Man pages for rcdk
Interface to the 'CDK' Libraries
| Atoms | Operations on Atoms |
| bpdata | Boiling Point Data |
| cdkFormula-class | Class cdkFormula, ac class for handling molecular formula |
| cdk.version | Get the current CDK version used in the package. |
| compare.isotope.pattern | Compare isotope patterns. |
| convert.implicit.to.explicit | Convert implicit hydrogens to explicit. |
| copy.image.to.clipboard | copy.image.to.clipboard |
| do.aromaticity | do.aromaticity |
| do.isotopes | do.isotopes |
| 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.atomic.desc.names | Get class names for atomic descriptors |
| get.atomic.number | get.atomic.number |
| get.atom.index | get.atom.index |
| 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.stereocenters | Identify which atoms are stereocenters. |
| get.stereo.types | Obtain the stereocenter type for atom. |
| 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 |
| 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 |
| 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. |
| 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. |
