Cheminformatics Tutorials - Herong's Tutorial Examples

∟Generating SVG Pictures with Open Babel

∟"obabel ... -o svg -xd" - Hide Molecule Name

This section provides a tutorial example on how to hide molecule names in SVG output pictures with '-xd' option using Open Babel.

By default, Open Babel will display the molecule name in SVG output format, if the input data contain one. If multiple molecules are included in a sing SVG output, displaying their names helps to identify different molecules.

But there is only one molecule in the SVG output, you may want to hide the molecule name by using the "-xd" option.

For example, the following molecule SDF input file contains the molecule name, "Tyrosine", in the first line:

Tyrosine
 OpenBabel09202120492D

 13 13  0  0  1  0  0  0  0  0999 V2000
    0.8660   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8660   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8660   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660    1.5000    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    1.7321    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7321    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5981    1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660    2.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  3 13  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
$$$$

You can run the following commands and view those two resulting SVG pictures to see the impact of the "-xd" option.

herong$ obabel tyrosine.sdf -O tyrosine-with-name.svg 

herong$ obabel tyrosine.sdf -O tyrosine-without-name.svg 

Table of Contents

 About This Book

 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

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB

"obabel ... -o svg -xd" - Hide Molecule Name - Updated in 2023, by Herong Yang