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. 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.
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