Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel ... -o svg -xC" - Hide Terminal C in SVG
This section provides a tutorial example how to hide carbon symbol 'C' on a terminal carbon atoms in a molecule SVG picture using the Open Babel 'obabel ... -o svg -xC' command.
By default, Open Babel displays carbon (C) symbols in SVG format, if they are terminal atoms in the molecule structure.
If you want to hide those C symbols for terminal carbon atoms, you can use the "-o svg -xC" option with the "obabel" command.
Here is how the "-xC" option is described in Open Babel help document: "C - do not draw terminal C (and attached H) explicitly The default is to draw all hetero atoms and terminal C explicitly, together with their attached hydrogens."
For example, the following command generates a SVG picture without C symbols for terminal carbon atoms for the Aspirin molecule:
herong$ obabel "-:O=C(Oc1ccccc1C(=O)O)C" -O aspirin-no-carbon.svg -xC 1 molecule converted
As a comparison, running the following command generates a SVG picture with C symbols for terminal carbon atoms for the same molecule:
herong$ obabel "-:O=C(Oc1ccccc1C(=O)O)C" -O aspirin.svg 1 molecule converted
Open both output files, aspirin.svg and aspirin-no-carbon.svg, in a Web browser, you see the differences:
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