Man pages for rcdk
Interface to the 'CDK' Libraries

AtomsOperations on Atoms
bpdataBoiling Point Data
cdkFormula-classClass cdkFormula, ac class for handling molecular formula
cdk.versionGet the current CDK version used in the package.
compare.isotope.patternCompare isotope patterns.
convert.implicit.to.explicitConvert implicit hydrogens to explicit.
copy.image.to.clipboardcopy.image.to.clipboard
do.aromaticitydo.aromaticity
do.isotopesdo.isotopes
eval.atomic.descCompute descriptors for each atom in a molecule
eval.descCompute descriptor values for a set of molecules
generate.2d.coordinatesGenerate 2D coordinates for a molecule.
generate.formulagenerate.formula
generate.formula.itergenerate.formula.iter
get.adjacency.matrixGet adjacency matrix for a molecule.
get.alogpCompute ALogP for a molecule
get.atom.countGet the number of atoms in the molecule.
get.atomic.desc.namesGet class names for atomic descriptors
get.atomic.numberget.atomic.number
get.atom.indexget.atom.index
get.atomsGet the atoms from a molecule or bond.
get.bond.orderGet an object representing bond order
get.bondsGet the bonds in a molecule.
get.chargeget.charge
get.chem.object.builderGet the default chemical object builder.
get.connected.atomGet the atom connected to an atom in a bond.
get.connected.atomsget.connected.atoms
get.connection.matrixGet connection matrix for a molecule.
get.depictorget.depictor
get.desc.categoriesList available descriptor categories
get.desc.namesGet descriptor class names
get.element.typesObtain the type of stereo element support for atom.
get.exact.massget.exact.mass
get.exhaustive.fragmentsGenerate Bemis-Murcko Fragments
get.fingerprintGenerate molecular fingerprints
get.formal.chargeget.formal.charge
get.formulaget.formula
get.hydrogen.countget.hydrogen.count
get.isotope.pattern.generatorConstruct an isotope pattern generator.
get.isotope.pattern.similarityConstruct an isotope pattern similarity calculator.
get.isotopes.patternget.isotopes.pattern
get.largest.componentGets the largest component in a disconnected molecular graph.
get.mcsget.mcs
get.mol2formulaget.mol2formula
get.murcko.fragmentsGenerate Bemis-Murcko Fragments
get.natural.massget.natural.mass
get.point2dget.point2d
get.point3dget.point3d
get.propertiesGet all properties associated with a molecule.
get.propertyGet a property value of the molecule.
get.smilesGenerate a SMILES representation of a molecule.
get.smiles.parserGet a SMILES parser object.
get.stereocentersIdentify which atoms are stereocenters.
get.stereo.typesObtain the stereocenter type for atom.
get.symbolget.symbol
get.titleGet the title of the molecule.
get.total.chargeget.total.charge
get.total.formal.chargeget.total.formal.charge
get.total.hydrogen.countGet total number of implicit hydrogens in the molecule.
get.tpsaCompute TPSA for a molecule
get.volumeCompute volume of a molecule
get.xlogpCompute XLogP for a molecule
iload.moleculesLoad molecules using an iterator.
is.aliphaticis.aliphatic
is.aromaticis.aromatic
is.connectedTests whether the molecule is fully connected.
is.in.ringis.in.ring
is.neutralTests whether the molecule is neutral.
isvalid.formulaisvalid.formula
load.moleculesLoad molecular structures from disk or URL
matchesmatches
MoleculeOperations on molecules
parse.smilesParse SMILES strings into molecule objects.
rcdk-deprecatedDeprecated functions in the rcdk package.
remove.hydrogensRemove explicit hydrogens.
remove.propertyRemove a property associated with a molecule.
set.atom.typesset.atom.types
set.charge.formulaset.charge.formula
set.propertySet a property value of the molecule.
set.titleSet the title of the molecule.
smiles.flavorsGenerate flag for customizing SMILES generation.
view.image.2dview.image.2d
view.molecule.2dview.molecule.2d
view.tableview.table
write.moleculesWrite molecules to disk.
rcdk documentation built on Sept. 26, 2022, 5:09 p.m.