Open Babel 2.1.0

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Open Babel 2.1.0 was released on 2007-04-07.

Release Notice

This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include a new framework for molecular mechanics force fields, a framework for canonical, unique atom numbering (i.e., an open source canonical SMILES implementation), new scripting interfaces in Ruby and Java, enhancements to the developer API, several highly-requested file formats, and many, many bug fixes and improvements.

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.
  • New obrotamer tool - generate random rotational isomers for conformational searching.
  • 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