Difference between revisions of "Open Babel 2.0.0"

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** Titles - eliminated -- can be produced with SMILES -xt
** Titles - eliminated -- can be produced with SMILES -xt

Revision as of 22:10, 5 December 2005

Open Babel 2.0.0 was released on 2005-11-26, one day after the 4th anniversary of the formation of the Open Babel project.

Release Notice

The Open Babel project is extremely proud to announce the release of Open Babel 2.0.0, the latest stable version of the free chemistry file translation program and chemistry software library. This release marks the fourth "birthday" of the Open Babel project and a milestone for a stable, flexible interface for developers and users alike.

OpenBabel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling, computational chemistry and related areas.

Highlights of the 2.0 release include a new conversion framework making it easier to develop new translators, dramatically improved support for merging, splitting, and batch conversion, a framework for molecular fingerprints, similarity searching, a fast molecular database format, support for Perl and Python scripting "wrappers," automatic support for reading .gz (gzip) compressed files, support for the new IUPAC/NIST InChI identifiers and more.

What's New from 1.100.2

  • 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, etc.
  • Support for fingerprinting and calculation of Tanimoto coefficients for similarity consideration. (A flexible fingerprint framework is available for developers.)
  • New support for PerlWrapper and PythonWrapper "wrappers" of the Open Babel library.
  • Many enhancements to the Open Babel API, including the new conversion framework: 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 and improve Open Babel data)
  • Improved z-matrix code (CartesianToInternal / InternalToCartesian).
  • Countless bug fixes.

New File Formats

  • 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