rcdk

Operations on Atoms

Operations on molecules

Boiling Point Data

Get the current CDK version used in the package.

Class cdkFormula, ac class for handling molecular formula

Compare isotope patterns.

Convert implicit hydrogens to explicit.

copy.image.to.clipboard

do.aromaticity

do.isotopes

do.typing

Compute descriptors for each atom in a molecule

Compute descriptor values for a set of molecules

Generate 2D coordinates for a molecule.

generate.formula

generate.formula.iter

Get adjacency matrix for a molecule.

Compute ALogP for a molecule

Get the number of atoms in the molecule.

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 class names for atomic descriptors

Get the atomic number of the atom.

Get the atoms from a molecule or bond.

Get the bonds in a molecule.

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 the default chemical object builder.

Get the atom connected to an atom in a bond.

Get atoms connected to the specified atom Returns a 'list“ of atoms that are connected to the specified atom.

Get connection matrix for a molecule.

get.depictor

List available descriptor categories

Get descriptor class names

Obtain the type of stereo element support for atom.

get.exact.mass

Generate Bemis-Murcko Fragments

Generate molecular fingerprints

Get the formal charge on the atom. By default the formal charge will be 0 (i.e., NULL is never returned).

get.formula

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

Construct an isotope pattern generator.

Construct an isotope pattern similarity calculator.

get.isotopes.pattern

Gets the largest component in a disconnected molecular graph.

get.mcs

get.mol2formula

Generate Bemis-Murcko Fragments

get.natural.mass

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 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 all properties associated with a molecule.

Get a property value of the molecule.

Generate a SMILES representation of a molecule.

Get a SMILES parser object.

Obtain the stereocenter type for atom.

Identify which atoms are stereocenters.

Get the atomic symbol of the atom. Get the atomic symbol of the atom.

Get the title of the molecule.

get.total.charge

get.total.formal.charge

Get total number of implicit hydrogens in the molecule.

Compute TPSA for a molecule

Compute volume of a molecule

Compute XLogP for a molecule

Load molecules using an iterator.

Tests whether an atom is aliphatic. This assumes that the molecule containing the atom has been appropriately configured.

Tests whether an atom is aromatic. This assumes that the molecule containing the atom has been appropriately configured.

Tests whether the molecule is fully connected.

Tests whether an atom is in a ring. This assumes that the molecule containing the atom has been appropriately configured.

Tests whether the molecule is neutral.

isvalid.formula

Load molecular structures from disk or URL

matches

Parse SMILES strings into molecule objects.

Remove explicit hydrogens.

Remove a property associated with a molecule.

set.charge.formula

Set a property value of the molecule.

Set the title of the molecule.

Generate flag for customizing SMILES generation.

view.image.2d

view.molecule.2d

Write molecules to disk.