Bugfixes

• Import/Export

  • OLE objects created by Accelrys Draw 4.1 and further versions could not be redirected by MarvinOLE server.

  • OLE opened in 3D rotation mode (F7) mode.

Bugfixes

• Applet

  • Communication problem involving JavaScript was fixed.

New features and improvements

• Image I/O

  • New image IO parameter "aminoAcidBondColoringEnabled" has been introduced for peptide bond coloring.

• Import/Export

  • SKC

    • If they are set to visible in ISIS, "Atom numbers" are imported as atom mapping from SKC.

Bugfixes

• Clipboard handling

  • If a structure had been pasted onto an empty canvas and MarvinSketch was closed without modifying the structure, the structure was not saved.

  • Files with "smiles" extension did not load by dragging them and dropping into MarvinSketch.

  • Clicking on the Transfer button (of MarvinSketch) after editing a structure in MarvinView caused NPE.

• Editing

  • If a template was merged to an atom of an abbreviated group which did not have any attachment point, the abbreviated group was not ungrouped.

  • Bond shortcuts did not work until the user pressed the "Bond" button on the "Tools" toolbar.

• Image I/O

  • Bond set coloring image export parameter was not effective, and in some cases it was able to modify the atom set coloring.

  • When saving a structure in pdf format, the image was cut too narrow.

  • Circled charge was not copied into PDF clipboard format on Mac. Currently it is represented without the circle.

• Molecule Representation

  • Valence Check

    • False valence error appeared on aromatic rings containing Nitrogen-like atoms in their aromatic form.

  • S-groups

    • The direction of S-group labels was changed at wrong angle.

• Painting

  • The " * " character was not supported in (among others) Arial, Times New Roman, and Lucida font family.

  • The leftname/rightname rendering of abbreviated groups have been incorrect in several cases such as "OMe".

• Name to Structure (n2s)

  • Some substituents separated by a space from an acid parent were wrongly interpreted as esters.

  • The naming webservice was not working in the applet.

New features and improvements

• Painting

  • Bond properties are displayed on the canvas.

• Clipboard handling

  • When the clipboard format is not recognized as a chemical object, the format chooser dialog is not displayed and Marvin does not import anything. Forum

• MarvinSketch Menu

  • The "Switch Transformation" menu item is removed from the "Edit > Transform" menu.

  • The "Graph Invariants" menu option is removed from the "View > Advanced" menu.

• MarvinSketch Dialogs

  • Look&Feel option has been eliminated from the "Preferences" dialog.

• Import/Export

  • CXSMILES, CXSMARTS

    • R-logic is supported by the CXSMILES and CXSMARTS formats.

    • Atom properties of homology groups are supported by the CXSMILES/CXSMARTS formats.

  • CDX, CDXML

    • 3-letter abbreviated amino acid labels can be imported from CDX. Forum

  • Name to Structure (n2s)

    • Japanese Name to Structure is supported. It requires a separate license.

    • The custom dictionary can be encoded in UTF-16 (both UTF-16BE and UTF-16LE variants) even if the system default encoding is different. The file needs to start with a byte order mark (BOM) character.

  • Document to Structure (d2s)

    • OSRA 2.0 is supported.

    • A format option has been introduced allowing the user to select an optical structure recognition tool: CLiDE, OSRA or Imago when more than one is installed on the computer. For instance, d2s:osra will request OSRA to be used.

  • Structure to Name (s2n)

    • Locants with a number and an atom type are written, for instance, as N6 instead of 6-N following the latest IUPAC recommendations.

• Molecule Representation

  • Method chemaxon.struc.MolBond.equals() compares the bonds by reference and not by the end points.

  • Clean 2D

    • Clean 2D of structures containing explicit hydrogen atoms is improved. Forum

• Applet

  • When the Marvin Applet does not work because the Java version is outdated, a proper warning message is displayed.

• Licensing

  • Reading of licenses has changed: now licenses in the ChemAxon home directory are read even if the CHEMAXON_LICENSE_URL environment variable or the chemaxon.license.url java system property is set.

• Structure Checker

  • "Double Bond Stereo Error Checker" has been introduced, which searches for invalid either double bonds. Its corresponding fixer converts the invalid either double bonds to plain double bonds. Documentation

  • "Stereo Inversion Retention Mark Checker" has been introduced, which identifies stereo inversion/retention marks on single molecules and in reactions. Its associated fixer removes the stereo inversion/retention marks from the structures. Documentation

  • "Valence Error Checker" detects all valence errors in Markush structures, even if the valence error is inside R-group definitions. Its fixer corrects all fixable valence errors in Markush structures.

• Calculations

  • Solubility

    • Aqueous Solubility Predictor has been added to Calculator Plugins. Documentation

  • Stereo Analysis

    • Available via cxcalc and Chemical Terms. Documentation

  • Conformations

    • Advanced conformational search. Documentation

Bugfixes

• Editing

  • Trying to merge an S-group on a multicenter atom threw a NullPointerException.

  • Hovering over a rounded rectangle with the mouse cursor caused a NullPointerException.

  • Replacing a selected single atom with a hydrogen using the toolbar button resulted in a "HH" atom.

  • Bonds could not be drawn from hydrogen atoms to other atoms.

  • The "Absolute" chiral flag disappeared from the canvas when the reaction arrow was deleted.

  • The brackets of an S-group disappeared when the group became part of a reaction.

  • Replacing an amino acid in a sequence merged the new amino acid in the wrong direction.

  • When single atoms in a chain were replaced by amino acids, attachment orders were incorrect.

  • Rotation of molecules in 3D did not work properly.

  • If a query property was set for an atom and - in a later step- a bond was drawn from this atom, the value of the atomic query property changed to zero regardless from its original setting.

• Load/Save handling in UI

  • Changing the background color when a 3D structure was converted to 2D, then saving in PNG format saved the structure with the earlier, 3D background color.

• Clipboard handling

  • Structure display options were not preserved when structures were copy-pasted as Marvin OLE objects.

  • Pasting a file in a one-line molecule format (e.g., SMILES) on the canvas merged the lines of the file content. Currently, only the first line of the file is pasted.

• MarvinView GUI

  • The "Save Selection..." menu option could not be used for selecting structures for saving from a multimolecule file.

• Import/Export

  • MRV, CML

    • CML and MRV import threw java.lang.ArrayIndexOutOfBoundsException when reading parallel bonds atoms. Now chemaxon.formats.MolFormatException is thrown instead.

  • SMILES, SMARTS

    • SMARTS string starting with parentheses was recognized as SMILES.

  • CXSMILES, CXSMARTS

    • Chiral flag (or molecular absolute stereo) was not exported to CXSMILES if enhanced stereo existed in the molecule.

  • InChi, InChiKey

    • Coordinate bond was exported as single bond to InChi. From now, we do not export these bonds according to the IUPAC recommendation.

  • Name to Structure (n2s)

    • The multiplying prefix "eicosa", a non-IUPAC variant of "icosa" was not supported.

    • The Chinese names of some alkanoic acids, such as ????, were not supported.

    • Some common names containing "chloride" were imported without a chlorine atom.

    • Some chiral heterocenters were reversed in anhydrides.

    • Some names with cis and trans stereodescriptors for rings were imported without stereochemistry.

    • Entries in the custom dictionary that consist of an empty structure failed to be imported.

    • The stereochemistry of some sugars, for example, 1-(2-Deoxy-2,2-difluoro-β-L-erythro-pentofuranos-1-yl)uracil, was wrong.

    • Stereochemistry was missing on some chiral centers of steroid derivatives.

  • Document to Structure (d2s)

    • The encoding of HTML files was not always detected from the META tag.

    • When the extraction of OLE embedded structures from Office documents was disabled using the d2s:-ole format option, the optical structure recognition of images was disabled as well.

    • The character position field of structures was sometimes higher by a few characters when extracted from HTML documents with CRLF (\r\n) line endings.

    • The CLiDE optical structure recognition tool was not automatically detected on 64 bit versions of Windows.

    • When using OSRA, some structures with implicit hydrogens were wrongly filtered out.

    • After processing only a part of an HTML document, the processing of the next HTML document could give some incorrect results.

  • Structure to Name (s2n)

    • IUPAC numbering was not displayed for some classes of structures, for instance, secondary amines.

    • The common names generated for some structures with a chloride counter-ion did not include the ending "chloride".

    • In a few cases, generated traditional names were imperfect, for instance, "nitrobenzeen" instead of "nitrobenzene".

• Molecule Representation

  • Clean 2D

    • Clean failed on atoms having two chain ligands with the same length.

  • Implicit/Explicit Hydrogen Conversion

    • Hydrogen atoms were added with invalid coordinates to carbon atoms having triple bond in 3D. Forum

• Image I/O

  • R/S stereo labels on chiral atoms were partly covered by bonds during EMF export. Forum

• Structure Checker

  • "Bond Angle Error Checker" reported incorrectly for molecules containing S-groups.

  • The first letter of a typed word did not appear in the search box of the "Configure Checkers" panel.

• Calculations

  • Remove Predictor from Marvin GUI, Chem Term, cxcalc and cxtrain.

  • Conformers

    • Lowest energy conformer calculation has been fixed.

    • Marvin - Conformers Plugin options has been improved along with corresponding documentation.

Deprecated and removed methods

• Deprecated and removed methods

Known issue

• Structure Checker

  • Online documentation help link does not work on Linux OS.