Open Babel 2.3.0
Open Babel 2.3.0 was released on 2010-10-XX.
This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include a completely rewritten stereochemistry engine, 2D depiction, improved 3D coordinate generation, ..... Many formats are improved or added, including CIF, .... , and more. Improved developer API and scripting support and many, many bug fixes are also included.
What's New from 2.2.3
- Completely rewritten stereochemistry perception, including support for tetrahedral, square planar, and higher-order stereochemistry.
- Dramatically improved canonicalization algorithm (Note that in general, canonical SMILES have changed since the 2.2.x release.)
- 2D depiction, including SVG vector graphics generation.
- New Spectrophore generation, contributed by Silicos NV.
- New ChargeMethod API including support for partial charge assignment from Gasteiger, MMFF94, Qeq, QTPIE methods and plugin interface for adding more.
- Improved 3D coordinate generation.
- New conformer generation framework, including support for diverse conformer generation and genetic algorithm lowest-energy searching.
- Improved user documentation.
- Improved aromaticity / Kekule bond assignment.
- Improved unit test suite using the CMake-based CTest program.
- Improved support for crystallographic unit cells (e.g., in CIF format).
- Improved UFF force field method, including hypervalent 5, 6, 7 and higher coordination numbers.
- Support for the GAFF (Generalized Amber Force Field) method.
- Support for reading geometry optimizations as multiple conformers from Gaussian, GAMESS-US, and other quantum chemistry packages.
- Support for reading molecular orbital energies from quantum chemistry formats.
- Several memory leaks fixed.
- Fixed many compiler warnings.
- Fixed support for MinGW and Cygwin environments.
- Fixed bugs with Gaussian 09 output files.
- Latest released version of the InChI library (1.0.3) generating standard InChI.
- Many more bug fixes and small feature improvements.
New Command-Line Operations
- --canonical: Output atoms in canonical order for any file format (i.e., not just SMILES)
- --conformer: Run a conformer search on the input molecules (has many options)
- --gen2D: Generate a 2D depiction of the molecule
- --partialcharge <model>: Use the partial charge model supplied to generate charges (i.e., instead of default Gasteiger sigma model)
- --sort <descriptor>: Sort molecules by a specified descriptor
- --unique: Only output unique molecules (as determined by InChI generation)
New File Formats
- Import & Export:
- DL-POLY CONFIG
- FHIaims XYZ
- Import only:
- DL-POLY HISTORY
- Genbank / EMBL
- GULP output
- PWscf output
- Export only:
- MNA (Multilevel Neighborhoods of Atoms)
- SVG vector graphics