Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel ... -o svg -xX" - Hide Implicit H in SVG
This section provides a tutorial example how to hide implicit hydrogen symbol 'H' on a non-carbon terminal atoms in a molecule SVG picture using the Open Babel 'obabel ... -o svg -xX' command.
By default, non-carbon terminal atoms have implicit hydrogen connections, Open Babel will display them as chemical formula showing implicit hydrogen counts in SVG format.
If you want to hide those implicit hydrogen counts, you can use the "-o svg -xX" option with the "obabel" command.
Here is how the "-xX" option is described in Open Babel help document: "X - All atoms are explicitly declared. Useful if we don't want any extra hydrogens drawn to fill the valence."
For example, the following command generates a SVG picture with no implicit hydrogen symbols for the tyrosine molecule:
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-no-hydrogen.svg -xX 1 molecule converted
As a comparison, running the following command generates a SVG picture with implicit hydrogen symbols of the same molecule:
herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.svg 1 molecule converted
Open both output files, tyrosine.svg and tyrosine-no-hydrogen.svg, in a Web browser, you see the differences:
Note that "-xX" option was added since Open Babel 2.4 for SVG format.
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
"obabel -o svg" - Molecule Picture in SVG
"obabel -:... -o svg" - Generate SVG from SMILES
"obabel ... -o svg -xi" - Show Atom Indices in SVG
"obabel ... -o svg -xS" - Ball/Stick Depiction in SVG
►"obabel ... -o svg -xX" - Hide Implicit H in SVG
"obabel ... -o svg -xC" - Hide Terminal C in SVG
"obabel ... -o svg -xP300" - Control Image Size
"obabel ... -o svg" - Two "svg" XML Tag Levels
"obabel ... -o svg -xd" - Hide Molecule Name
"babel ... -o svg -xd -xP300" - Open Babel 2.4 Bug
Scale SVG Images using "viewBox" Attribute
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.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