Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel ... -o svg -xP300" - Control Image Size
This section provides a tutorial example on how to control molecule SVG image size using the Open Babel 'obabel ... -o svg -xPnnn' command.
The default behavior of Open Babel on scaling and centering SVG images is different depending on which release you are using.
With Open Babel 2.4 or newer the molecule SVG image is defaulted in the center of a 200x200 square.
With Open Babel 2.3 or older, the molecule SVG image is defaulted in a rectangular area calculated as the boundary boxing all atom's x and y coordinates.
If you want to place the molecule SVG image in the center of a given square area, you can use the "-o svg -xPnnn" option with the "obabel" command.
Here is how the "-xPnnn" option is described in Open Babel help document: "P# - px Single mol in defined size image The General option --px # is an alternative to the above."
For example, the following command generates a SVG picture of a carbon chain displayed in the center of a 300x300 square area.
herong$ obabel -:CCCCCCC -O carbon-chain-centered.svg -xC -xt -xP300 1 molecule converted
As a comparison, running the following command with Open Babel 2.3 generates a SVG picture of a carbon chain displayed in rectangular area just large enough to cover all carbon atoms.
herong$ obabel -version Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:48 herong$ obabel -:CCCCCCC -O carbon-chain-default.svg -xC -xt 1 molecule converted
Put both images, carbon-chain-default.svg and carbon-chain-centered.svg, in an HTML document with grey background, 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