Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Write Stereoinformation to Output by Open Babel
This section provides a quick introduction on how stereoinformation is written to output by Open Babel.
Stereoinformation is being written to output data based on stereo centers maintained by Open Babel according the following rules:
1. 3D Stereoinformation - By default, 3D coordinates are copied over from input data to output data without any changes.
If needed, you can specify "--gen3d" option to re-generate 3D coordinates.
2. 2D Stereoinformation - By default, 2D Stereoinformation is always re-generated from perceived stereo centers. And there is no option to change this behavior.
In other words, the file writers re-generate the wedges or hashes from the stereo data at the point of writing; in other words, the particular location of the wedge/hash (or even whether it is present) may change on writing. This was done to ensure that the written structure accurately represents Open Babel’s internal view of the molecule; passing wedges/hashes through unchanged may not represent this (consider the case where a wedge bond is attached to a tetrahedral center which cannot be a stereocenter).
3. 0D Stereoinformation - 0D Stereoinformation is always written to output data according stereo centers perceived by Open Babel from input data. 0D Stereoinformation from input data fully replaced.
As you can see, Open Babel is not simply copy Stereoinformation from input to output. It reads stereoinformation from input, constructs stereo centers, and writes normalized stereoinformation to output.
This may cause some confusions as we presented in next tutorials.
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
Read Stereoinformation from Input with Open Babel
Stereo Perception Performed by Open Babel
►Write Stereoinformation to Output by Open Babel
Wedge-Hash Bond Changed by Open Babel
Hash Bond with Solid Line by Open Babel
Hash over Double Bond by 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.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