Marvin 5.8.0 beta is available for testing

Dear users,

Marvin 5.8.0 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/5.8.0beta

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

 

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Marvin 5.8.0 beta changes:

New features and improvements

• MarvinSketch GUI
  
  
  
  
  • Group types on "group creation" dialoge can be configured.
  
  
  • The icon of manual atom mapping has been changed.
  
  
  • A new radical electron setting and the corresponding toolbar icon group has been introduced, solely for educational purposes: Up to four radical electrons can be defined for an atom, and it is arranged evenly in the empty space around the atom label.
  
  
  • Recent file list length has been increased up to 50. (The default is 25.)
  
  
  
  


• MarvinView GUI
  
  
  
  
  • Atom mark and atom highlight display can be enabled/disabled.
  
  
  
  


• Import/Export
  
  
  
  
  • Structure to Name (s2n)
    
    
    
    
    • New name format option: "source" has been introduced to print the names present in the source molecule data. For instance, molconvert name:source input.sdf.
    
    
    
    
  
  
  • Name to Structure (n2s)
    
    
    
    
    • Automatic text OCR (optical character recognition) has been added to support document to structure conversion of scanned (non searchable) PDF documents.
    
    
    • n2s handles stereochemistry of cyclic monosaccharides.
    
    
    • Extended support for common names: n2s can convert 123 thousand common names – including synonyms – corresponding to 34 thousand structures instead of the previous 63 and 28 thousand, respectively.
    
    
    
    
  
  
  • MRV
    
    
    
    
    • The information on the selected atoms and bonds can be stored in MRV format.
    
    
    • MRV format has been changed: there is no indentation, there are line-breakes only after the header and after the documents. The original format (including line-breakes and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications. See export options here.
    
    
    
    
  
  
  • SMARTS
    
    
    
    
    • ChemAxon Extended SMARTS represents R-group (Markush) structures.
    
    
    
    
  
  
  • CML
    
    
    
    
    • CML bondStereo implementation has been completed with atom references.
    
    
    • CML format has been changed: there is no indentation, there are line-breakes only after the molecules and after the header. The original format (including line-breakes and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications. See export options here.
    
    
    
    
  
  
  
  


• Calculator Plugins
  
  
  
  
  • New integrated component: NMR Predictor Beta has been implemented.
  
  
  • "Consider tautomerization" option has been renamed to "Consider tautomerization/resonance" in logP and logD calculator plugins.
  
  
  • "Tools" menu content has been moved to "Calculations" menu.
  
  
  
  


• Data transfer
  
  
  
  
  • Native PDF format as the default image pasteboard format is used on MAC systems. It allows the user to copy a structure (which was originally created by either Marvin or ChemDraw) from a Microsoft Office 2011 document and to paste it to Marvin.
  
  
  • More verbose logging from from OLE Dotnet panel (catching managed bridge exceptions via COM) has been introduced.
  
  
  
  

Bugfixes

• MarvinView
  
  
  
  
  • Sometimes molecules were lost when switching from "Spreadsheet mode" (Table>Options>Table Type) to "Molecule matrix" mode.
  
  
  • When a zero length structure file was opened, the content of the previous file remained in the viewer until the first repainting.
  
  
  • Scrolling up and down increased the number of molecules and changed their orders.
  
  
  
  


• Painting
  
  
  
  
  • Until the first repaint, textbox was smaller than required, and the content was cropped to its size.
  
  
  
  


• Import/Export
  
  
  
  
  • Structure to Name (s2n)
    
    
    
    
    • Incorrect name was generated for chiral allenes, for instance: (2M)-1,3-dichloropropa-1,2-diene, the correct is 1M. (The locant was previously in the middle of the cumulated double bond system, but is now at the beginning of it, as prescribed by IUPAC.)
    
    
    • Fixed generation of names in the case where a radical marker "yl" was missing, for instance "...(4-methylbenzene)sulfonyl..." instead of the correct form "...(4-methylphenyl)sulfonyl..."
    
    
    
    
  
  
  • Name to Structure (n2s)
    
    
    
    
    • Automatic name format recognition failed for names containing unicode prime characters.
    
    
    • CAS number cache could get corrupted and created failures.
    
    
    
    
  
  
  • Document to Structure (d2s)
    
    
    
    
    • The total length (getEstimatedTotalCharacters) was not available to progress listeners during Document to Structure conversion of PDFs using the API.
    
    
    
    
  
  
  • SMILES
    
    
    
    
    • CXSMILES IO error due to non-escaped characters appeared.
    
    
    • The name imported from SMILES format was wrong in rare cases, when special characters (e.g., |) were in the fields part of the extended SMILES.
    
    
    
    
  
  
  
  


• Calculator Plugins
  
  
  
  
  • logP and pKa calculations threw error at heavy atom count 300.
  
  
  
  

I am trying to convert IUPAC names to structures in Marvin Draw 5.11.4 (cut and paste)

Structures with unicode characters do not get generated, though it is reported fixed as of 5.8 "Fixed: Automatic name format recognition failed for names containing unicode prime characters." as indicated in this thread.

Example name:

5-chloro-2,15-dimethyl-14-(6-methylheptan-2-yl)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-7-ene Could you please give some advice?

I checked it and I can confirm that this is a bug in versions 5.11.4 and 5.11.5. It was fixed in version 5.12 . Thank you for reporting it, we will corect the release notes.

Best Regards,

Efi

I can confirm this is working since version 5.12. The corresponding message in the change log is:

Name to structure now also works when bridge and spiro numberings are represented by using unicode superscript numbers, such as: tetracyclo[12.4.0.02,6.07,12]octadecane