Marvin 5.9.0 beta is available for testing

Dear users,

Marvin 5.9.0 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/5.9.0beta2

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

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March 2nd, 2012: Marvin 5.9.0 Beta

New features and improvements

• MarvinSketch GUI
  
  
  
  • Drawing electron flow arrow in a reaction has been enabled.
  
  
  
  


• MarvinView GUI
  
  
  
  • Document to Structure on PDF documents can display the first structures without waiting to process the whole document.
  
  
  
  


• Import/Export
  
  
  
  • CML, MRV
    
    
    
    • New option to MRV and CML export, :CN, is introduced, where 0 < N ≤ 9 and N is the length of the decimals of the exported coordinates. For example, mrv:C5
    
    
    
    
  
  
  • Name to Structure (n2s)
    
    
    
    • Conversion of systematic names has been increased by about 5%, and increased accuracy of the generated structures.
    
    
    • Prefix "nor" has been implemented (e.g., 17-Hydroxy-19-norpregn-4-ene).
    
    
    • Name with stereo-markers "r" or "s" where such stereoconfiguration cannot be present are now interpreted as "R" or "S". This allows names that have been completely lowercased to be converted correctly.
    
    
    
    
  
  
  • Document to Structure (d2s)
    
    
    
    • Document to Structure supports the following common office document formats: doc, docx, ppt, pptx, xls, xls, odt in addition to pdf, xml, html and txt.
    
    
    • Format options have been added to d2s, to specify what input formats should be converted (for CAS, SMILES and inchi). Format option "insideTag=<tag>" to restrict conversions to the content of a specific tag (for instance in HTML).
    
    
    • The type of source text used for the conversion is included in generated structures. Possibly values: systematic, generic, common (for names), smiles, InChI, CAS# (for text formats), cdx, mrv, symyx (for embedded structures in office documents).
    
    
    • Processing speed has been increased: doubled on typical documents including chemical names, and tripled on documents with few chemical names.
    
    
    
    
  
  
  
  


• Molecule Representation
  
  
  
  • Molecule/atom/bond properties
    
    
    
    • ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
    
    
    
    
  
  
  • Valence Check
    
    
    
    • A new option is provided which enables to turn off the valence check of nitrogen, phosphorus, or boron atoms in those cases when they are in aromatic compounds.
    
    
    
    
  
  
  
  


• Calculations
  
  
  
  • Isomers (tautomer., reson.)
    
    
    
    • Tautomerization can take into account the possibility of ring closure when "All tautomers" function is selected.
    
    
    
    
  
  
  • NMR Predictor Beta
    
    
    
    • "Copy to Clipboard" and "Export Prediction to PDF" actions have been implemented.
    
    
    
    
  
  
  
  


• cxcalc
  
  
  
  • Advanced logging in cxcalc: logging errors and execution times is available.
  
  
  
  


• Structure Checker
  
  
  
  • Chiral flag error checker options have been improved.
  
  
  • Custom fixers use annotations replacing property files. Backward compatibility is ensured for both custom checkers and fixers.Documentation
  
  
  • Pattern based report file generation is available as a new option in structurecheck commandline.
  
  
  
  


• MarvinSpace
  
  
  
  • Default aromatization method in MarvinSpace is the Basic aromatization (the same as in MarvinSketch).
  
  
  
  

Bugfixes

• MarvinSketch GUI
  
  
  
  • MarvinView 3D window could not be opened from the sketcher if MarvinView 2D window had been opened before.
  
  
  
  


• Applet
  
  
  
  • Applet settings could influence the client side desktop application settings.
  
  
  
  


• Painting
  
  
  
  • The query properties were wrongly painted in some cases and covered the atom labels.
  
  
  • 3D rotate action activated automatically when joining a structure in hand to a bond of a 2D structure on the canvas.
  
  
  • Double bond was not painted in centered position in case of terminal bonds when the label of the connected atom was displayed or both of the atom labels were displayed.
  
  
  • Single arrow type brackets were not painted.
  
  
  • The orientation of explicit hydrogens was incorrect when explicit hydrogens were added to the (selected) upper methylene C atom of a cyclohexane.
  
  
  
  


• Import/Export
  
  
  
  • MOL, SDF, RXN, RDF
    
    
    
    • Handling of special characters (-, ", space) in extended MDL MOL format IO was wrong.
    
    
    • RDF file exported by Instant JChem was not imported correctly to ISIS/Base.
    
    
    
    
  
  
  • SMILES, SMARTS
    
    
    
    • In some rare cases, the unique SMILES of a molecule depended on the numbering of the atoms.
    
    
    
    
  
  
  • CML, MRV
    
    
    
    • Parity value in CML format was stored the opposite way as the CML standard defines it. Now the correct value is stored which leads to backward inconsistency with CML files generated by ChemAxon applications in previous versions, but correct values are read from standard CML files. To avoid running into similar problems in the future, now a version information is stored both in CML and MRV formats. This information contains a version number of the file format and the application version by which the file was generated. The parity value is changed to opposite in MRV format as well to be consistent with the CML format but it does not lead to backward inconsistency in this case: parity values stored in not versioned MRV files are converted to their opposite while parity values from versioned MRV files are not.
    
    
    
    
  
  
  • PDF
    
    
    
    • View settings were not applied in exported pdf file.
    
    
    
    
  
  
  • VMN
    
    
    
    • VNM format sometimes was recognized wrongly as mol2.
    
    
    
    
  
  
  • Image I/O
    
    
    
    • The molecule source was generated in unnecessary cases.
    
    
    • javax.imageio left temp files open if the ImageOutputStream was not closed properly.
    
    
    
    
  
  
  • Structure to Name (s2n)
    
    
    
    • The generated names for bridged and spiro ring systems were missing E/Z stereodescriptors for double bonds in large rings.
    
    
    • Some unconventional names were generated with suffixes such as amido, sulfonyl, carbonyl, ... mentioned as prefixes. For instance 2-[(2-chlorophenyl)amido]benzoate for [O-]C(=O)C1=C(NC(=O)C2=C(Cl)C=CC=C2)C=CC=C1. The generated names is now 2-(2-chlorobenzamido)benzoate.
    
    
    
    
  
  
  • Name to Structure (n2s)
    
    
    
    • Stereochemistry was not indicated in the displayed structure when cis or trans is used to specify the configuration of the two substituents of a ring system.
    
    
    • Cycloalkane substituents of fused ring systems were aromatized.
    
    
    • The stereochemistry of chiral atoms in subsitutents was sometimes inverted.
    
    
    • Name to Structure was blocked on some very long names with unbalanced parentheses.
    
    
    
    
  
  
  • Document to Structure (d2s)
    
    
    
    • Some types of smiles strings were not recognized by Document to Structure, in particular those with stereochemistry or acyclic structures with two-letter heteroatoms.
    
    
    
    
  
  
  • Peptide
    
    
    
    • Numbers or sign "-" in the name of custom aminoacids were not accepted during the import of peptides (exception was thrown).
    
    
    
    
  
  
  
  


• Molecule Representation
  
  
  
  • Molecule/atom/bond properties
    
    
    
    • ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
    
    
    • Molecule.implicitizeHydrogens() threw "java.lang.IndexOutOfBoundsException" after fragmentation if the molecule contained information in MDocument field.
    
    
    
    
  
  
  • Valence Check
    
    
    
    • Valence Check gave false valence error for aromatic oxygen having +1 charge.
    
    
    
    
  
  
  
  


• Structure Checker
  
  
  
  • Aromaticity Error checker options could not be set.
  
  
  
  

Known issue

• Structure Checker
  
  
  
  • R-group Reference Error Checker cannot find circular and selfreferring R-atoms and R-groups.
  
  
  
  

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.

---

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.