Interface to the 'CDK' Libraries


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Documentation for package ‘rcdk’ version 3.4.7.1

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bpdata Boiling Point Data
cdk.version Get Current CDK Version
cdkFormula-class Class cdkFormula, a class for handling molecular formula
charge Get the Total Charges for the Molecule
compare.isotope.pattern Compare isotope patterns.
convert.implicit.to.explicit Operations on molecules
copy.image.to.clipboard View and Copy 2D Structure Diagrams
depict View and Copy 2D Structure Diagrams
do.aromaticity Perform Aromaticity Detection, atom typing or isotopic configuration
do.isotopes Perform Aromaticity Detection, atom typing or isotopic configuration
do.typing Perform Aromaticity Detection, atom typing or isotopic configuration
eval.atomic.desc Evaluate an Atomic Descriptor
eval.desc Evaluate a Molecular Descriptor
fragment Molecule Fragmentation Methods
generate.2d.coordinates Generate 2D Coordinates from Connectivity Information
generate.formula Generate molecular formulae given a target mass and a set of elements and counts.
generate.formula.iter Generate molecular formulae given a target mass and a set of elements and counts.
get.adjacency.matrix Get adjacency matrix for a molecule.
get.alogp Commonly Used Molecular Descriptors
get.atom.count Get the atoms from a molecule or bond
get.atom.index Operations on atoms
get.atomic.desc.names Get the names of the available atomic descriptors
get.atomic.number Operations on atoms
get.atoms Get the atoms from a molecule or bond
get.bonds Get the bonds from a molecule
get.charge Operations on atoms
get.connected.atom Get the atom connected to an atom in a bond
get.connected.atoms Operations on atoms
get.connection.matrix Get connection matrix for a molecule.
get.depictor View and Copy 2D Structure Diagrams
get.desc.categories Get Descriptor Class Names
get.desc.names Get Descriptor Class Names
get.element.types Obtain the type of stereo element support for atom.
get.exact.mass Operations on molecules
get.exhaustive.fragments Molecule Fragmentation Methods
get.fingerprint Evaluate Fingerprints
get.formal.charge Operations on atoms
get.formula Get the formula object from a formula character.
get.hydrogen.count Operations on atoms
get.isotope.pattern.generator Construct an isotope pattern generator.
get.isotope.pattern.similarity Construct an isotope pattern similarity calculator.
get.isotopes.pattern Generate the isotope pattern.
get.largest.component Get the Largest Component in a Disconnected Molecule
get.mcs Perform Substructure Searching & MCS Detection
get.mol2formula Parser a molecule to formula object.
get.murcko.fragments Molecule Fragmentation Methods
get.natural.mass Operations on molecules
get.point2d Operations on atoms
get.point3d Operations on atoms
get.properties Get All Property Values of a Molecule
get.property Get the Value of a Molecule Property
get.smiles Get the SMILES for a Molecule
get.smiles.parser Get a SMILES Parser
get.stereo.types Obtain the stereocenter type for atom.
get.stereocenters Identify which atoms are stereocenters.
get.symbol Operations on atoms
get.title Get the Value of a Molecule Property
get.total.charge Get the Total Charges for the Molecule
get.total.formal.charge Get the Total Charges for the Molecule
get.total.hydrogen.count Get the Total Hydrogen Count for a Molecule
get.tpsa Commonly Used Molecular Descriptors
get.volume Commonly Used Molecular Descriptors
get.xlogp Commonly Used Molecular Descriptors
hasNext Does This Iterator Have A Next Element
hasNext.iload.molecules Does This Iterator Have A Next Element
iload.molecules Load Molecular Structures From Disk
is.aliphatic Operations on atoms
is.aromatic Operations on atoms
is.connected Get the Largest Component in a Disconnected Molecule
is.in.ring Operations on atoms
is.neutral Operations on molecules
is.subgraph Perform Substructure Searching & MCS Detection
isvalid.formula Validate a cdkFormula object.
load.molecules Load Molecular Structures From Disk
match Perform Substructure Searching & MCS Detection
matches Perform Substructure Searching & MCS Detection
mcs Perform Substructure Searching & MCS Detection
parse.smiles Parse a Vector of SMILES Strings
remove.hydrogens Remove Hydrogens from a Molecule
remove.property Remove A Property From a Molecule
set.charge.formula Set the charge to a cdkFormula object.
set.property Set A Property On A Molecule
show-method Class cdkFormula, a class for handling molecular formula
smarts Perform Substructure Searching & MCS Detection
smiles.flavors Generate flag for customizing SMILES generation.
substructure Perform Substructure Searching & MCS Detection
view.image.2d View and Copy 2D Structure Diagrams
view.molecule.2d View and Copy 2D Structure Diagrams
view.table View 2D Structures With Data
write.molecules Write Molecules To Disk