Open Babel 2.3.1
From Open Babel
Open Babel 2.3.1 was released on 2011-10-14.
Contents |
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
