Open Babel 2.3.1#

Released on 2011-10-14.

This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Open Babel. Many bugs and enhancements have been added since the 2.3.0 release.

After 10 years, we finally published a paper discussing Open Babel. Please consider citing this work if you publish work which used Open Babel: Noel M. O’Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch and Geoffrey R. Hutchison. “Open Babel: An open chemical toolbox.” Journal of Cheminformatics 2011, 3:33.

What’s new from 2.3.0#

  • Better support for unknown stereochemistry, including a “wobbly” bond in 2D depiction.

  • Many fixes for rare bugs with stereochemical conversions, including unusual valences.

  • Significantly improved 2D depiction code, improving performance and cis/trans stereochemical accuracy

  • Added support for direct 2D depiction to PNG files using the Cairo library, if available.

  • PNG files from Open Babel contain molecular information and can be read to give the MDL Molfile.

  • SVG files with 2D depiction can now include a grid of molecules with embedded JavaScript to zoom and scroll.

  • Molecular formulas now include the total charge (e.g., HCO2-)

  • Added the EEM partial charge model from Bultinck, et. al.

  • Fixed problems with FastSearch databases larger than 4GB, now checking for large files.

  • Improved performance with force field minimization, particularly the UFF and GAFF methods.

  • Several MMFF94 atom typing bugs fixed.

  • Updated GAFF parameters from the AmberTools distribution.

  • Improvements in 3D coordinate generation, particularly more accurate sp3 bond angles

  • Fixed tests for auto-typing molecules with force fields when running through different isomers.

  • Improvements in scripting bindings, particularly Python, Ruby, and Java

  • Pybel now uses the built-in 2D depiction, and no longer needs OASA.

  • Added initial support for MM3 atom typing with the Tinker package

  • Significant bug fixes for the PDBQT format.

  • Reading FASTA files can now generate 3D coordinates for single-stranded DNA in addition to the default double-strand.

  • Support for reading/writing unit cell information from MOPAC files.

  • Support for re-numbering SMILES by specifying the first and last atoms with -xf and -xl flags.

  • Better support for InChI -> InChI key generation by direct conversion, rather than re-perception of the InChI.

  • Fix for rare stack overflow crash in SMARTS perception.

  • Improved UNIX man pages.

  • Many bug fixes and small enhancements

New File Formats#

  • Import and Export:

** Gromacs GRO * Import: ** ABINIT ** XCrySDen XSF * Export: ** InChI Key