Release notes for 5.2.x releases

September 11th, 2009: Marvin 5.2.5

New features and improvements

• Import/Export:
  • Structures can be saved in InChiKey format from the GUI. InChiKey can also be selected in the Edit > Source window.
  • Support rel- relative stereo names in name import.
  • Support of nucleosides and nucleotides in name import.
  • Better support for traditional names in name import (over 15% more names supported from NCI database).
  • Better support of stereo descriptors in name import: cis-, trans- is supported.
• Documentation
  • New public example demonstrating the usage of text boxes with formatted text.
• API
  • New getter and setter methods in MolPrinter API for trancparency, ballRadius, stickThickness, wireThickness, lonePairsAutoCalculated, carbonVisibility, boundingRectangle.
  • Name to structure extraction from text and html documents API has been added to the name-to-structure infrastructure (see the api documentation of chemaxon.naming.DocumentExtractor.
  • Custom name conversion plugin API has been added to the name-to-structure infrastructure (see the api documentation of chemaxon.naming.NameConverters). This allows for instance the integration of a large in-house structure dictionary (including names) stored in a local or remote database into name-to-structure and document-to-structure conversions.
  • Deprecated asynchronous molecule setting methods in MViewPane API: setM(int, String), setM(int, String, String) and setM(int, File, String).
• .NET integration
  • MarvinBeans for .NET snapshot version is available (download, documentation).

Bugfixes

• MarvinView
  • MView table cell resizing is not working (forum topic).
• Import/Export
  • Aliphatic property was not added to aliphatic C with doublebond and any bond during SMARTS (forum topic).
  • MarvinView and MarvinSketch sometimes crashed when bad InChI was imported.
• Chemical Structure Painting
  • The Wireframe with Knobs display option did not work.
• Clean 2D
  • Explicit H atoms having parity were improperly added with the Clean option.
  • 2D cleaning of a bridged ring having another ring as neighbor was wrong.
• Licenses
  • Resonance plugin displayed a warning without a license (although it is a free plugin).
  • There was a minor bug in license key verification.

August 11th, 2009: Marvin 5.2.4

New features and improvements

• MarvinSketch
  • New icon is added to the "Add Attachment Point" action (forum topic).
  • New keyboard shortcuts: 5 - Single Up, 6 - Single Down, 7 - Wiggly bond.
• Molecule representation
  • Add function that returns improved information of parity.

Bugfixes

• MarvinSketch
  • Custom menus were not loaded after restarting MarvinSketch.
• MarvinView
  • Print All did nothing if multiple pages were sent to the printer from MarvinView.
• Licenses
  • Fixed the displayed state of licenses to be installed. (Replaced "Invalid" with "To be installed".)
• Applet
  • Complete the missing isLeopardSafari() method in marvin.js (marvin/sketch/index.jsp did not load in Mac Safari) (forum topic).
• Import/Export
  • Partial charges numeric format in mol2 is fixed (forum topic).
• Molecule representation
  • Nitrogen with double bond and explicit H gets stereo value (forum topic).
  • Bug was in setDim method in RgMolecule.
• Chemical Structure Painting
  • Bracket overwrote lone pairs, image generation clipped off lone pairs/charge symol ( forum topic).
• Calculator Plugins
  • Canonical tautomer calculation threw ArrayIndexOutOfBoundsException in some cases (forum topic).

July 29th, 2009: Marvin 5.2.3.2

New features and improvements

• API
  • New functions are added that return improved information of parity: Parity.asymmetricAtoms(MoleculeGraph), Parity.chiralAtoms(MoleculeGraph).

Bugfixes

• MarvinSketch
  • Initialization problem in MarvinSketch if it was initialized through MarvinOLEServer.
• Calculator Plugins
  • The chiralCenterCount function in TopologyAnalyser plugin returned now zero for the number of chiral centers of 1,4-dimethylcyclohexane.

July 15th, 2009: Marvin 5.2.3.1

No changes

July 8th, 2009: Marvin 5.2.3

New features and improvements

• MarvinSketch
  • A splash screen image is shown during the initialization of the MarvinSketch standalone version.
• Import/Export
  • Partial charges are saved in mol2 file format based on the calculation result of the charge plugin (charge license required; if it is not found then the mol2 file is created without charges). (forum topic).
  • Relative stereo descriptors (using enhanced stereo OR groups) is supported in name export.
  • Amino acid recognition in Name import has been improved: substituents are recognized, D/L configuration is supported.
  • Importing non standard names is more flexible: more freedom at numbering, bracers and dashes.
  • Cis/trans releated information is supported in name import.
• Clean 2D
  • The arrangement of wedge bonds using the 'Clean wedge bonds' option has been improved. (forum topic).
• Applet
  • The loading of MSketch Applet is sped up: the total size of the files downloaded during the first initialization has been reduced by 14% compared to the previous version.
  • The value of the "legacy_lifecycle" parameter is true in default in Marvin applets if you use marvin.js (see applet parameters).
  • New methods have been introduced in marvin.js, which return with the generated applet source instead of writing it into the html source: msketch_end_to_string(), mview_end_to_string() and mspace_end_to_string().
  • A new applet parameter has been introduced ("appletid") to identify applet in the propertychange event notification sent to JavaScript.
  • The marvin.js uses ID attribute instead of NAME to refer to the applet.
• Chemical Terms
  • New Chemical Terms functions have been introduced:
    • importMol()
    • isMarkush() (forum topic)
    • whereIsValenceError()
    • hasAromatizationError()
• Calculator plugins
  • A new method has been implemented in the Structural Frameworks plugin of the Geometry plugin: checkMolecule().
  • The major tautomer generation has been sped up (forum topic).
  • Stereoisomer plugin can generate stereoisomers with given chirality as constraint (forum topic).

Bugfixes

• MarvinSketch
  • The 'Recent file list' contained two separate (and incorrect) items if the filename contained a comma character (divided at the comma).
  • OLE failed with some repaint events when the canvas was in the background of other java components.
• Applet
  • The JVM version in the EMBED and the OBJECT tag in the marvin.js generated code was not up-to-date. In addition to the update the NAME attribute was changed to ID (forum topic).
  • The "viewCarbonVisibility" applet parameter did not work (forum topic).
• Import/Export
  • Some R/S and E/Z stereo descriptors were missing in generated names.
  • Failing on name generation of very complex structures was not handled too gracefully.
  • cxsmarts:h failed (forum topic).
  • MOLFiles with incorrect spaces at the end of the new type of Atom list definition lines can now be imported without error.
  • CDX import failed at some reaction mapping.
• Molecule representation
  • There was a NullPointerException in aromatization (forum topic).
  • Copy/paste and import/export of a molecule in mrv format having an S-Group with only one atom did not work (forum topic).
  • The getAromaticAndAliphaticRings method threw NullPointerException (forum topic).
• Calculator plugins
  • The exceptions of the Structural Frameworks plugin were sometimes improper (now it throws PluginException on error).
  • Projected surface area prediction produced inconsistent values (forum topic).
• Template handling
  • Homology templates were missing in applets.
• Installation
  • Marvin/JChem batch files could not handle quotes in the parameter list (forum topic).
• Licenses
  • The use of the setLicense or setLicenseFile API resulted in unusable client licenses unless they had the "Server Mode Allowed" field (forum topic).

May 27th, 2009: Marvin 5.2.2

New features and improvements

• MarvinSketch:
  • The Clear Atom List button is added to the Periodic System dialog window (forum topic).
  • Icon for Reaxys Generics is added.
• MolConverter:
  • Option -m produces multiple output files from multi-molecule input (forum topic).
• Applet:
  • New applet parameters for setting license files (forum topics: #3715, #4796).
• Import/Export:
  • InChi 1.02 version has been integrated.
  • InChiKey can be exported. New export option: inchi:key
• Calculator Plugins:
  • Added average microspecies charge calculations to cxcalc (averagemicrospeciescharge) and Chemical Terms (averageMicrospeciesCharge()) (forum topic).
• Documentation:
  • chemaxon.marvin.MolPrinter and chemaxon.formats.MolConverter API are improved.
• API:
  • Named constants for applet and bean parameters are available in the API: chemaxon.marvin.common.ParameterConstants.
  • New MolRenderer API available: chemaxon.marvin.beans.MolRenderer.
  • Deprecated methods in chemaxon.formats.MolImporter: parameterless constructor, setOptions(String), setFileName(String).

Bugfixes

• MarvinSketch:
  • Undo sets viewport to lower-right corner/Undo-Redo scaling.
  • Number of missing from menu label AND1 and AND2 in Atom > Stereo > Enhanced menu.
• MarvinView:
  • Selected cell becomes unselected after changing table options.
• Import/Export:
  • Pseudoatom export bug in MDL Molfile export.
  • Chiral center had wrong connectivity at atom. (forum topic).
  • chemaxon.util.MolHandler threw ClassCastException by SMILES.
  • Unique SMILES export bugs.
  • ClassCastException threw by endless loop for invalid SMILES import. (forum topic)
  • Reaction arrow was not visible by creating JPEG reaction images.
  • MRV import failed for polymer in abbreviated S-group.
  • IUPAC name import bug by certain structures.
• Molecule representation:
  • The chemaxon.marvin.MolPrinter.setMol method ignored atom sets.
• Chemical structure and graphical object painting:
  • NullPointerException in a MolPrinter example (forum topic).
  • The Get Sketch Image button on Marvin Beans example (examples/beans/sketch-images/SketchImages) generated misplaced drawing.
• Calculator Plugins:
  • 3D flexible alignment throws NullPointerException if molecules are too dissimilar to align.
  • Timelimit setting added to 3D flexible alignment API.
• Licenses:
  • Name to Structure was not running freely from Marvin.

April 14th, 2009: Marvin 5.2.1

New features and improvements

• MarvinSketch
  • Copy actions run in background thread.
  • Speed up OLE copy: MarvinOLEServer running in the background permanently.
• Applet
  • Customizable applet splash screen which is displayed while the applet is loading (live example).
• Import/Export
  • Allows aromatic boron in cxsmiles.
  • cxsmarts format stores attachment point data.
  • Support for atom values in cxsmiles.
  • Keep wedge arrangement in cxsmiles (forum topic).
• Calculator Plugins
  • Structural frameworks plugin is moved to Other plugin group, 3D Alignment plugin is moved to Conformation plugin group.
  • Added stereoDoubleBondCount calculation to TopologyAnalyserPlugin.
• Licenses
  • The Alignment plugin can be used with Conformation Plugin license.
• API
  • CGraph.cloneCopy() copies all relevant cached calculated data.

Bugfixes

• MarvinSketch
  • The first alteration of the structure couldn't be undone in MarvinSketch opened through MarvinView.
  • The .H+/.H- buttons could not be used in some cases.
  • Do not show carbon atoms when charge is on bracket.
  • Bold font is used for superscripts in case of charge for better visibility.
  • Missing bond problem after OLE copy: reimplementing bond-crossing drawing.
  • Missing bond crossing visualization when crossing a bond with a bond vertically.
  • The Insert > Groups dialog contained some empty elements.
• MarvinView
  • MarvinView hid the right side of text boxes.
  • MarvinView did not display SD file property when first entries are missing the value.
  • MarvinView freezing when molecule subset start index set to invalid value.
• MarvinSpace
  • MSpace debug printout is removed.
• Import/Export
  • Rdf conversion lost the reaction number (forum topic).
  • Fixed fusion bridge wrong lettering in name export (forum topic).
• Molecule Representation
  • Ungrouping of multilevel S-groups with Molecule.DEFAULT_UNGROUP caused NPE.
  • Empty DataSgroup-s are removed if an S-group gets empty (API, GUI).
  • Merge Brackets popup menu item was not available in some cases.
  • Rings were not cleaned perfectly.
• Calculator Plugins
  • MarkushEnumerationPlugin.getRandomStructure() did not return random structures, always the first enumerated was returned.
• Licenses
  • Markush license exception was incorrectly thrown by JChemSearch.
• API
  • MolImporter.getRecordCount returned 2* the expected number.
  • First (record number) column displays the value returned by MDocSource.getDocLabel.

March 10th, 2009: Marvin 5.2

New features and improvements

• Compatibility
  • Minimum Java requirement of Marvin is 1.5.
• MarvinSketch
  • Truly transparent structure painting method: higher quality drawings at crossing bonds and atom labels.
  • Vector graphics (EMF) copy place transparent picture to the clipboard.
  • New color schema options on the Periodic System dialog.
  • Charge can be assigned to the S-group and displayed on the molecule bracket.
  • Drawing attachment points outside S-groups.
  • Homology group drawing.
• MarvinView
  • Copy/Paste transfers molecule properties.
  • "Go To" option in Table menu.
  • New values of edited data fields and molecules are stored permanently in memory even in case of large (cached) viewer tables.
• Import/Export
  • Extended support for the generation of fused names (from 75% to 80%) in IUPAC name export.
  • CAS naming and simple fused systems supported in name import.
  • Transparent background in image export (EMF, SVG, PNG).
• Molecule representation
  • New option for adding an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.
• Calculator Plugins
  • New plugin: Flexible 3D alignment of multiple molecule structures to each other.
  • New plugin: structural framework calculation including Bemis-Murcko.
  • Markush enumeration:
    • Enumeration of homology groups.
    • Enumeration of X pseudo atoms [F,Cl,Br,I].
  • pKa calculator is trainable.
  • Total charge calculation in cxcalc ("totalcharge") (forum topic).
  • "Take major tautomeric form" option in MajorMicrospeciesPlugin.
  • 23 new ring related functions in TopologyAnalyser.
  • Resonance Plugin was moved to "Other" plugin group, and it can be used without license key (free) (forum topic).
• Chemical Terms
  • Flexible plugin parameter setting in Evaluator: "name1:value1 name2:value2 ...". (Example: markushEnumerations('random:true id:true', '1,2', 5).)
  • hasRadical(), radicalCount(), and hasIsotope() functions in Chemical Terms.
  • fragments() function in Chemical Terms (forum topic).
  • CT Editor is available in Marvin API.
• API
  • Transfer button: optional button to send the molecule to the specified target after closing MarvinSketch window.
  • Specify own background color separately for each cell in MarvinView via (applet) parameter.
  • New metal types can be specified in Periodic system.
  • Structure checker core classes and functions are implemented.
  • MViewPane enhanced table support.
  • PluginFactory creates new plugin and display instances for each getPlugin() and getDisplay() call in case of multimol display; added MOLECULES result domain type and canRepeat() in CalculatorPlugin

Bugfixes

• MarvinSketch
  • Disabled tooltips in menus.
  • The copied and generated structure with Data S-group is much bigger than needed (forum topic).
• MarvinView
  • Print All displayed only the first row on each page.
  • Multi-line SDF properties seem to be truncated in the cells until somone clicks on them (then a scrollbar appears).
  • Page Up/Page Down not working in spreadsheet view.
  • NullPointerException in empty mview when the "Show Fields" option was selected.
• Import/export
  • Cis Trans info defined by aromatic bonds in SMART / SMILES import. (forum topic
  • SMILES export of SuperAtom S-group in SuperAtom S-group did not work (forum topic).
• Molecule representation
  • Clean 2D improvement (forum topic).
• Calculator Plugins
  • Double bond stereoisomers of molecules containing wiggly type double bonds are generated correctly (forum topic).
  • Ungrouping grouped molecules before calculating functions in ElementalAnalyser.
  • cxcalc in concurrent mode always used ReusableInputProducer and hence plugin objects are always re-set in the working units.

What's new in Marvin 5.2?

• MarvinSketch
  • Truly transparent structure painting method: higher quality drawings at crossing bonds and atom labels.
    
  • Vector graphics (EMF) copy place transparent picture to the clipboard.
  • New color schema options on the Periodic System dialog.
    
  • Charge can be assigned to the S-group and displayed on the molecule bracket.
    
  • Drawing attachment points outside S-groups.
  • Homology group drawing.
    
  • A splash screen image is shown during the initialization of the standalone version.
    
• MarvinView
  • Copy/Paste transfers molecule properties.
  • "Go To" option in Table menu.
  • New values of edited data fields and molecules are stored permanently in memory even in case of large (cached) viewer tables.
• MolConverter:
  • Option -m produces multiple output files from multi-molecule input.
• Applet:
  • The loading of MSketch Applet is sped up: the total size of the files downloaded during the first initialization has been reduced by more than 20% between 5.2.0 and 5.2.3.
  • New applet parameters for setting license files.
• Import/Export
  • Extended support for the generation of fused names (from 75% to 80%) in IUPAC name export.
  • CAS naming and simple fused systems supported in name import.
  
  
  • Transparent background in image export (EMF, SVG, PNG).
  • InChiKey can be exported. New export option: inchi:key.
  • Partial charges are saved in mol2 file format based on the calculation result of the charge plugin.
• Molecule representation
  • New option for adding an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.
• Calculator Plugins
  • New plugin: Flexible 3D alignment of multiple molecule structures to each other.
  
  
  • New plugin: structural framework calculation including Bemis-Murcko.
  • Markush enumeration:
    • Enumeration of homology groups.
    • Enumeration of X pseudo atoms [F,Cl,Br,I].
  • pKa calculator is trainable.
  • The major tautomer generation has been sped up.
  • Total charge calculation in cxcalc ("totalcharge").
  • "Take major tautomeric form" option in MajorMicrospeciesPlugin.
  • New ring related functions in TopologyAnalyser.
  • Resonance Plugin was moved to "Other" plugin group, and it can be used without license key (free).
  • Added average microspecies charge calculations to cxcalc (averagemicrospeciescharge) and Chemical Terms (averageMicrospeciesCharge()).
• Chemical Terms
  • Flexible plugin parameter setting in Evaluator.
  • New functions: hasRadical(), radicalCount(), hasIsotope(), fragments().
  • CT Editor is available in Marvin.
• API
  • Transfer button: optional button to send the molecule to the specified target after closing MarvinSketch window.
  • Specify own background color separately for each cell in MarvinView via (applet) parameter.
  • New metal types can be specified in Periodic system.
  • Structure checker core classes and functions.
  • MViewPane enhanced table support.
  • PluginFactory creates new plugin and display instances for each getPlugin() and getDisplay() call in case of multimol display; added MOLECULES result domain type and canRepeat() in CalculatorPlugin.
  • Named constants for applet and bean parameters are available.
  • New MolRenderer API available.