Open Babel, or how I learned to love the chemistry file format

The latest version of this documentation is available in several formats from http://openbabel.org/docs/dev/.

• Introduction
  • Goals of the Open Babel project
  • Frequently Asked Questions
  • Thanks
• Install Open Babel
  • Install a binary package
  • Compiling Open Babel
• obabel and babel - Convert, Filter and Manipulate Chemical Data
  • Synopsis
  • Options
  • Examples
  • Differences between babel and obabel
  • Format Options
  • Append property values to the title
  • Generating conformers for structures
  • 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™
• obabel vs Chemistry Toolkit Rosetta
  • Heavy atom counts from an SD file
  • Convert a SMILES string to canonical SMILES
  • Report how many SD file records are within a certain molecular weight range
  • Convert SMILES file to SD file
  • Report the similarity between two structures
  • Find the 10 nearest neighbors in a data set
  • Depict a compound as an image
  • Highlight a substructure in the depiction
  • Align the depiction using a fixed substructure
  • Perform a substructure search on an SDF file and report the number of false positives
  • Calculate TPSA
  • Working with SD tag data
  • Unattempted tasks
• 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
• Contributing to Open Babel
  • Overview
  • Developing Open Babel
  • 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 formats
  • Utility formats
  • Other cheminformatics formats
  • Computational chemistry formats
  • Crystallography formats
  • Reaction formats
  • Image formats
  • 2D drawing formats
  • 3D viewer formats
  • Kinetics and Thermodynamics formats
  • Molecular dynamics and docking formats
  • Volume data formats
  • Miscellaneous formats
  • Biological data formats
  • Obscure formats