Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel -x..." - Extra Options for Output Writing
This section provides a tutorial example on how to pass extra options to Open Babel 'obabel' command for writing molecule data in a specific format.
When you are writing molecule data in a specific input format, Open Babel "obabel" command may support some extra options just for that data format.
If you want to pass extra options for "obabel" to write output data of a specific format, you need to use one or more "-x..." options in the "obabel" command line as shown in the following syntax:
babel input_section output_section [-xA...] [-xB...] ... # "A..." and "B..." are extra options for writing output data.
For example, when "obabel" is writing output data in "svg" format, it supports an option called "t", which tells "obabel" to write thicker lines for bonds. To specify this "t" option for writing data, you can enter it as "-xt" in the command line as shown below:
herong$ obabel molecule.sdf -O molecule.svg -xt 1 molecule converted
If you view "molecule.svg" in a Web browser, bonds will be displayed in thicker lines.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
►Using Open Babel Command: "obabel"
"obabel -i ..." - Input Data Format and Source
"obabel -o ... -O" - Output Data Format and Destination
"obabel -... --..." - Generic Conversion Options
"obabel" Command Option Argument Syntax
"obabel ... --gen2D" - Calculated 2D Coordinates
"obabel ... -f # -l #" - Split Large Molecule File
"obabel -h/-d" - Add/Remove Hydrogens in Molecule Data
"obabel --append ..." - Calculate Molecule Properties
"obabel -L formats" - List of File Formats Supported
"obabel -a..." - Extra Options for Input Reading
►"obabel -x..." - Extra Options for Output Writing
"obabel" vs. "babel" Open Babel Commands
Generating SVG Pictures with Open Babel
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