Release notes for 5.1.x releases

February 14th 2009 Marvin 5.1.5
- MarvinSketch
  - Explicit valence setting of atoms is available from menu (forum topic).
- Applet
  - New MarvinView applet parameter: celli_j and the possibility to escape characters.
- Import/Export
  - Text format import from cdx.
- Installer
  - Marvin Beans installer for Linux with Java.
- API
  - Save/load MSketchPane toolbar and menu configuration : reset active configuration fix.
  - New method in MolAtom (getLonePairCount()) that returns the same value as MoleculeGraph().getLonePairCount(int i) is implemented. (forum topic).
December 19th 2008 Marvin 5.1.4
- MarvinSketch
  - Arrows group is restructured in the toolbar and in the menubar (forum topic).
  - The Insert > Groups menu is replaced by a more convenient dialog.
- Import/Export
  - Unique SMILES should implicitize plain Hydrogens (forum topic).
- Calculator Plugins
  - Unique Markush code can be generated for each enumerated structure.
  - logP and logD calculations are significantly faster.
- API
  - New methods in chemaxon.beans.MViewPane: isViewWindowOpened(int), isSketchWindowOpened(int) and closeSketcher(int).
  - PDBReader and related classes were moved from chemaxon.modules to chemaxon.marvin.io.formats.pdb.
  - MacroMolecule and related classes were moved from chemaxon.modules to chemaxon.struc.
November 13th 2008 Marvin 5.1.3_2
- Bugfixes.
November 11th 2008 Marvin 5.1.3_1
- Bugfix.
November 7th 2008 Marvin 5.1.3
- MarvinSketch
  - Slight improvement in multimolecule file opening, the index of the stucture in the preview is automatically offered.
- MarvinView
  - New helper API ( chemaxon/marvin/beans/MViewParams ) that generates the value to the molecule table parameters of MarvinView.
  - Support MDLCT format in OLE Object.
- Licenses
  - Important change in the licensing of calculator plugins: all plugins work in evaluation mode without a license.
- Import/Export
  - Encoding detection when the default system encoding is not suitable for the input file. It tries to recognize UTF-8, UTF-16, EUC-JP and Shift_JIS. If all fails, then it also tries ISO-8859-1 and windows-1252. The guessed encoding can be printed using molconvert query-encoding.
  - Energy is stored in the second line of XYZ files.
  - MDL formats
    - Import of SDfiles without structure fields.
    - Energy is imported from the header line, the "Energy" SDF property is removed.
    - Format recognition optimized: other recognizers are not called any more if the first 12 lines match at least one MDL format.
  - API
    - PositionedInputStream.skipLine() method created to speed up pre-reading of huge multimolecule files. It should be called in MRecordReader.skipRecord() implementations instead of readLine() if the line contents are unimportant.
- Clean 2D
  - Clean 2D considers electron flow arrows (forum topic).
- Calculator Plugins
  - Huckel orbital coefficient calculation in HuckelAnalysisPlugin (forum topic)
  - Markush enumeration ID can be generated for enumerated molecules.
  - logP calculation methods were introduced; available methods: "VG", "KLOP", "PHYS", "user defined", "weighted".
  - logP calculation is trainable, the "user defined" logP calculation method can be trained with experimental logP values provided by the user.
  - Cxcalc can be used for training the plugin calculations (currently only logP is trainable).
October 1st 2008 Marvin 5.1.2
- MarvinSketch/View
  - New option/parameter to display the label of carbon atoms in structures.
September 1st 2008 Marvin 5.1.1
- MarvinSketch
  - New, explicit way of defining lone pair and radical elecrons on atoms.
  - The following menus were (temporarily) removed from the Template Library: File > Close, Options menu (the functions are out of order).
  - The Structure > Clean 3D > Select Conformer menu option is renamed to Display Stored Conformers.
- Applet
  - New applet parameter to remove the on-the-fly customizability of the Advanced Template Toolbar.
- Import/Export
  - The lone pair and radical electrons can be exported to cxsmiles format.
  - Also recognize names that are part of the traditional dictionary (now that name recognition should only be tried when most others have failed, it is not as problematic to load the dictionary during recognition).
- Chemical Terms
  - Evaluator config files defined by the user are read from .chemaxon/MARVIN_MAJOR_VERSION (UNIX / Linux) or chemaxon/MARVIN_MAJOR_VERSION (Windows) directory.
- API:
  - Renderer (chemaxon.marvin.beans.MViewRenderer) and editor (chemaxon.marvin.beans.MViewEditor) components for JTables are part of the public API.
- Bugfixes
August 7th 2008 Marvin 5.1.0
- MarvinSketch:
  - Conversion of IUPAC Names to structure.
  - OLE 2 support.
  - Accelerated initialization of MarvinSketch and MarvinView at startup.
  - Flip Group option.
  - Recent file list.
  - The magnification of a molecule can be saved in MRV format.
- MarvinView:
  - (Batch) conversion of IUPAC Names to structure when opening .name files.
  - Printing has been redesigned. New options: Print to PDF and Print Preview.
- Applet:
  - New applet parameter to listen for mouse events.
  - Calculator Plugins are accessible from JavaScript via Chemical Terms.
- Import/Export:
  - IUPAC name import has been implemented.
  - IUPAC name export: improved support for amino-acids and peptides.
  - Compressed base64 encoded (cx)SMILES/(cx)SMARTS output.
  - Unique SMILES export has been changed because of.
  - UTF-8 character encoding support for applet parameters.
- Molecule Representation:
  - N with valence 5 in aromatic rings is allowed.
  - Aromatization accepts all atom types in aromatic rings.
  - M, MH, X, XH are not aromatic query atom.
- Clean 3D:
  - Major Clean 3D core modifications.
  - New Dreiding force field implementation.
- Calculator Plugins:
  - Tautomerization Plugin
    - Generic tautomer generation.
    - New tautomerization options.
  - Topology Analyser Plugin
    - New calculations.
  - Geometry Plugin
    - Molecule projection calculations.
  - Markush Enumeration Plugin
    - Structure coloring and scaffold aligning options in Markush enumeration.
    - Position variation bonds in Markush enumeration.
    - New Markush enumeration options: orienting scaffold uniformly and coloring enumerated structures.
    - Speeding up random enumeration.
  - Huckel Analysis Plugin
    - Eigenvalue and eigenvector calculations.
    - Some cxcalc calculations have been renamed.
    - Removed aromatic restriction from Huckel E/Nu order calculations.
  - logP plugin
    - The calculation algorithm has been improved using the PhysProp database.
- Chemical Terms:
  - Chemical Terms is available from Marvin in command line and API.
  - It can also be used in Java scripts (in applets).
  - New functions and options have been implemented.
  - Evaluator command line application can list available functions.
  - AND, OR, NOT boolean operators.
- API:
  - Both aromatization methods aromatize query atoms if they have double and single bonds in the ring.
  - Atoms belonging to some atomgroups can be recognized by the name of the group (e.g. alkali, alkaline earth, etc.).
  - MoleculeIterator interface is moved to chemaxon.util.iterator.
  - Calculator Plugins:
    - New caluclations in GeometryPlugin.
    - New calculations in TopologyAnalyser and TopologyAnalyserPlugin.
    - New calculations and options in TautomerizationPlugin.
    - New calculations and options in MarkushEnumerationPlugin.
    - New and renamed calculations in HuckelAnalysisPlugin.
  - Molecule file format recognizers are called in the priority order. Deprecated Recognizer.getPriority().
- Documentation:
  - Updated developer's guide and examples.
- Bugfixes