Marvin 5.10.0 Beta version is available for testing!

 

Dear users,

Marvin 5.10.0 beta is available for testing. For a full list of changes, please see below.

Download: https://www.chemaxon.com/download.php?d=/data/download/marvin/5.10.0beta

Bug reports: if you found a bug in this beta release, please let us know through the regular support channels.

 

 

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June 08th, 2012: Marvin 5.10.0

New features and improvements

• MarvinSketch GUI
  
  
  
  • New graphical arrows: equilibrium arrow, curved arrow, dashed arrow, and crossed arrow has been introduced. Documentation, Forum topic
  
  
  • The built-in abbreviated groups can be easily extended and overridden with custom abbreviated group definitions. Documentation
  
  
  • New display option has been introduced:peptide sequence can be visualized in 1-letter form besides the original 3-letter form.
  
  
  • Cleaning preset is added to template sets. It can be controlled on the Template library dialog.
  
  
  • When opening an item of the Recent File list fails, the entry is deleted.
  
  
  • All query atoms and query properties are available from menu and toolbar by customization.
  
  
  • Names of homology groups on "Advanced" tab of "Periodic System Dialog" and in "Template Library" have been updated.
  
  
  • The elements of the Advanced tab on the Periodic System dialog are now available from MarvinSketch by typing as shortcuts.
  
  
  • The picture of custom defined templates appear at the mouse tooltip when the name of the structure is unknown.
  
  
  • The name of reaction arrow: "Resonance" and graphical arrow "Two-Headed Arrow" have been changed. Forum topic
  
  
  
  


• MarvinSketch Printing
  
  
  
  • The page format settings on the print dialog is now stored and do not need to be reset when starting a printing job from MarvinSketch or MarvinView. Forum topic
  
  
  
  


• Import/Export
  
  
  
  • Load/Save handling in UI
    
    
    
    • Disconnected molecules can be saved separately in MSketch. Documentation.
    
    
    • When saving a document opened by d2s in MView, MRV is offered as default format.
    
    
    
    
  
  
  • Structure to Name (s2n)
    
    
    
    • Extended and updated structure to common name dictionary.
    
    
    • L-amino acid structures are all converted to L- traditional name.
    
    
    
    
  
  
  • Name to Structure (n2s)
    
    
    
    • Improved conversion of systematic names, notably names expressed as amides of acids, such as "pyridine-4-carboxylic acid (2-methoxy-ethyl)-methyl-amide".
    
    
    • Extended and updated common name to structure dictionary.
    
    
    • All peptide abbreviations are now consistently converted to the L- stereo form structure.
    
    
    
    
  
  
  • Document to Structure (d2s)
    
    
    
    • Document to Structure can be instructed to process only a subset of pages in a document using the new startPage and endPage format options.
    
    
    
    
  
  
  • DNA/RNA
    
    
    
    • DNA nucleid acid sequence can be imported in four ways: ACGT, A-C-G-T, dAdCdGdT or dA-dC-dG-dT. RNA nucleic acid import accepts sequences like both ACGU and A-C-G-U.
    
    
    
    
  
  
  
  


• Molecule Representation
  
  
  
  • Molecule/atom/bond properties
    
    
    
    • Similarly to MolAtom, general properties are possible to be added to MolBond.
    
    
    • New, simple way is provided to replace isotopes.data and elements.zip used in PeriodicSystem.java. Documentation.
    
    
    
    
  
  
  • S-groups
    
    
    
    • New method is introduced to set a data S-group to behave as relative after specifying its absolute position
    
    
    
    
  
  
  • R-groups
    
    
    
    • A new, fast method is available to delete one or more molecules from an R-group definition.
    
    
    
    
  
  
  
  


• Calculations
  
  
  
  • Isomers (tautomer., reson.)
    
    
    
    • Rational tautomer generation option has been introduced. Generation of All tautomers and Canonical tautomer can take this new option into consideration. Documentation
    
    
    
    
  
  
  • NMR Predictor
    
    
    
    • NMR Predictor is available in MarvinSketch. It accurately predicts ¹³C and ¹H NMR spectra of standard organic molecules. See Product page and Documentation for more information.
    
    
    
    
  
  
  • Services
    
    
    
    • LocalService allows to set URL based JAR path.
    
    
    
    
  
  
  
  


• Structure Checker
  
  
  
  • New checker: Absent Chiral Flag checker; when the molecule is chiral and all stereo centers are precisely marked, absolute chiral flag can be applied to the molecule. Documentation
  
  
  • R-group Reference Error Checker is deprecated and has been split into three separate checkers:
    
    
    
    • Circular R-group Reference Checker;
    
    
    • Missing R-group Checker;
    
    
    • Unused R-group Checker.
    
    
    
    
  
  
  • Partial clean fixer is available for certain structure checkers: it can fix the erroneous part of the molecule exclusively.
  
  
  
  


• Stereochemistry
  
  
  
  • A new method is available that finds atoms that can become (s) or (r) stereo centers after the stereo arrangement of the bonds around the atom is specified.
  
  
  
  


• API
  
  
  
  • New parameter to set accessibility of special nodes in Advanced tab of Periodic System dialog: Documentation (Forum topic).
  
  
  
  

Bugfixes

• MarvinSketch
  
  
  
  • When MarvinSketch was launched from command line with -h or --help option, the application was not terminated after printing of help message.
  
  
  • When using MSketchPane from an application, and pop it up as a modal dialog, its children could disappear behind the main application (e.g. DialogLauncher example).
  
  
  
  


• MarvinSketch GUI
  
  
  
  • Scaling bug occured on the button of the template toolbar if there was a contracted group displayed on the button.
  
  
  • "Calculations" menu did not appear in ISIS/Draw-like configuration.
  
  
  
  


• MarvinView GUI
  
  
  
  • The title of the MView application window was not updated on file open and save.
  
  
  
  


• Applet
  
  
  
  • Although a valid URL was given in sketchHelp applet parameter, Marvin applet loaded the default help by selecting Help->Help Content instead of the given URL.
  
  
  • "My templates" became unavailable in applet after modifying it from template library. Forum topic.
  
  
  
  


• Painting
  
  
  
  • The rb* atomic query property was not displayed at the mouse tooltip when it was set through its keyboard shortcut: ".rb*".
  
  
  
  


• Chemical Structure Painting
  
  
  
  • Positioning of R-group labels was incorrect.
  
  
  
  


• Datatransfer
  
  
  
  • Clipboard handling
    
    
    
    • Copy as PDF used 100x100px as image metrics and not the appropriate size for the current scale in Mac OSX.
    
    
    
    
  
  
  
  


• Import/Export
  
  
  
  • MOL, SDF, RXN, RDF
    
    
    
    • The subscript information of the S-group generic bracket was not exported to MOL V3000 and V2000 formats.
    
    
    • Export of compressed MOL files allowed too large coordinate values, which caused distortion in the molecule after importing it.
    
    
    • After importing an RDfile that contains an empty S-group, its brackets didn't appear.
    
    
    
    
  
  
  • SDF
    
    
    
    • Data S-groups were lost after exporting it to SDF format.
    
    
    
    
  
  
  • SMILES, SMARTS
    
    
    
    • Export to abbreviated group format did not work since 5.8.
    
    
    
    
  
  
  • CXSMILES, CXSMARTS
    
    
    
    • CXSMILES import added radicals to atoms that have coordinate bond to a central, metal atom.
    
    
    • I/O of atom alias "," was not working in CXSMILES format.
    
    
    
    
  
  
  • CML, MRV
    
    
    
    • Format mrv had missing closing tags at the end of the generic S-group lines.
    
    
    • MolExporter exported to MRV format using operating system specific line ending, '\n'.
    
    
    
    
  
  
  • CDX
    
    
    
    • Standalone list atoms and labels were read as text boxes from CDX files.
    
    
    • Component grouping was not recognized during CDX import.
    
    
    
    
  
  
  • SKC
    
    
    
    • During the export to SKC format, chiral flags were lost and "AND enantiomer" flags were displayed.
    
    
    
    
  
  
  • CDX/SKC
    
    
    
    • When opening a ChemDraw .cdx file or an ISIS/Draw .skc file containing structures with abbreviated groups, the attachment point of these groups was rendered incorrectly.
    
    
    
    
  
  
  • Structure to Name (s2n)
    
    
    
    • There were extraneous numbers in generated names for structures containing atom values.
    
    
    • Generation of IUPAC names for large structures might have stopped before the timeout.
    
    
    
    
  
  
  • Name to Structure (n2s)
    
    
    
    • The n2s import option to specify the location of the custom dictionary was not thread-safe, and was not accessible in d2s.
    
    
    • Name to structure failed to return a result on some very long names (several hundreds of characters).
    
    
    
    
  
  
  • Document to Structure (d2s)
    
    
    
    • Non-chemical data in embedded structures, for instance text labels, were not extracted from embedded documents.
    
    
    • Some embedded structures were not extracted from office documents.
    
    
    • Reactions embedded in documents were not extracted.
    
    
    
    
  
  
  • Molconvert
    
    
    
    • A NullPointerException appeared in the console instead of an error message when using molconvert to convert an image with skiperror parameter set without OSRA installed.
    
    
    
    
  
  
  
  


• Molecule Representation
  
  
  
  • Valence Check
    
    
    
    • Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
    
    
    • False positive valence error was on aromatic rings which have sulfur ligand that is part of a ring.
    
    
    • Removing explicit hydrogen atoms from LiH, CaH₂, SH₄, PH₅, PbH₂, PbH₄ did not keep the original hydrogen count.
    
    
    • Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
    
    
    
    
  
  
  • S-groups
    
    
    
    • Bracket positioning did not take the implicit hydrogen atoms into account.
    
    
    • If data were added as "relative", the cleaning or arrange methods did not take them along with the fragment/component/molecule.
    
    
    • The chirality of expanded S-group's atom changed, when there wasn't enough space in the canvas for the expanded S-group.
    
    
    • After expanding S-groups, atoms of the molecule could overlap.
    
    
    • Removal of explicit hydrogen being the only atom of an S-group was unsuccessful. New flag, SGROUP_H, has been introduced, fo remove such hydrogens.
    
    
    • Exception was occurred when an abbreviated group was copied then pasted.
    
    
    • Method MulticenterTransform.transformMulticenters(Molecule mol) and MulticenterTransform.restoreMulticenters(Molecule mol) changed the number of implicit hydrogens of atoms.
    
    
    
    
  
  
  • R-groups
    
    
    
    • Fragmantation of an Rg-molecule resulted inconsistent molecules.
    
    
    
    
  
  
  
  


• Clean 2D
  
  
  
  • In case of selection, stereoinformation of the molecule during two dimensional cleaning was lost.
  
  
  
  


• Aromatization/dearomatization
  
  
  
  • General aromatization worked incorrectly in case of molecules with a bond connecting 2 rings but not being part of any ring. Solving this problem, deprecated method int[] getSSSRBondSet(), was removed and, instead, BitSet getSSSRBondSet() was introduced.
  
  
  
  


• Calculations
  
  
  
  • Isomers (tautomer., reson.)
    
    
    
    • Tautomer generation was very slow on proteins.
    
    
    • Some deuterium atoms were removed during tautomer generation. Forum.
    
    
    • The structure of the generated tautomer was not cleaned if the input molecule contained abbreviated group(s).
    
    
    
    
  
  
  
  


• Structure Checker
  
  
  
  • Clean Wedge fixer of Wedge Error checker had no effect in case of wedge bond between two chiral centers.
  
  
  
  


• Elemental Analyzer
  
  
  
  • Elemental analyser calculated wrong molecular formula for molecules, that contains bond to a centroid.