<?xml version="1.0" encoding="utf-8"?>
<changelog xmlns="http://cdk.sf.net/schema/changelog"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
  xsi:schemaLocation="http://cdk.sf.net/schema/changelog changelog.xsd">

  <release id="20050826">
    <addition contributor="egonw">
      Added a cdk.tools.ProteinBuilderTool to build protein structures
    </addition>
    <addition contributor="egonw">
      Added a AminoAcid class that extends Monomer
    </addition>
    <addition contributor="chhoppe">
      Added MM2AtomTypeMatcher to cdk
    </addition>
    <addition contributor="shk3">
      BondTools contains a method if a double bond configuration is cis or trans
    </addition>
    <addition contributor="shk3 tohel">
      For the embedded component, the menu can be exported and integrated into mparent application
    </addition>
    <addition contributor="shk3 tohel">
      Embedded component has own context menu with file related functions
    </addition>
    <addition contributor="shk3 tohel">
      Drawing area has a defined size, currently only A4
    </addition>
    <addition contributor="shk3 tohel">
      Menu/Tool/Statusbar can be hidden and by hiding all the editor looks like an viewer
    </addition>
    <addition contributor="shk3 tohel">
      When double clicking on embedded drawing panel, new editor/viewer frame pops up with model of exisiting frame
    </addition>
    <addition contributor="shk3 tohel">
      Applets for editor and viewer exist
    </addition>
    <addition contributor="shk3 tohel">
      Splitting of JCP in editor and viewer as separate applications
    </addition>
    <addition contributor="chhoppe">
      Added MMFF94AtomTypeMatcher to cdk
    </addition>
    <apiChange closes="1208740">
      Deprecated RTools which should be removed in the first release after the
      next; it's outdated, contains a few bugs, and redundant. Use 
      UniversalIsomorphismTester instead.
    </apiChange>
    <bugfix contributor="irilenia thanser" closes="1208740">
      Fixed copying and matching of aromatic bonds.
    </bugfix>
    <bugfix contributor="meklund" closes="1193703">
      Fixed broken Junit test when coffein.pdb is read. Corrected way of setting
      element symbol in PDBAtom.
    </bugfix>
    <addition contributor="egonw">
      Added an option for flipping a selected molecule horizontally or vertically.
    </addition>
    <addition contributor="egonw">
      Insert from SMILES in JChemPaint now really inserts, instead of adding a new
      model.
    </addition>
    <addition contributor="egonw">
      Added copy/paste functionality to JChemPaint.
    </addition>
    <addition contributor="steinbeck">
      Added classes for permuting the order of atoms in an AtomContainer 
      (graph.AtomContainerAtomPermutor)
    </addition>
    <addition>
      AtomPlacer now draws 180 deg geometry when encountering triple bonds
    </addition>
    <addition contributor="steinbeck">
      JChemPaint sources reintegrated to applications.jchempaint package
    </addition>
    <addition>
      Added new method MFAnalyser.getHTMLMolecularFormulaWithCharge()
    </addition>
    <addition>
      Added new methods SetOfAtomContainers.removeAtomContainer()
    </addition>
    <addition>
      Added a CDKRXNWriter.
    </addition>
    <addition contributor="egonw" implements="1062516">
      Atom type list for PDB atom codes
    </addition>
    <addition contributor="egonw" implements="824133">
      Implemented an iterating (event based) CML reader
    </addition>
    <addition contributor="egonw">
      ReaderFactory now uses the new CDK set io-formats instead of
      hardcoding the recognized formats
    </addition>
    <addition contributor="egonw" implements="954356">
      The PluginManager now adds the plugin menu to the plugin window
    </addition>
    <addition contributor="egonw">
      Jmol API and IO from CVS HEAD on 10.05
    </addition>
    <addition contributor="meklund">
      Added AminoAcid templates
    </addition>
    <addition>
      The libio.cml.Convertor now also accepts AtomContainer
    </addition>
    <addition implements="949751">
      Added customization of atom color for Renderer[2D|3D]Model
    </addition>
    <addition contributor="egonw">
      Added the new method CDKPluginInterface.getPluginLicense()
    </addition>
    <addition contributor="egonw">
      Added the new method CDKEditBus.runScript()
    </addition>
    <addition contributor="egonw">
      CML2 from Jumbo 4.6 was uploaded (for Java 1.4 and 1.5)
    </addition>
    <addition contributor="egonw">
      Added rendering of radicals (SingleElectron)
    </addition>
    <addition contributor="egonw">
      Added reading of 'M  RAD' from MDL molfiles
    </addition>
    <addition contributor="egonw">
      Added writing and reading of radicals in CML2
    </addition>
    <addition>
      Added getRelevantAtomContainer(ChemObject, Bond) to cdk.tools.manipulators
    </addition>
    <addition contributor="egonw" implements="1177112">
      Implemented reading of data items from MDL SD files
    </addition>
    <addition contributor="egonw">
      Added cdk.index.CASNumber.calculateCheckBit()
    </addition>
    <addition contributor="egonw">
      Added the new class PDBAtom with field for PDB specific information
    </addition>
    <addition contributor="egonw">
      Added a CML Customizer interface which reduces the CDK module dependency
      of the libio-cml module
    </addition>
    <addition contributor="egonw">
      Added two new module for outputting data for specific CDK modules:
      pdb-cml for outputing PDBAtom information, and qsar-cml for outputing
      QSAR-descriptor information
    </addition>
    <bugfix contributor="egonw" closes="1260766">
      Removed exponential growth of the ChemSequence length.
    </bugfix>
    <bugfix contributor="ulif" closes="1212219">
      Fixed output of mass number information in MDL files.
    </bugfix>
    <bugfix contributor="thanser" closes="1110537 999330">
      Fixed problem with UniversalIsomorphism. Under certain conditions extra subgraphs
      were found, breaking symmetry.
    </bugfix>
    <bugfix>
      Fixed KabschAlignment so that the rotation matrixi, U, is returned properly
    </bugfix>
    <bugfix>
      Fixed junit-test and run-test: missing cdk-data.jar
    </bugfix>
    <bugfix>
      Don't consume Exceptions while writing MDL
    </bugfix>
    <bugfix closes="1118689">
      Removed entry for 'D' in the isotope list; '2H' is still present
    </bugfix>
    <bugfix>
      Fail more informative on (corrupt) MDL files that lack the property block
    </bugfix>
    <bugfix contributor="egonw">
      Fixed API detection in CDKPluginManager when distributing change events
    </bugfix>
    <bugfix>
      Fixed returning of SingleElectron's with AtomContainer
      .getConnectedElectronContainers(Atom)
    </bugfix>
    <bugfix>
      Fixed retaining LonePair's and SingleElectron's when using
      ConnectivityChecker.partitionIntoMolecules()
    </bugfix>
    <bugfix>
      Fixed showing ElectronContainers in the cdk.apps.swing.ChemObectTree
    </bugfix>
    <bugfix contributor="egonw" closes="1172425">
      The IteratingMDLReader can now also read MDL molfiles with only one
      molecule
    </bugfix>
    <bugfix>
      Fixed output of CML2 for reactions with IDs
    </bugfix>
    <bugfix closes="1169385" contributor="egonw">
      CDK IO is now fully supports InputStream
    </bugfix>
    <bugfix closes="1185991">
      Fixed error in isotope list
    </bugfix>
    <bugfix>
      Fixed reading of Z from CrystClust files
    </bugfix>
    <bugfix closes="937743" contributor="steinbeck">
      AtomPlacer now draws linear geometries for C#C and C=C=C
    </bugfix>
    <bugfix contributor="egonw" closes="1175478">
      Fixed reading of explicit single bonds in SMILES
    </bugfix>
    <bugfix contributor="steinbeck" closes="934819 931608">
      Fixed false handling of terminal branched groups in Fingerprinter
    </bugfix>
    <bugfix contributor="steinbeck" closes="938761">
      No overlapping atoms in layout
    </bugfix>
    <bugfix contributor="cpudney" closes="1185551">
      Fixed misuse of ready() in MDLReader which cause problems when reading
      over the internet
    </bugfix>
    <apiChange>
      Moved IsotopeFactory from cdk-standard to the cdk-core module
    </apiChange>
    <apiChange contributor="egonw">
      Descriptor.calculate() now returns a DescriptorValue instead of 
      DescriptorResult
    </apiChange>
    <apiChange contributor="egonw" closes="1150670">
      Removed LoggingTool(boolean) and LoggingTool(Object, boolean)
      because configuration should be done at application level
    </apiChange>
    <apiChange>
      Renamed ValencyCheckerInterface.calculateMissingHydrogen() to
      .calculateNumberOfImplicitHydrogens()
    </apiChange>
    <apiChange contributor="egonw">
      PDB fields are now read into the new PDBAtom fields instead of the previously
      used ChemObject properties defined in CDKConstants
    </apiChange>
    <apiChange implements="1175952">
      The cdk.layout.TemplateHandler now uses CML2 files
    </apiChange>
    <apiChange>
      reaction.ReactionBalancer: removed init method, constructor no longer takes a
      Reaction object, the isBalanced and balance method do so now.
    </apiChange>
    <apiChange contributor="meklund">
      Refactored Strand out of Polymer into BioPolymer.
    </apiChange>
  </release>
</changelog>
