Difference between revisions of "Open Babel 2.2.0"

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(Initial pass at new formats)
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==What's New from 2.1.1==
 
==What's New from 2.1.1==
  
* New support for 3D coordinate generation using the OBBuilder class
+
* New support for 3D coordinate generation using the OBBuilder class.
** Note that this  
+
** 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).
 
* Significantly faster force fields (up to 200x faster).
 
* New force fields, including complete UFF, MMFF94, and MMFF94s implementations.
 
* New force fields, including complete UFF, MMFF94, and MMFF94s implementations.
* Monte Carlo conformer search support, including the new obconformer tool.
+
* Monte Carlo conformer search support, including a new obconformer tool.
* Unified framework for plugin classes, allowing new types...
+
* 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.
 
* 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.
 
* 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, including coordinate generation, 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.
 
* Code for integrating Open Babel and the BOOST graph library.
* Improved scripting support, including new bindings for C#.
+
* 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.
 
* Space group support and thoroughly revised and improved CIF format.
 
* 3D Point group symmetry perception.
 
* 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.)
 
* 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.
 
* Initial support for reading trajectories and animations.
 +
* Improved support for reaction formats, including CML, RXN, and Reaction SMILES.
 
* 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.
 
* 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.
 
* Framework to support "aliases" for group abbreviations, partially implemented for MDL formats.
Line 49: Line 53:
 
* Export only:
 
* Export only:
 
** MSMS
 
** MSMS
** ADF inport
+
** ADF input
 +
** InChI Keys

Revision as of 13:12, 1 July 2008

Open Babel 2.2.0 will be released on 2008-07-04.

Release Notice

This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include ...

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).
  • 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.
  • 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.
  • 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
    • GAMESS-UK
    • Gaussian Cube
    • Gaussian Z-matrix
    • GROMACS xtc trajectories
    • MCDL
    • mmCIF
    • OpenDX cube (e.g., from APBS)
    • Reaction SMILES
  • Import only:
    • ADF output
    • ADF Tape41 ASCII data
    • Molden
    • MSI msi format
    • PNG (for embedded chemical data)
    • PQR
  • Export only:
    • MSMS
    • ADF input
    • InChI Keys