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. |