Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
RDKit GenerateDepictionMatching2DStructure(m, s) - Substructure Orientation
This section provides a tutorial example on how to draw multiple molecules with the same orientation as a common substructure.
If a substructure is found in multiple molecules, you may want them to be display in the same orientation as the substructure.
This can be done using the AllChem.GenerateDepictionMatching2DStructure(m, s) method as shown below: in a Jupyter Notebook:
from rdkit import Chem
l = ['O=C(O)c2cc1ccc(Cl)n1cn2', 'c1ccc2c(c1)ncn3cccc23',
'c1ccc3c(c1)cc2ccncn23']
ms = []
for i in l:
m = Chem.MolFromSmiles(i)
ms.append(m)
from rdkit.Chem import Draw
Draw.MolsToGridImage(ms)
from rdkit.Chem import AllChem
s = Chem.MolFromSmiles('c1nccc2n1ccc2')
AllChem.Compute2DCoords(s)
for m in ms:
AllChem.GenerateDepictionMatching2DStructure(m, s)
Draw.MolsToGridImage(ms)
As you can see from the output, molecules in the bottom images all have the same orientation as the substructure.
By the way, rdkit.Chem.Draw.MolsToGridImage(ms) allows you to draw multiple molecules in a single image.
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
rdkit.Chem.Draw - Handle Molecule Images
►Molecule Substructure Search with RDKit
RDKit m.HasSubstructMatch(s) - Substructure Match
►RDKit GenerateDepictionMatching2DStructure(m, s) - Substructure Orientation
RDKit rdMolDraw2D.PrepareAndDrawMolecule - Substructure Highlight
RDKit Substructure Search with SMARTS
rdkit.Chem.rdFMCS - Maximum Common Substructure
rdkit.Chem.rdSubstructLibrary - Substructure Library
Substructure Library in Binary and SMILES Formats
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