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Open Babel, or how I learned to love the chemistry file format
¶
Introduction
Goals of the Open Babel project
Frequently Asked Questions
Thanks
Install Open Babel
Install a binary package
Compiling Open Babel
babel and obabel - Convert, Filter and Manipulate Chemical Data
Synopsis
Options
Examples
Differences between babel and obabel
Format Options
Append property values to the title
Filtering molecules from a multimolecule file
Substructure and similarity searching
Sorting molecules
Remove duplicate molecules
Aliases for chemical groups
The Open Babel GUI
Basic operation
Options
Multiple input files
Wildcards in filenames
Local input
Output file
Graphical display
Using a restricted set of formats
Other features
Example files
Molecular fingerprints and similarity searching
Fingerprint format
Spectrophores™
Write software using the Open Babel library
The Open Babel API
C++
Python
Java
Perl
CSharp and OBDotNet
Ruby
Cheminformatics 101
Cheminformatics Basics
Representing Molecules
Substructure Searching with Indexes
Molecular Similarity
Chemical Registration Systems
Radicals and SMILES extensions
The need for radicals and implicit hydrogen to coexist
How Open Babel does it
In radicals either the hydrogen or the spin multiplicity can be implicit
SMILES extensions for radicals
Miscellaneous topics
Lazy Evaluation
Errors and Warnings
Modular design of code base
Contributing to Open Babel
Overview
Developing Open Babel
Developer Resources
Version Control
Documentation
Testing the Code
Software Archaeology
Adding plugins
How to add a new file format
Adding new operations and options
Supported File Formats and Options
Common cheminformatics
Utility
Other cheminformatics
Computational chemistry
Crystallography
Reactions
Images
2D drawing
3D viewers
Kinetics and Thermodynamics
Molecular dynamics and docking
Volume data
Miscellaneous
Biological data
Obscure formats
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Open Babel v2.3.0 documentation
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