Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Hash Bond with Solid Line by Open Babel
This section provides a tutorial example demonstrating how Open Babel 'correcting' wedge-hash bond representations of stereo centers from molecule input data.
Sometimes, when a hash bond is located on a ring structure, Open Babel adds a solid line to the hash bond.
Here is an example SDF/Mol file, Hash-with-Solid-Line.sdf, that has 4 stereo centers on a ring structure.
Hash-with-Solid-Line
HerongYang.com
15 16 0 0 0 0 0 0 0 0999 V2000
3.6373 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2124 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4249 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8497 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0622 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8497 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4116 2.4271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0622 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8497 4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6373 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4249 4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2124 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
3 1 1 0 0 0 0
4 5 1 0 0 0 0
1 4 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
4 8 1 6 0 0 0
3 6 1 6 0 0 0
2 9 1 1 0 0 0
5 10 1 6 0 0 0
11 12 1 0 0 0 0
12 13 1 0 0 0 0
5 11 1 0 0 0 0
14 15 1 0 0 0 0
13 14 1 0 0 0 0
2 15 1 0 0 0 0
M END
If we view this SDF/Mol with Open Babel, JSME and pccdb.org, we get 3 different results:
As you can see, 3 tools behaved differently:
- Open Babel - Changed hash bonds to neighboring atoms. Hash style is changed by adding a solid line.
- JSME - Kept everything as given in the input.
- pccdb.org - Made the same changes on the hash bonds. and changed the formation of the ring structure.
So has bond with a solid line is a way to indicate a single bond on a ring going toward the back of the display screen.
By the way, pccdb.org changed the formation of the ring structure, because our input data does not match the real molecule structure. If we allow Open Babel to regenerate the 2D coordinates, it will give us a structure similar to pccdb.org's result.
herong$ obabel Hash-with-Solid-Line.sdf -O output.svg -xd --gen2D herong$ chrome output.svg
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