User Guide

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/

• Introduction
  • Goals of the Open Babel project
  • Frequently Asked Questions
  • Thanks
• Install Open Babel
  • Install a binary package
  • Compiling Open Babel
• obabel - Convert, Filter and Manipulate Chemical Data
  • Synopsis
  • Options
  • Examples
  • 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
  • Forcefield energy and minimization
  • Aligning molecules or substructures
  • Specifying the speed of 3D coordinate generation
• 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
• Tutorial on using the GUI
  • Converting chemical file formats
  • Filtering structures
  • Substructure and similarity searching a large dataset
• 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
• 2D Depiction
  • Molecular graphics
• 3D Structure Generation
  • Generate a single conformer
  • Generate multiple conformers
• Molecular Mechanics and Force Fields
  • Generalized Amber Force Field (gaff)
  • Ghemical Force Field (ghemical)
  • MMFF94 Force Field (mmff94)
  • Universal Force Field (uff)
• Write software using the Open Babel library
  • The Open Babel API
  • C++
  • Python
  • Java
  • Perl
  • CSharp and OBDotNet
  • Ruby
  • Updating to Open Babel 3.0 from 2.x
• Cheminformatics 101
  • Cheminformatics Basics
  • Representing Molecules
  • Substructure Searching with Indexes
  • Molecular Similarity
  • Chemical Registration Systems
• Stereochemistry
  • Accessing stereochemistry information
  • The Config() object
  • Modifying the stereochemistry
  • Stereo perception
  • Miscellaneous stereo functions in the API
• Handling of aromaticity
  • How is aromaticity information stored?
  • Perception of aromaticity
  • SMILES reading and writing
  • Effect of modifying the structure
• 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
  • Other Supported Extensions
• Contributing to Open Babel
  • Overview
  • Developing Open Babel
  • Documentation
  • Adding a new test
  • Software Archaeology
• Adding plugins
  • How to add a new file format
  • Adding new operations and options
  • How to add a new descriptor
• Supported File Formats and Options
  • Common cheminformatics formats
  • Utility formats
  • Other cheminformatics formats
  • Computational chemistry formats
  • Molecular fingerprint 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
  • JSON formats
  • Miscellaneous formats
  • Biological data formats
  • Obscure formats
• Descriptors
  • Numerical descriptors
  • Textual descriptors
  • Descriptors for filtering
• Charge models
  • Cheminformatics charge models
  • Special charge models
• Release Notes
  • Open Babel 3.1.0
  • Open Babel 3.0.0
  • Open Babel 2.4.0
  • Open Babel 2.3.1
  • Open Babel 2.3.0
  • Open Babel 2.2.3
  • Open Babel 2.2.2
  • Open Babel 2.2.1
  • Open Babel 2.2.0
  • Open Babel 2.1.1
  • Open Babel 2.1.0
  • Open Babel 2.0.2
  • Open Babel 2.0.1
  • Open Babel 2.0
  • Open Babel 1.100.2
  • Open Babel 1.100.1
  • Open Babel 1.100.0
  • Open Babel 1.99