Open Babel 2.1.0

From Open Babel

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

• Import & Export:
  • Carine's ASCII Crystal (ACR)
  • ChemDraw CDX & CDXML
  • Crystallographic Interchange Format (CIF)
  • Fasta Sequence
  • Thermo Format
• Import only:
  • Gaussian fchk
  • InChI
• Export only:
  • Open Babel MolReport
  • Titles