Release notes for 5.7.x releases

December 12th, 2011: Marvin 5.7.1

Bugfixes

• Molecule Painting
  • Valences higher than nine were wrongly displayed if the valence property visibility was turned off.
• Calculator Plugins
  • Some property calculations threw ArrayIndexOutOfBoundsException when the input molecule contained multiple fragments.
• Build/Installation
  • OLE defect occured during side-by-side installations.

November 4th, 2011: Marvin 5.7.0

New features and improvements

• MarvinSketch GUI
  • New bond type: "Hashed bond" has been introduced.
  • "Coordinate" Bond Line Style – in the Edit>Preferences>Bonds menu – allows changing the type of coordinate bonds between the default ones (arrow for single atom and hashed for multicenter) and solid.
  • Selected structures can be aligned or distributed relative to each other horizontally or vertically. The Align&Distribute function aligns and distribute the objects at the same time.
  • New chain drawing tool: Curved chain tool. Instead of creating a straight chain it modifies the direction of the last bond of the chain based on the mouse movement. Curved chains or macrocycles can be created that way.
  • The chain drawing direction is mirrored based on the direction of the mouse movements.
  • Selection can be moved in greater units with SHIFT + arrow keys.
• Import/Export
  • Structure to Name
    • Traditional name for known class names (e.g. acylcholine) is generated.
  • Name to Structure
    • "Name to structure" converter supports more systematic names (6% to 50% measured on various sets of names extracted from patents). For instance, names representing esterification with locants (e.g. 1,4-di-tert-butyl piperazine-1,4-dicarboxylate).
    • Optional support for CAS numbers in Document2Structure.
    • Faster loading of PDFs by Document to Structure (from 25% to 75% speedup in most cases). Names can be extracted from more types of PDFs.
  • CDX/CDXML
    • Hashed bond type has been implemented in Marvin. "Hashed to Down Wedge" conversion has been changed to "Hashed to Hashed" conversion.
• Clean 3D/optimization
  • Verbose mode has been added to Generate3D. Use option "[verbose]" to switch on; use "molconvert -H3D" for detailed help.
• Datatransfer
  • Native pasteboard for Macintosh has been implemented. It solves general copy/paste issues, e.g. copy/paste between Marvin and other chemical sketcher programs (e.g., ChemDraw).
  • Marvin supports conversion of other Vendors (currently ISIS and Symys) embedded OLE objects to Marvin OLE.
• Structure Checker
  • New checkers are available:
    • R-atom Checker: detects R-atoms (all, disconnected, generic, linker, nested).
    • R-group Attachment Error Checker: detects attachment differences between R-atoms and R-group members. A new fixer corrects the attachment bond types and adds missing attachments in unambiguous cases.
    • R-group Reference Error Checker: detects missing R-atoms, missing R-groups, self or circular references of nested R-atoms.
  • Checker and fixer classes implemented by the user are loaded from given jar file.
• API
  • chemaxon.marvin.util.ColorGenerator class provides an easy way to generate the required number of different colors.
  • Several core functions are deprecated. See this table for details.
  • API support for running checkers and fixers multiple times automatically.

Bugfixes

• MarvinSketch
  • The Java beans and applet parameter for switching the valence property visibility OFF was missing.
• MarvinSketch GUI
  • Scrolling with mousewheel or arrow keys enlarged Marvin Sketch canvas.
  • Moving selection with arrow keys could not be undone.
  • Attachment points were not highlighted by green when they were selected.
  • Sugar templates: D-furanoses had S label on carbon 5.
  • Double click selection did not work when it pointed to an atom.
• MarvinView
  • MViewPane did not refresh when UserSettings changed.
• MarvinView printing
  • Several MarvinView display property was missing in MolPrinter
• Painting
  • Error highlight was partially visible and often disappeared on mouse move.
• Molecule Painting
  • Positive charge of hydrogen was not scaled properly in case of small magnification.
• Import/Export
  • Structure to Name
    • Incorrect names where generated when the parent structure has identical substituents orientated differently, for instance: 4-formamido-1H-pyrazole-3-carboxamide
  • Inchi Key
    • Inchi slowdown with inchikey call for 10000s of structures.
  • PDF
    • OSRA did not work in Marvin unless its library was set in the PATH.
  • SMILES/SMARTS
    • A molfile or sketch is carrying an 'rb*' flag on any atom(s) was translated incorrectly to SMARTS ('x' atomic primitive).
    • cxsmiles IO of Data sgroup was incorrect.
    • mol format from smarts wich contained "[C,!N]" (representing "Carbon , not Nitrogen") was converted incorrectly.
• Molecule representation
  • Connecting an additional bond to an abbreviated group freezed Marvin Sketch.
• Stereochemistry
  • Allene parity lost by removing explicit hydrogens.
• Aromatization/dearomatization
  • Aromatization of an aromatized structure created new aromatic ring
• Elemental analysis
  • The Elemental Analyzer did not support Position-Variation bonds in formula calculation. Known issue: Dot-disconnected formula calculation is not working correctly in case of Position-Variation bonds.

What's new in Marvin 5.7?

Latest version: Marvin 5.9.4

Download Marvin's latest version

See all new features and bug fixes in change log

New bond type: Hashed bond has been introduced.	Selected structures can be aligned or distributed relative to each other horizontally or vertically. The Align&Distribute function aligns and distribute the objects at the same time.
"Coordinate" Bond Line Style – in the Edit>Preferences>Bonds menu – allows changing the type of coordinate bonds between the default ones (arrow for single atom and hashed for multicenter) and solid.	Curved chain tool has been introduced. Instead of creating a straight chain it modifies the direction of the last bond of the chain based on the mouse movement.
API: Several core functions are deprecated. See this table for details.	Name to structure converter supports more systematic names(6% to 50% measured on various sets of names extracted from patents).
Native pasteboard for Macintosh has been implemented. It solves general copy/paste issues, e.g. copy/paste between Marvin other chemical sketcher programs.	New version number policy: the first 3 digit indicates the version number of the release, the last part is an internal build ID that is a helper info for deploying packages.

Change log

Release notes archive 5.6, 5.5, 5.4, 5.3, 5.2, 5.1, 5.0, 4.1, 4.0, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2.0, 1.3, 1.2, 1.1, 1.0