Open Babel 2.1.0
Open Babel 2.1.0 was released on 2007-04-07.
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
- Export only:
- Open Babel MolReport