page
$<-,_p_OpenBabel__OBFFCalculation2-method Man page
$,_p_OpenBabel__OBFFCalculation2-method Man page
[[<-,_p_OpenBabel__OBFFCalculation3,character-method Man page
$<-,_p_OpenBabel__OBFFCalculation3-method Man page
$,_p_OpenBabel__OBFFCalculation3-method Man page
[[<-,_p_OpenBabel__OBFFCalculation4,character-method Man page
$<-,_p_OpenBabel__OBFFCalculation4-method Man page
$,_p_OpenBabel__OBFFCalculation4-method Man page
[[<-,_p_OpenBabel__OBFFConstraint,character-method Man page
$<-,_p_OpenBabel__OBFFConstraint-method Man page
$,_p_OpenBabel__OBFFConstraint-method Man page
$,_p_OpenBabel__OBFFConstraints-method Man page
[[<-,_p_OpenBabel__OBFFParameter,character-method Man page
$<-,_p_OpenBabel__OBFFParameter-method Man page
$,_p_OpenBabel__OBFFParameter-method Man page
$,_p_OpenBabel__OBFingerprint-method Man page
$,_p_OpenBabel__OBForceField-method Man page
$,_p_OpenBabel__OBFormat-method Man page
$,_p_OpenBabel__OBGenericData-method Man page
$,_p_OpenBabel__OBGlobalDataBase-method Man page
$,_p_OpenBabel__OBGridData-method Man page
[[<-,_p_OpenBabel__OBInternalCoord,character-method Man page
$<-,_p_OpenBabel__OBInternalCoord-method Man page
$,_p_OpenBabel__OBInternalCoord-method Man page
$,_p_OpenBabel__OBIsotopeTable-method Man page
$,_p_OpenBabel__OBMatrixData-method Man page
$,_p_OpenBabel__OBMessageHandler-method Man page
$,_p_OpenBabel__OBMolAngleIter-method Man page
[[<-,_p_OpenBabel__OBMolAtomBFSIter,character-method Man page
$<-,_p_OpenBabel__OBMolAtomBFSIter-method Man page
$,_p_OpenBabel__OBMolAtomBFSIter-method Man page
[[<-,_p_OpenBabel__OBMolAtomDFSIter,character-method Man page
$<-,_p_OpenBabel__OBMolAtomDFSIter-method Man page
$,_p_OpenBabel__OBMolAtomDFSIter-method Man page
[[<-,_p_OpenBabel__OBMolAtomIter,character-method Man page
$<-,_p_OpenBabel__OBMolAtomIter-method Man page
$,_p_OpenBabel__OBMolAtomIter-method Man page
[[<-,_p_OpenBabel__OBMolBondBFSIter,character-method Man page
$<-,_p_OpenBabel__OBMolBondBFSIter-method Man page
$,_p_OpenBabel__OBMolBondBFSIter-method Man page
[[<-,_p_OpenBabel__OBMolBondIter,character-method Man page
$<-,_p_OpenBabel__OBMolBondIter-method Man page
$,_p_OpenBabel__OBMolBondIter-method Man page
$,_p_OpenBabel__OBMol-method Man page
$,_p_OpenBabel__OBMolPairIter-method Man page
[[<-,_p_OpenBabel__OBMolRingIter,character-method Man page
$<-,_p_OpenBabel__OBMolRingIter-method Man page
$,_p_OpenBabel__OBMolRingIter-method Man page
$,_p_OpenBabel__OBMolTorsionIter-method Man page
$,_p_OpenBabel__OBOp-method Man page
$,_p_OpenBabel__OBOrbitalData-method Man page
$,_p_OpenBabel__OBOrbital-method Man page
$,_p_OpenBabel__OBPairData-method Man page
$,_p_OpenBabel__OBPlugin-method Man page
$,_p_OpenBabel__OBRandom-method Man page
[[<-,_p_OpenBabel__OBResidueAtomIter,character-method Man page
$<-,_p_OpenBabel__OBResidueAtomIter-method Man page
$,_p_OpenBabel__OBResidueAtomIter-method Man page
$,_p_OpenBabel__OBResidueData-method Man page
$,_p_OpenBabel__OBResidueIter-method Man page
$,_p_OpenBabel__OBResidue-method Man page
[[<-,_p_OpenBabel__OBRing,character-method Man page
$,_p_OpenBabel__OBRingData-method Man page
$<-,_p_OpenBabel__OBRing-method Man page
$,_p_OpenBabel__OBRing-method Man page
$,_p_OpenBabel__OBRingSearch-method Man page
$,_p_OpenBabel__OBRingTyper-method Man page
$,_p_OpenBabel__OBRotationData-method Man page
$,_p_OpenBabel__OBRTree-method Man page
$,_p_OpenBabel__OBSerialNums-method Man page
$,_p_OpenBabel__OBSetData-method Man page
$,_p_OpenBabel__OBSmartsMatcher-method Man page
$,_p_OpenBabel__OBSmartsPattern-method Man page
$,_p_OpenBabel__OBSqrtTbl-method Man page
$,_p_OpenBabel__OBSSMatch-method Man page
$,_p_OpenBabel__OBStopwatch-method Man page
$,_p_OpenBabel__OBSymmetryData-method Man page
$,_p_OpenBabel__OBTorsionData-method Man page
$,_p_OpenBabel__OBTorsion-method Man page
$,_p_OpenBabel__OBTypeTable-method Man page
[[<-,_p_OpenBabel__OBUnitCell,character-method Man page
$<-,_p_OpenBabel__OBUnitCell-method Man page
$,_p_OpenBabel__OBUnitCell-method Man page
$,_p_OpenBabel__OBVectorData-method Man page
$,_p_OpenBabel__OBVibrationData-method Man page
$,_p_OpenBabel__OBVirtualBond-method Man page
$,_p_OpenBabel__SpaceGroup-method Man page
$,_p_OpenBabel__transform3d-method Man page
$,_p_OpenBabel__vector3-method Man page
prop_OB Man page
[[<-,_p_std__pairT_unsigned_int_unsigned_int_t,character-method Man page
$<-,_p_std__pairT_unsigned_int_unsigned_int_t-method Man page
$,_p_std__pairT_unsigned_int_unsigned_int_t-method Man page
$,_p_std__vectorT_double_std__allocatorT_double_t_t-method Man page
$,_p_std__vectorT_int_std__allocatorT_int_t_t-method Man page
$,_p_std__vectorT_OpenBabel__OBBond_std__allocatorT_OpenBabel__O Man page
$,_p_std__vectorT_OpenBabel__OBGenericData_p_std__allocatorT_Ope Man page
$,_p_std__vectorT_OpenBabel__OBInternalCoord_p_std__allocatorT_O Man page
$,_p_std__vectorT_OpenBabel__OBMol_std__allocatorT_OpenBabel__OB Man page
$,_p_std__vectorT_OpenBabel__OBResidue_std__allocatorT_OpenBabel Man page
$,_p_std__vectorT_OpenBabel__OBRing_p_std__allocatorT_OpenBabel_ Man page
$,_p_std__vectorT_OpenBabel__OBRing_std__allocatorT_OpenBabel__O Man page
$,_p_std__vectorT_OpenBabel__vector3_std__allocatorT_OpenBabel__ Man page
$,_p_std__vectorT_std__pairT_unsigned_int_unsigned_int_t_std__al Man page
$,_p_std__vectorT_std__string_std__allocatorT_std__string_t_t-me Man page
$,_p_std__vectorT_std__vectorT_int_std__allocatorT_int_t_t_std__ Man page
$,_p_std__vectorT_std__vectorT_OpenBabel__vector3_std__allocator Man page
$,_p_std__vectorT_std__vectorT_std__pairT_unsigned_int_unsigned_ Man page
$,_p_std__vectorT_unsigned_int_std__allocatorT_unsigned_int_t_t- Man page
$,_p_stringp-method Man page
smartsSearch_OB Man page

Files

ChemmineOB/DESCRIPTION
ChemmineOB/INSTALL
ChemmineOB/LICENSE
ChemmineOB/NAMESPACE
ChemmineOB/R
ChemmineOB/R/ChemmineOB.R ChemmineOB/R/wrappers.R
ChemmineOB/README.md
ChemmineOB/build
ChemmineOB/build/vignette.rds
ChemmineOB/cleanup
ChemmineOB/configure
ChemmineOB/configure.ac
ChemmineOB/inst
ChemmineOB/inst/NEWS.Rd
ChemmineOB/inst/doc
ChemmineOB/inst/doc/ChemmineOB.R
ChemmineOB/inst/doc/ChemmineOB.Rmd
ChemmineOB/inst/doc/ChemmineOB.html
ChemmineOB/inst/openbabel_data
ChemmineOB/inst/openbabel_data/CMakeLists.txt
ChemmineOB/inst/openbabel_data/MACCS.txt
ChemmineOB/inst/openbabel_data/SMARTS_InteLigand.txt
ChemmineOB/inst/openbabel_data/UFF.prm
ChemmineOB/inst/openbabel_data/aromatic.txt
ChemmineOB/inst/openbabel_data/atomtyp.txt
ChemmineOB/inst/openbabel_data/babel_povray3.inc
ChemmineOB/inst/openbabel_data/bin2hex.pl
ChemmineOB/inst/openbabel_data/bondtyp.txt
ChemmineOB/inst/openbabel_data/element.txt
ChemmineOB/inst/openbabel_data/fragments.txt
ChemmineOB/inst/openbabel_data/gaff.dat
ChemmineOB/inst/openbabel_data/gaff.prm
ChemmineOB/inst/openbabel_data/genheaders.sh
ChemmineOB/inst/openbabel_data/ghemical.prm
ChemmineOB/inst/openbabel_data/isotope-small.txt
ChemmineOB/inst/openbabel_data/isotope.txt
ChemmineOB/inst/openbabel_data/logp.txt
ChemmineOB/inst/openbabel_data/mm2.prm
ChemmineOB/inst/openbabel_data/mmff94.ff
ChemmineOB/inst/openbabel_data/mmff94s.ff
ChemmineOB/inst/openbabel_data/mmffang.par
ChemmineOB/inst/openbabel_data/mmffbndk.par
ChemmineOB/inst/openbabel_data/mmffbond.par
ChemmineOB/inst/openbabel_data/mmffchg.par
ChemmineOB/inst/openbabel_data/mmffdef.par
ChemmineOB/inst/openbabel_data/mmffdfsb.par
ChemmineOB/inst/openbabel_data/mmffoop.par
ChemmineOB/inst/openbabel_data/mmffpbci.par
ChemmineOB/inst/openbabel_data/mmffprop.par
ChemmineOB/inst/openbabel_data/mmffs_oop.par
ChemmineOB/inst/openbabel_data/mmffs_tor.par
ChemmineOB/inst/openbabel_data/mmffstbn.par
ChemmineOB/inst/openbabel_data/mmfftor.par
ChemmineOB/inst/openbabel_data/mmffvdw.par
ChemmineOB/inst/openbabel_data/mpC.txt
ChemmineOB/inst/openbabel_data/mr.txt
ChemmineOB/inst/openbabel_data/patterns.txt
ChemmineOB/inst/openbabel_data/phmodel.txt
ChemmineOB/inst/openbabel_data/plugindefines.txt
ChemmineOB/inst/openbabel_data/psa.txt
ChemmineOB/inst/openbabel_data/qeq.txt
ChemmineOB/inst/openbabel_data/resdata.txt
ChemmineOB/inst/openbabel_data/ringtyp.txt
ChemmineOB/inst/openbabel_data/space-groups.txt
ChemmineOB/inst/openbabel_data/space-groups.xsl
ChemmineOB/inst/openbabel_data/splash.png
ChemmineOB/inst/openbabel_data/superatom.txt
ChemmineOB/inst/openbabel_data/svgformat.script
ChemmineOB/inst/openbabel_data/templates.sdf
ChemmineOB/inst/openbabel_data/torlib.txt
ChemmineOB/inst/openbabel_data/types.txt
ChemmineOB/inst/unitTests
ChemmineOB/inst/unitTests/test_conversions.R
ChemmineOB/inst/unitTests/test_main.R
ChemmineOB/man
ChemmineOB/man/OB-classes.Rd ChemmineOB/man/canonicalNumbering_OB.Rd ChemmineOB/man/convertFormat.Rd ChemmineOB/man/convertFormatFile.Rd ChemmineOB/man/exactMass_OB.Rd ChemmineOB/man/fingerprint_OB.Rd ChemmineOB/man/forEachMol.Rd ChemmineOB/man/prop_OB.Rd ChemmineOB/man/smartsSearch_OB.Rd
ChemmineOB/src
ChemmineOB/src/ChemmineOB.cpp
ChemmineOB/src/Makevars.in
ChemmineOB/src/Makevars.win
ChemmineOB/src/canonical.cpp
ChemmineOB/tests
ChemmineOB/tests/runTests.R
ChemmineOB/vignettes
ChemmineOB/vignettes/ChemmineOB.Rmd
ChemmineOB/vignettes/ChemmineOB.Rmd_bootstrap
ChemmineOB/vignettes/Makefile_bootstrap
ChemmineOB/vignettes/header.html
ChemmineOB/vignettes/html.template_bootstrap
ChemmineOB/vignettes/references.bib

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