Open Babel 2.0¶
Released on 2005-11-26.
What’s new from 1.100.2¶
This release represents Open Babel’s fourth “birthday” and a milestone for a stable, flexible interface for developers and users alike.
- New conversion framework. The new framework allows dynamic
- loading/unloading of file translator modules (i.e., shared libraries, DLLs, DSO, etc.). More importantly, it facilitates adding new formats, since each format is self-contained and no editing of other files is required.
- Improved support for XML chemistry formats, including CML, PubChem XML,
- Support for fingerprinting and calculation of Tanimoto coefficients for
- similarity consideration. (A flexible fingerprint framework is available for developers.)
- New support for Perl and Python “wrappers” of the Open Babel library.
- Many enhancements to the Open Babel API: See the Developers API Notes for
- more information. Some code will require updating, see the Developer’s Migration Guide for details.
- Support for automatically reading .gz compressed files.
- (e.g., 1abc.pdb.gz is uncompressed and treated as a PDB file) Use of the -z flag creates gzip-compressed output files.
- Support for the new IUPAC InChI identifiers.
- Improved bond order typing, including flexible SMARTS matching in
- bondtyp.txt.
- New Kekulization routine – improves aromaticity detection in aromatic amines
- like pyrroles, porphyrins, etc.
- Improved support for radicals and spin multiplicity, including
- assignment of hydrogens to radicals.
- Improved support for 2D vs. 3D file formats.
- New error logging framework keeps an “audit log” of changes to files
- (hydrogen addition, bond order assignment) and different levels of error reporting / debugging. Use the “—errorlevel 4” flag to access this information.
- Improved atom typing and hydrogen addition rules.
- Improved obfit utility will output RMSD and find matches with the
- best RMSD.
- Updated isotope data from 2003 IUPAC standard.
- Updated elemental data from the Blue Obelisk Data Repository.
- (project started, in part, to validate the old Open Babel data)
- Improved z-matrix code (CartesianToInternal / InternalToCartesian).
- Countless bug fixes.
New File Formats¶
- Import & Export:
- ChemDraw CT (Connection Table) CML Reaction files MDL Molfile V3000 MDL Rxn files Open Babel free-form fractional (crystallographic coordinates) Open Babel fastsearch database format Open Babel fingerprint formats PCModel format YASARA.org YOB format Turbomole Improved CML support Improved Gaussian 98/03 support Improved SMILES import / export
- Import-Only:
- PubChem XML
- Export-Only:
- MPQC input Open Babel “copy” format (i.e., copy the raw input file) Sybyl MPD descriptor format IUPAC InChI descriptor
- Changed formats:
- MMADS - eliminated
- bin - OpenEye binary v 1, eliminated
- GROMOS96 - changed from separate g96a & g96nm types to a unified g96 type. Defaults to output Angstroms, Use -xn to output nm.
- Titles - eliminated – can be produced with SMILES -xt