Open Babel 2.1.0#

Released on 2007-04-07.

What’s new from 2.0.2#

  • Now handles molecules with >65536 atoms or bonds. Some PDB entries,

    in particular have such large molecular systems.

  • New features for molecular mechanics force fields, including energy

    evaluation and geometry optimization. Ultimately, this will enable coordinate generation and refinement for SMILES and other formats. (A flexible force field framework is available for developers.)

  • Implementation of the open source Ghemical all atom force field.

  • Framework for canonical atom numbering, including a new canonical

    SMILES format.

  • New support for Ruby and Java interfaces to the Open Babel library.

  • Improved scripting interfaces through Perl and Python, including the new “pybel” module with a more Python-like syntax.

  • Automatically handles reading from text files with DOS or Mac OS 9

    line endings.

  • Many enhancements to the Open Babel API: See the Developers API Notes for

    more information.

  • New obenergy tool - evaluate the energy of a molecule using

    molecular mechanics.

  • New obminimize tool - optimize the geometry of structures using

    molecular mechanics.

  • Improved obprop tool - outputs a variety of molecular properties including

    Topological Polar Surface Area (TPSA), Molar Refractivity (MR), and logP.

  • The babel tool can now setting program keywords for some quantum mechanics

    formats from the command-line, including: GAMESS, Gaussian, Q-Chem, and MOPAC. (This feature can also be accessed by developers and expanded to other formats.)

  • New options for babel tool, including:

    -e for continuing after errors -k for translating computational keywords (e.g., GAMESS, Gaussian, etc.) –join to join all input molecules into a single output –separate to separate disconnected fragments into separate molecular records -C (combine mols in first file with others having the same name) –property to add or replace a property (e.g., in an MDL SD file) –title to add or replace the molecule title –addtotitle to append text to the current molecule title –addformula to append the molecular formula to the current title

  • Many more bug fixes and small feature improvements.

New File Formats#

Import & Export:

Carine’s ASCII Crystal (ACR) ChemDraw CDX & CDXML Crystallographic Interchange Format (CIF) Fasta Sequence Thermo Format


Gaussian fchk InChI


Open Babel MolReport Titles