Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"babel ... -o svg -xd -xP300" - Open Babel 2.4 Bug
This section provides a tutorial example demonstrating a code bug in 'babel -o svg -xd -xP300' command in Open Babel 2.4.
"-xd" for "svg" output format is a nice option in Open Babel that removes molecule title in the output SVG image.
But there seems to be a code bug in Open Babel 2.4 release, where "-xd" option requires a parameter. If you use "-xd" option and follow by another option, the "babel -o svg" command will give you an error: "Option -d takes a parameter">
herong$ obabel -:CCCCCCC -O carbon-chain.sdf --gen2D 1 molecule converted herong$ babel carbon-chain.sdf carbon-chain.svg -xd -xP300 Option -d takes a parameter
The workaround is to put the "-xd" option at the end of the command line as shown below:
herong$ babel carbon-chain.sdf carbon-chain.svg -xP300 -xd 1 molecule converted 20 audit log messages
However, the "obabel -o svg -xd -xP300" works perfectly in Open Babel 2.4 release.
herong$ obabel -:CCCCCC -o svg -O carbon-chain.svg -xd -xP300 1 molecule converted
So we should use "obabel" instead of "babel", since "babel" is deprecated now and will be removed in a future release.
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