What Is rdkit.Chem.rdchem Module

Cheminformatics Tutorials - Herong's Tutorial Examples

∟What Is rdkit.Chem.rdchem Module

This section provides a quick introduction of the core module of the RDKit library, rdkit.Chem.rdchem, which provides core chemistry functionalities to create and convert molecules and related objects.

What Is rdkit.Chem.rdchem Module? - rdkit.Chem.rdchem Module is core module of the RDKit library. It provides core chemistry functionalities to create and convert molecules and related objects.

rdkit.Chem.rdchem contains the following main classes:

rdkit.Chem.rdchem.Mol - Represents a molecule with atoms, bonds and other properties.

rdkit.Chem.rdchem.Atom - Represents a standalone atom or an atom within a molecule.

rdkit.Chem.rdchem.Bond - Represents a bond within a molecule.

rdkit.Chem.rdchem.RWMol - Represents a molecule with read and write functionalities.

rdkit.Chem.rdchem.Conformer - Represents an instance of molecule conformations expressed in 2-D or 3-D space.

rdkit.Chem.rdchem.EditableMol - Represents a molecule with editing functionalities. EditableMol is a less-performant version of the RWMolecule class. It is recommended to use RWMolecule instead of EditableMol.

rdkit.Chem.rdchem.MolBundle - Represents a group of related molecules.

rdkit.Chem.rdchem.PeriodicTable - Represents the periodic table with methods to retreive chemical element information.

To simplify access names, rdkit.Chem.rdchem module members are also imported at the rdkit.Chem package level. So you can access module members at both levels: the rdkit.Chem package level and the rdkit.Chem.rdchem module level, as shown below:

herong$ python
>>> import rdkit.Chem.rdchem
>>> m = rdkit.Chem.rdchem.RWMol()
>>> exit()

herong$ python
>>> import rdkit.Chem
>>> m = rdkit.Chem.rdchem.RWMol()
>>> exit()

herong$ python
>>> from rdkit.Chem import rdchem
>>> m = rdchem.RWMol()
>>> exit()

herong$ python
>>> from rdkit import Chem
>>> m = Chem.rdchem.RWMol()
>>> exit()

rdkit.Chem.rdchem module classes can also accessed directly from the package name "rdkit.Chem" without module name "rdchem" as shown below:

herong$ python
>>> from rdkit import Chem

>>> m = Chem.rdchem.RWMol()
>>> type(m)
<class 'rdkit.Chem.rdchem.RWMol'>

>>> m = Chem.RWMol()
>>> type(m)
<class 'rdkit.Chem.rdchem.RWMol'>

>>> Chem.rdchem.BondType.SINGLE
rdkit.Chem.rdchem.BondType.SINGLE

>>> Chem.BondType.SINGLE
rdkit.Chem.rdchem.BondType.SINGLE