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.