Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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
For more information, see rdkit.Chem.rdchem module reference document at https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
►rdkit.Chem.rdchem - The Core Module
►What Is rdkit.Chem.rdchem Module
rdkit.Chem.rdchem.Mol - The Molecule Class
rdkit.Chem.rdchem.Atom - The Atom Class
rdkit.Chem.rdchem.Bond - The Bond Class
rdkit.Chem.rdchem.RWMol - The RWMol Class
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction