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