Interface to the 'CDK' Libraries


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Documentation for package ‘rcdk’ version 3.6.0

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Atoms Operations on Atoms
bpdata Boiling Point Data
cdk.version Get the current CDK version used in the package.
cdkFormula-class Class cdkFormula, ac class for handling molecular formula
charge Tests whether the molecule is neutral.
compare.isotope.pattern Compare isotope patterns.
convert.implicit.to.explicit Convert implicit hydrogens to explicit.
copy.image.to.clipboard copy.image.to.clipboard
deprecated_rcdk_function Deprecated functions in the rcdk package.
do.aromaticity do.aromaticity
do.isotopes do.isotopes
do.typing Deprecated functions in the rcdk package.
eval.atomic.desc Compute descriptors for each atom in a molecule
eval.desc Compute descriptor values for a set of molecules
generate.2d.coordinates Generate 2D coordinates for a molecule.
generate.formula generate.formula
generate.formula.iter generate.formula.iter
get.adjacency.matrix Get adjacency matrix for a molecule.
get.alogp Compute ALogP for a molecule
get.atom.count Get the number of atoms in the molecule.
get.atom.index Get the index of an atom in a molecule. Acces the index of an atom in the context of an IAtomContainer. Indexing starts from 0. If the index is not known, -1 is returned.
get.atomic.desc.names Get class names for atomic descriptors
get.atomic.number Get the atomic number of the atom.
get.atoms Get the atoms from a molecule or bond.
get.bond.order Get an object representing bond order
get.bonds Get the bonds in a molecule.
get.charge Get the charge on the atom. This method returns the partial charge on the atom. If charges have not been set the return value is 'NULL', otherwise the appropriate charge.
get.chem.object.builder Get the default chemical object builder.
get.connected.atom Get the atom connected to an atom in a bond.
get.connected.atoms Get atoms connected to the specified atom Returns a 'list" of atoms that are connected to the specified atom.
get.connection.matrix Get connection matrix for a molecule.
get.depictor get.depictor
get.desc.categories List available descriptor categories
get.desc.names Get descriptor class names
get.element.types Obtain the type of stereo element support for atom.
get.exact.mass get.exact.mass
get.exhaustive.fragments Generate Bemis-Murcko Fragments
get.fingerprint Generate molecular fingerprints
get.formal.charge Get the formal charge on the atom. By default the formal charge will be 0 (i.e., 'NULL' is never returned).
get.formula get.formula
get.hydrogen.count Get the implicit hydrogen count for the atom. This method returns the number of implicit H's on the atom. Depending on where the molecule was read from this may be 'NULL' or an integer greater than or equal to 0
get.isotope.pattern.generator Construct an isotope pattern generator.
get.isotope.pattern.similarity Construct an isotope pattern similarity calculator.
get.isotopes.pattern get.isotopes.pattern
get.largest.component Gets the largest component in a disconnected molecular graph.
get.mcs get.mcs
get.mol2formula get.mol2formula
get.murcko.fragments Generate Bemis-Murcko Fragments
get.natural.mass get.natural.mass
get.point2d Get the 2D coordinates of the atom. In case, coordinates are unavailable (e.g., molecule was read in from a SMILES file) or have not been generated yet, 'NA''s are returned for the X & Y coordinates.
get.point3d Get the 3D coordinates of the atom. In case, coordinates are unavailable (e.g., molecule was read in from a SMILES file) or have not been generated yet, 'NA''s are returned for the X, Y and Z coordinates.
get.properties Get all properties associated with a molecule.
get.property Get a property value of the molecule.
get.smiles Generate a SMILES representation of a molecule.
get.smiles.parser Get a SMILES parser object.
get.stereo.types Obtain the stereocenter type for atom.
get.stereocenters Identify which atoms are stereocenters.
get.symbol Get the atomic symbol of the atom. Get the atomic symbol of the atom.
get.title Get the title of the molecule.
get.total.charge get.total.charge
get.total.formal.charge get.total.formal.charge
get.total.hydrogen.count Get total number of implicit hydrogens in the molecule.
get.tpsa Compute TPSA for a molecule
get.volume Compute volume of a molecule
get.xlogp Compute XLogP for a molecule
hydrogen Get the implicit hydrogen count for the atom. This method returns the number of implicit H's on the atom. Depending on where the molecule was read from this may be 'NULL' or an integer greater than or equal to 0
iload.molecules Load molecules using an iterator.
is.aliphatic Tests whether an atom is aliphatic. This assumes that the molecule containing the atom has been appropriately configured.
is.aromatic Tests whether an atom is aromatic. This assumes that the molecule containing the atom has been appropriately configured.
is.connected Tests whether the molecule is fully connected.
is.in.ring Tests whether an atom is in a ring. This assumes that the molecule containing the atom has been appropriately configured.
is.neutral Tests whether the molecule is neutral.
isvalid.formula isvalid.formula
load.molecules Load molecular structures from disk or URL
matches matches
Molecule Operations on molecules
parse.smiles Parse SMILES strings into molecule objects.
rcdk-deprecated Deprecated functions in the rcdk package.
remove.hydrogens Remove explicit hydrogens.
remove.property Remove a property associated with a molecule.
set.atom.types Set the CDK atom types for all atoms in the molecule Calling this method will overwrite any pre-existing type information. Currently there is no way to choose other atom typing schemes
set.charge.formula set.charge.formula
set.property Set a property value of the molecule.
set.title Set the title of the molecule.
show-method Class cdkFormula, ac class for handling molecular formula
smiles.flavors Generate flag for customizing SMILES generation.
view.image.2d view.image.2d
view.molecule.2d view.molecule.2d
view.table view.table
write.molecules Write molecules to disk.