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OpenBabelGUI Changelog

What's new in OpenBabelGUI 2.3.0a

Aug 12, 2011
  • This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include a completely rewritten stereochemistry engine, Spectrophore fingerprint generation, 2D depiction, improved 3D coordinate generation, conformer searching, and more. Many formats are improved or added, including CIF, PDBQT, SVG, and more. Improved developer API and scripting support and many, many bug fixes are also included.

New in OpenBabelGUI 2.2.3 (Aug 12, 2011)

  • Completely rewritten stereochemistry perception, including support for tetrahedral, square planar, and higher-order stereochemistry.
  • Dramatically improved canonicalization algorithm (Note that in general, canonical SMILES have changed since the 2.2.x release.)
  • 2D depiction, including SVG vector graphics generation using code from MCDL.
  • New Spectrophore generation, contributed by Silicos NV.
  • New ChargeMethod API including support for partial charge assignment from Gasteiger, MMFF94, QEq, QTPIE methods and plugin interface for adding more.
  • Improved 3D coordinate generation.
  • New conformer generation framework, including support for diverse conformer generation and genetic algorithm lowest-energy searching. Improved user documentation.
  • Improved aromaticity / Kekule bond assignment.
  • Improved unit test suite using the CMake-based CTest program.
  • Improved support for crystallographic unit cells (e.g., in CIF format). Improved UFF force field method, including hypervalent 5, 6, 7 and higher coordination numbers.
  • Support for the GAFF (Generalized Amber Force Field) method.
  • Support for reading geometry optimizations as multiple conformers from Gaussian, GAMESS-US, and other quantum chemistry packages. Support for reading molecular orbital energies from quantum chemistry formats. Several memory leaks fixed.
  • Fixed many compiler warnings.
  • Fixed support for MinGW and Cygwin environments.
  • Fixed bugs with Gaussian 09 output files.
  • Latest released version of the InChI library (1.0.3) generating standard InChI.
  • Many more bug fixes and small feature improvements.
  • New Command-Line Operations
  • -canonical: Output atoms in canonical order for any file format (i.e., not just SMILES)
  • conformer: Run a conformer search on the input molecules (has many options)
  • gen2D: Generate a 2D depiction of the molecule
  • partialcharge : Use the partial charge model supplied to generate charges (i.e., instead of default Gasteiger sigma model)
  • sort : Sort molecules by a specified descriptor
  • unique: Only output unique molecules (as determined by InChI generation)
  • New File Formats:
  • Import & Export:
  • DL-POLY CONFIG
  • FHIaims XYZ
  • PDBQT
  • Import only:
  • DL-POLY HISTORY
  • GULP output
  • PWscf output
  • Text Export only:
  • MNA (Multilevel Neighborhoods of Atoms) SVG vector graphics

New in OpenBabelGUI 2.2.0 (Jan 27, 2009)

  • 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.