Difference between revisions of "Open Babel 2.3.1"

Latest revision as of 01:32, 18 October 2011

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