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Finishing touches for 2.2.0
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Geoffrey Hutchison
@@ -9,6 +9,7 @@ The Open Babel project is currently loosely managed by:
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Michael Banck
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Geoff Hutchison
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Chris Morley
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Tim Vandermeersch
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Full list of contributors can be found on the Open Babel website:
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<http://openbabel.sourceforge.net/wiki/THANKS>
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<http://openbabel.org/wiki/THANKS>
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@@ -1,3 +1,8 @@
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2008-07-03 Geoffrey Hutchison <babel@geoffhutchison.net>
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* src/Makefile.am, src/CMakeLists.txt: Update SONAME to 3 for
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version 2.2.0 release.
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2008-07-03 Marcus D. Hanwell <marcus@cryos.org>
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* src/grid.cpp: Fixed the Init function to apply padding correctly.
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@@ -2,23 +2,81 @@ Open Babel 2.2.0 (2008-07-04)
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What's New from 2.1.1:
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- Significantly faster force fields (up to 200x faster).
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- New force fields, including complete UFF and MMFF94 implementations.
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- Monte Carlo conformer search support, including the new obconformer tool.
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- Code for integrating Open Babel and RDKit.
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This release represents a major update and should be a stable upgrade,
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strongly recommended for all users of Open Babel. Highlights include
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improved force fields and coordinate generation, conformer searching,
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enhanced plugins including molecular descriptors, filters, and
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command-line transformations. Many formats are improved or added,
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including CIF, mmCIF, Gaussian cube, PQR, OpenDX cubes, and
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more. Improved developer API and scripting support and many, many bug
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fixes are also included.
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- New support for 3D coordinate generation using the OBBuilder class.
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Note that this code directly supports non-chiral compounds
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Stereochemistry may or may not be supported in this release
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- Significantly faster force fields (up to 200x faster) and support
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for constrained optimization.
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- New force fields, including complete UFF, MMFF94, and MMFF94s implementations.
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- Monte Carlo conformer search support, including a new obconformer tool.
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- Unified framework for plugin classes, including easy-to program file
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formats, descriptors, filters, force fields, fingerprints, etc.
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- A new "descriptor" plugin framework for QSAR descriptors, etc.
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Initial descriptors include hydrogen-bond donors, acceptors,
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octanol/water partition, topological polar surface area, molar
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refractivity, molecular weight, InChI, SMARTS, titles, Lipinski
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Rule of Five, etc.
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- A new "filter" plugin framework for selecting molecules by title,
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molecular weight, etc.
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- Facility to add new "ops", commandline options or operations on the
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conversion process as plugin code.
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Initial operations include 3D coordinate generation, tautomer
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standarization, and addition of polar hydrogens.
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- Code for integrating Open Babel and the BOOST graph library.
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- New support for 3D coordinate generation using the OBBuilder class
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- A new "descriptor" plugin framework for QSAR descriptors.
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- A new "filter" plugin framework for selecting molecules by title, molecular weight, etc.
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- Facility to add new options on the conversion process as plugin code.
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- Space group support.
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- 3D Point group symmetry perception.
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- Improved support for "grids" or "cubes" of molecular data, such as from quantum mechanics programs. (See below for supported file formats.)
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- File format modules are now installed in a version-specific directory, preventing problems between 2.2.x and 2.1.x (or older) plugin libraries.
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- MDL SDF formats now support "aliases" for group abbreviations
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- Improved scripting support, including new bindings for C# and
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improved Java, Ruby, Python, and Perl bindings.
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- Space group support and thoroughly revised and improved CIF format.
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- Initial support for 3D point group symmetry perception.
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- Improved support for "grids" or "cubes" of molecular data, such as
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from quantum mechanics programs. (See below for supported file
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formats.)
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- Initial support for reading trajectories and animations.
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- Improved support for reaction formats, including CML, RXN, and
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Reaction SMILES.
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- Improved residue handling in PDB and Mol2 formats.
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- Improved pH-dependent hydrogen addition.
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- Latest released version of the InChI library, including use of the
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latest "preferred" options for InChI generation.
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- Support for the cross-platform CMake build system.
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- File format modules are now installed in a version-specific
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directory on unix, preventing problems between 2.2.x and 2.1.x (or
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older) plugin libraries.
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- Framework to support "aliases" for group abbreviations, partially
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implemented for MDL formats.
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- Many more bug fixes and small feature improvements.
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New formats:
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==New File Formats==
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Import & Export:
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Chemkin
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Gaussian Cube
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Gaussian Z-matrix
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GROMACS xtc trajectories
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MCDL
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mmCIF
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OpenDX cube (e.g., from APBS)
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Reaction SMILES
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Import only:
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Accelrys/MSI Cerius II MSI text format
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ADF output
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ADF Tape41 ASCII data
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GAMESS-UK input and output
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Molden structure
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PNG (for embedded chemical data)
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PQR
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Export only:
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MSMS input
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ADF input
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InChI Keys
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Open Babel 2.1.1 (2007-07-07)
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@@ -7,7 +7,7 @@ to search, convert, analyze, or store data from molecular modeling,
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chemistry, solid-state materials, biochemistry, or related areas.
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* Ready-to-use programs, and complete programmer's toolkit
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* Read, write and convert over 80 chemical file formats
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* Read, write and convert over 90 chemical file formats
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* Filter and search molecular files using SMARTS and other methods
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* Supports molecular modeling, cheminformatics, bioinformatics,
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organic chemistry, inorganic chemistry, solid-state materials,
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@@ -21,4 +21,4 @@ can be found in the file "COPYING" which should be included in your
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distribution.
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For more information, check the Open Babel website:
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<http://openbabel.sourceforge.net/>
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<http://openbabel.org/>
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+4
-3
@@ -189,14 +189,15 @@ top_srcdir = @top_srcdir@
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EXTRA_DIST = $(man_MANS) README.dioxin.pov README.povray babel31.inc \
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dioxin.mol2 dioxin.inc dioxin.png dioxin.pov \
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CMakeLists.txt \
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Doxyfile-man \
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FAQ.html OBTwoMigration.html \
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babel.html obchiral.html obfit.html obgrep.html \
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obprop.html obrotate.html obminimize.html obenergy.html \
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obrotamer.html # roundtrip.html
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obrotamer.html obprobe.html obgen.html obconformer.html
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man_MANS = babel.1 obchiral.1 obfit.1 obgrep.1 obrotate.1 obprop.1 \
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obminimize.1 obenergy.1 obrotamer.1 roundtrip.1
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obminimize.1 obenergy.1 obrotamer.1 \
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obprobe.1 obgen.1 obconformer.1 \
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roundtrip.1
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all: all-am
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