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
  • 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 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