Open Babel 2.3.1

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Open Babel 2.3.1 was released on 2011-10-14.

Release Notice

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.

Citation

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.

http://www.jcheminf.com/content/3/1/33

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