Difference between revisions of "Open Babel 2.3.0"

From Open Babel
Jump to: navigation, search
Line 8: Line 8:
  
 
* Completely rewritten stereochemistry perception, including support for tetrahedral, square planar, and higher-order stereochemistry.
 
* Completely rewritten stereochemistry perception, including support for tetrahedral, square planar, and higher-order stereochemistry.
−
* Dramatically improved canonicalization algorithm (typically assigning different canonical SMILES).
+
* 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.
 
* 2D depiction, including SVG vector graphics generation.
 +
* New [http://sourceforge.net/news/?group_id=40728&id=288972 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.
 
* 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.
 
* Improved 3D coordinate generation.
−
* New conformer generation framework.
+
* New conformer generation framework, including support for diverse conformer generation and genetic algorithm lowest-energy searching.
 
* Improved user documentation.
 
* Improved user documentation.
 
* Improved aromaticity / Kekule bond assignment.
 
* Improved aromaticity / Kekule bond assignment.
Line 28: Line 29:
 
* Many more bug fixes and small feature improvements.
 
* Many more bug fixes and small feature improvements.
  
−
==Added Command-Line Operations==
+
==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 <model>''': Use the partial charge model supplied to generate charges (i.e., instead of default Gasteiger sigma model)
 +
* '''--sort <descriptor>''': Sort molecules by a specified descriptor
 
* '''--unique''': Only output unique molecules (as determined by InChI generation)
 
* '''--unique''': Only output unique molecules (as determined by InChI generation)
−
 
  
 
==New File Formats==
 
==New File Formats==
  
 
* Import & Export:  
 
* Import & Export:  
−
** MNA
+
** DL-POLY CONFIG
 +
** FHIaims XYZ
 
** PDBQT
 
** PDBQT
−
** DL-POLY
 
  
 
* Import only:
 
* Import only:
 +
** DL-POLY HISTORY
 +
** Genbank / EMBL
 +
** GULP output
 +
** PWscf output
 +
** Text
  
 
* Export only:
 
* Export only:
 +
** MNA (Multilevel Neighborhoods of Atoms)
 
** SVG vector graphics
 
** SVG vector graphics
  
 
[[Category:Releases]]
 
[[Category:Releases]]

Revision as of 08:32, 18 October 2010

Open Babel 2.3.0 was released on 2010-10-XX.

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 completely rewritten stereochemistry engine, 2D depiction, improved 3D coordinate generation, ..... Many formats are improved or added, including CIF, .... , and more. Improved developer API and scripting support and many, many bug fixes are also included.

What's New from 2.2.3

  • 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.
  • 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 <model>: Use the partial charge model supplied to generate charges (i.e., instead of default Gasteiger sigma model)
  • --sort <descriptor>: 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
    • Genbank / EMBL
    • GULP output
    • PWscf output
    • Text
  • Export only:
    • MNA (Multilevel Neighborhoods of Atoms)
    • SVG vector graphics
Retrieved from "http:///en/w/index.php?title=Open_Babel_2.3.0&oldid=3325"