Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
What Is rdkit.Chem.rdDepictor Module
This section provides a quick introduction of the molecule file module of the RDKit library, rdkit.Chem.rdDepictor, which provides functionalities to depict a molecule in a 2 dimensional space.
What Is rdkit.Chem.rdDepictor Module? - rdkit.Chem.rdDepictor module provides functionalities to depict a molecule in a 2 dimensional space.
rdkit.Chem.rdDepictor contains the following main methods:
rdkit.Chem.rdDepictor.Compute2DCoords(m) - Computes 2 dimensional coordinates of atoms and bonds of a given molecule to depict it as a 2-D structure. This method is identical to the rdkit.Chem.rdchem.Mol.Compute2DCoords() method.
rdkit.Chem.rdDepictor.GenerateDepictionMatching2DStructure(m, ref) - Same as Compute2DCoords(m), except that orientation the 2-D structure should match the given reference molecule's structure.
rdkit.Chem.rdDepictor.GenerateDepictionMatching3DStructure(m, ref) - Same as GenerateDepictionMatching2DStructure(m, ref), except that the reference molecule is given with a 3-D structure.
To simplify access names, rdkit.Chem.rdchem module members are also imported at the rdkit.AllChem package level. So you can access module members at both levels: the rdkit.AllChem package level and the rdkit.Chem.rdDepictor module level, as shown below:
herong$ python >>> import rdkit.Chem >>> m = rdkit..Chem.rdmolfiles.MolFromSmiles('Cc1ccccc1') >>> import rdkit.Chem.rdDepictor >>> rdkit.Chem.rdDepictor.Compute2DCoords(m) 0 >>> print(rdkit.Chem.rdmolfiles.MolToMolBlock(m)) RDKit 2D 7 7 0 0 0 0 0 0 0 0999 V2000 2.5714 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0714 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3214 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1786 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9286 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1786 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3214 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 2 1 0 M END >>> from rdkit.Chem import AllChem >>> AllChem.Compute2DCoords(m) 0
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
rdkit.Chem.rdmolfiles - Molecular File Module
►rdkit.Chem.rdDepictor - Compute 2D Coordinates
►What Is rdkit.Chem.rdDepictor Module
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