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[Cdk-commits] SF.net SVN: cdk: [6676] trunk/cdk/changelog.20060714.txt
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From: <eg...@us...> - 2006-07-14 13:12:29
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Revision: 6676 Author: egonw Date: 2006-07-14 06:12:19 -0700 (Fri, 14 Jul 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6676&view=rev Log Message: ----------- Added changelog for this version, as copied from the wiki Added Paths: ----------- trunk/cdk/changelog.20060714.txt Added: trunk/cdk/changelog.20060714.txt =================================================================== --- trunk/cdk/changelog.20060714.txt (rev 0) +++ trunk/cdk/changelog.20060714.txt 2006-07-14 13:12:19 UTC (rev 6676) @@ -0,0 +1,157 @@ +===== ChangeLog 20060714 Release ===== + +Release 20060714 matches the source code from SVN revision 6673. + +General changes: + + * new build system that compiles modules one by one to have clear dependencies + * more use of @cdk.keyword for the topic index + * data files moved from cdk/data to cdk/src/data + * updated the FSF address + * code clean ups and JavaDoc improvement + * many bug fixes and new JUnit tests + * removed printf.jar which had a suspicious licence + * upgraded log4j version to 1.2.13 + * upgraded jgrapht version to 0.6.0 + * dependency on gnujaxp has been removed + +Below is an overview of major changes sorted per module. + +==== interfaces ==== + + * the interfaces are now located in org.openscience.cdk.interfaces + * many methods now make use of interfaces instead of implementations: generally a replace if ChemObject by IChemObject + * the data classes return interfaces now + * the interface cdk.ChemObjectListener is now known as cdk.IChemObjectListener + * added an IChemObjectBuilder interface with implementations + * IRingSet now extends ISetOfAtomContainers + * IChemObject.clone() now declares a 'throws CloneNotSupported' (as is normal in Java) + * the API now use the List interface instead of the Vector implementation + +==== data (+ data-debug + nonotify) ==== + + * Added a DefaultChemObjectBuilder for the data classes + * Added new set of data classes that debug calls to the classes (data-debug module) + * Added new set of data classes that do not trigger ChangedNotification calls (nonotify module) + * Added missing serialVersionUID fields to data classes + * Mapping now properly implements clone() + +==== core ==== + + * now only depends on interfaces, no longer on the data class implementations + * added a constructor CDKException(String message, Throwable cause) + * added a number of missing atom types from our lists + +==== standard ==== + + * added DeAromatizationTool which can convert 'aromatic' systems to Kekule systems + * removed the deprecated RTools + * added a method to calculate double bond equivalents (DBEs) + * added some methods to get all paths between 2 atoms and all paths starting from an atom of a given length + * added a method to get the actual shortest path between two atoms + * added a general IImplementationSpecification which DescriptorSpecification and ReactionSpecification now extend + * added getAtomCount() and getBondCount() to manipulators + * deprecated the manipulators' getAllInOneAtomContainer() convenience method as they pose a serious performance hit + * added a method in GeometryTools to rotate the coordinates of an atom in 3d around a line segment by a specified angle + * added an EState atom type matcher + +==== render ==== + + * added option to turn of rendering of reaction boxes + * added option to draw CDKConstants.TITLE + * added rendering of curly arrows + * extended highlighting posibilities: there are now three types of selection: + + - highlightAtom/Bond with highligh color, for hovering over + - selectedPart/selectedPartColor for internally selected part + - externalSelectdPart/externalHighlightColor for external selections + + * added 'compact' mode in which atoms are drawn like squares (like on PubChem) + * the renderer now uses cached screen coordinates instead of modifying the atomic coordinates all the time + * removed the unmaintained Java3D based 3D renderer + +==== io ==== + + * removed ChemObjectWriter.highestSupportedChemObject() + * no longer depends on a specific interfaces implementation + * the MDLWriter can now write IChemFile + * added a basic Mol2 writer + * the MDLReader is now more flexible with corrupt output from other programs + * ChemObjectIO.accepts(Object) is deprecated in favor of .accepts(Class) + * many chemical file formats were added defined in OpenBabel + * the MDLRXNReader now reads atom-atom mappings + * IChemFormat now extends IResourceFormat + * added the new methods IResourceFormat.getMIMEType(), getFileExtensions() and isXMLBased() + * added IChemFormat.getSupportedDataFeatures() + * added ReaderFactory.createReader(IChemFormat) and WriterFactory.createWriter(IChemFormat) + +==== valencycheck ==== + +==== extra ==== + + * Stereo center detection was refactored out of the SmilesGenerator into BondTools + * getAllChemObjects() were added to cdk.tools.manipulators classes + * namespace declarations in dictionaries and atom type lists were fixed + * added a GridGenerator + * added the Tanimoto similarity measure + * dictionaries can now be in OWL too, in addition to STMML (part of CML) + * the StructureDiagramGenerator no longer deletes E/Z stereochemistry + * the AbstractController now allows merging of Atoms + * added tool to determine the number of lone pair electrons for an atomtype + +==== pdb ==== + + * REMARK and COMPND are now read from PDB files + * mutliple MODEL in PDB files are now read into a ChemSequence + * PDBAtom was moved into the cdk.protein.data package + * added method PDBStrand.getMonomerNamesInSequentialOrder() + * the PDBReader performance was improved by some 30% + +==== qsar ==== + + * descriptors are moved to cdk.qsar.descriptors.molecular and descriptor.atomic + * added the Petitjean shape indices descriptor + * added Randic's weighted path descriptor + * added descriptors for the number of atoms in the longest aliphatic chain, longest chain and largest pi system + * added new interfaces IAtomicDescriptor, IBondDescriptor and IMolecularDescriptor + * added a few bond descriptors + * added Weka to build linear regression models + * R-CDK bridge now uses rJava/JRI instead of previous library + +==== forcefield ==== + + * added a line search algorithm for the Wolfe conditions and a cubic interpolation + * added MMFF94EnergyFunction.MMFF94EnergyFunction(IAtomContainer) to calculate for force field energy + +==== libio_cml (+ qsar_cml + pdb_cml) ==== + + * Uses Jumbo 5.2 now, with a XOM 1.1 based CMLDOM + +==== libio_biojava ==== + + * added tool to convert a BioJava SymbolList to a CDK IBioPolymer + * added customizing of Bond in the ICMLCustomizer API + +==== charges ==== + + * implemented Garsteiger pi charges + +==== reaction ==== + + * added cdk.reaction.IReactionProcess for describing reaction processes + * added a set of reaction types found in mass spectroscopy + * added a method in ReactionManipulator that returns the mapped ChemObject for a given ChemObject + * added a StructureResonanceGenerator that uses known reaction types from cdk.reaction.type + +==== smiles ==== + + * added four missing one char symbol elements in parser: K, U, V and Y + * added a DeduceBondSystemTool that is supposed to resolve double bond placement in delocalized systems + +==== builder3d ==== + +==== experimental ==== + + * added a ProteinPocket finder algorithm + * added a SubstructureFingerprinter (which still lacks a good optimized list of descriptive substructures. Anyone?) + * added generator for Murcko fragments This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |