[octet-devel] CDKTools-0.4.0 released.

[rich a. <che...@ya...>]

CDKTools-0.4.0 has been released
(http://octet.sourceforge.net). This package is a
complete rewrite that takes advantage of new features
introduced in Octet-0.4.1.

Highlights:

* Limited support of fractional CDK bond
orders/multiatom Octet BondingSystems is now
available. For example, if benzene is specified in CDK
with bond order = 1.5 for all six Bonds, this will be
interpreted as an Octet BondingSystem with six Atoms
and six electrons. Similarly, multiatom Octet
BondingSystems are interpreted as CDK Bonds with
fractional order.

* AtomContainerBuilder provides an abstraction layer
for the construction of any AtomContainer. For the
first time, it is possible to write file parsers (and
other molecule representation builders) that use the
Octet RepresentationBuilder API and which can be
incorporated with minimal effort into both Octet and
CDK.

* AdapterMolecule inherits the CDK Molecule
implementation and the Octet Molecule interface,
enabling it to work seamlessly with both Octet and
CDK. The Virtual Proxy Pattern is used to defer the
full cost of creating an AdapterMolecule until the
Octet Molecule interface is actually used.
AdapterMolecule can be constructed using either the
CDK Molecule API or the Octet RepresentationBuilder
API.

This release still has features that are not
implementented. CDK stereochemistry is not handled,
nor are CDK Atom charges. Properly handling the
mutablity of CDK's Atoms and Bonds still needs more
work. But what is implemented will take care of most
of the likely situations.

The package includes detailed JavaDoc with code
examples:

http://octet.sourceforge.net/javadoc/cdktools_0.4.0/index.html

The Octet homepage has an updated tutorial section
that illustrates the new API:

http://octet.sourceforge.net/tutorial.html#cdk

best,
rich


		
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