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.atom.index |
get.atomic.desc.names |
Get class names for atomic descriptors |
get.atomic.number |
get.atomic.number |
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.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.connected.atoms |
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.formal.charge |
get.formula |
get.formula |
get.hydrogen.count |
get.hydrogen.count |
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.point2d |
get.point3d |
get.point3d |
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.symbol |
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.hydrogen.count |
iload.molecules |
Load molecules using an iterator. |
is.aliphatic |
is.aliphatic |
is.aromatic |
is.aromatic |
is.connected |
Tests whether the molecule is fully connected. |
is.in.ring |
is.in.ring |
is.neutral |
Tests whether the molecule is neutral. |
isvalid.formula |
isvalid.formula |
load.molecules |
Load molecular structures from disk or URL |
match-SMARTS |
matches |
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.atom.types |
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. |