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
do.typingdo.typing
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 the atomic number of the atom.
get.atom.indexGet the index of an atom in a molecule. Acces the index of an...
get.atomsGet the atoms from a molecule or bond.
get.bondsGet the bonds in a molecule.
get.chargeGet the charge on the atom. This method returns the partial...
get.chem.object.builderGet the default chemical object builder.
get.connected.atomGet the atom connected to an atom in a bond.
get.connected.atomsGet atoms connected to the specified atom Returns a 'list" of...
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 the formal charge on the atom. By default the formal...
get.formulaget.formula
get.hydrogen.countGet the implicit hydrogen count for the atom. This method...
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 the 2D coordinates of the atom. In case, coordinates are...
get.point3dGet the 3D coordinates of the atom. In case, coordinates are...
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 the atomic symbol of the atom. Get the atomic symbol of...
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.aliphaticTests whether an atom is aliphatic. This assumes that the...
is.aromaticTests whether an atom is aromatic. This assumes that the...
is.connectedTests whether the molecule is fully connected.
is.in.ringTests whether an atom is in a ring. This assumes that the...
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.
remove.hydrogensRemove explicit hydrogens.
remove.propertyRemove a property associated with a molecule.
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
write.moleculesWrite molecules to disk.
rcdk documentation built on March 13, 2020, 1:30 a.m.