Open Babel 2.2.0#

Released on 2008-07-04.

What’s new from 2.1.1#

  • New support for 3D coordinate generation using the OBBuilder class.

    Note that this code directly supports non-chiral compounds Stereochemistry may or may not be supported in this release

  • Significantly faster force fields (up to 200x faster) and support

    for constrained optimization.

  • New force fields, including complete UFF, MMFF94, and MMFF94s implementations.

  • Monte Carlo conformer search support, including a new obconformer tool.

  • Unified framework for plugin classes, including easy-to program file formats, descriptors, filters, force fields, fingerprints, etc.

  • A new “descriptor” plugin framework for QSAR descriptors, etc. Initial descriptors include hydrogen-bond donors, acceptors, octanol/water partition, topological polar surface area, molar refractivity, molecular weight, InChI, SMARTS, titles, Lipinski Rule of Five, etc.

  • A new “filter” plugin framework for selecting molecules by title, molecular weight, etc.

  • Facility to add new “ops”, commandline options or operations on the conversion process as plugin code. Initial operations include 3D coordinate generation, tautomer standarization, and addition of polar hydrogens.

  • Code for integrating Open Babel and the BOOST graph library.

  • Improved scripting support, including new bindings for C# and improved Java, Ruby, Python, and Perl bindings.

  • Space group support and thoroughly revised and improved CIF format.

  • Initial support for 3D point group symmetry perception.

  • Improved support for “grids” or “cubes” of molecular data, such as from quantum mechanics programs. (See below for supported file formats.)

  • Initial support for reading trajectories and animations.

  • Improved support for reaction formats, including CML, RXN, and Reaction SMILES.

  • Improved residue handling in PDB and Mol2 formats.

  • Improved pH-dependent hydrogen addition.

  • Latest released version of the InChI library, including use of the

    latest “preferred” options for InChI generation.

  • Support for the cross-platform CMake build system.

  • File format modules are now installed in a version-specific

    directory on unix, preventing problems between 2.2.x and 2.1.x (or older) plugin libraries.

  • Framework to support “aliases” for group abbreviations, partially

    implemented for MDL formats.

  • Many more bug fixes and small feature improvements.

New File Formats#

Import & Export:

Chemkin Gaussian Cube Gaussian Z-matrix GROMACS xtc trajectories MCDL mmCIF OpenDX cube (e.g., from APBS) Reaction SMILES

Import only:

Accelrys/MSI Cerius II MSI text format ADF output ADF Tape41 ASCII data GAMESS-UK input and output Molden structure PNG (for embedded chemical data) PQR

Export only:

MSMS input ADF input InChI Keys