Improvements

2D Clean

• Cleaning of fullerene structures has been improved.

Bugfixes

Editing

• Peptide bond could not be deleted.

• Applying the Format>Restore Default from atom context menu ruined the atom coordinates.

Display

• In case when decimal mark was set as comma, the analysis box showed wrong result.

Import/export

• If a group with very long bonds was exported from MDL MOL file format and imported back, the position of the brackets was wrong.

Improvements:

Editing

• Aromatic ring calculation in case of 3D rotated ring has been revised.

• 'Apply for Selection Only' option for coloring has been introduced enabling different coloring of the atom label and adherent bonds.

Bugfixes:

Editing

• The Analysis box was not updated properly in case of alias or pseudo atoms.

Bugfixes:

Editing:

• The feedback of expanded abbreviated group showed the formatting.

Improvements:

GUI

• Ctrl+M shortcut has been introduced for Copy as MRV command.

• 3D rotate (F6) mouse mode has been removed.

• On atom format panel, atom label size can set instead of the former scale option.

Bugfixes:

Editing

• In some cases placing a reaction arrow deleted the "No Structure".

• Name of the items was displayed on the canvas even it they had been set off on the Preferences dialog or the Analysis box editing dialog.

• Editing analysis box: changing the order of the items did not work for name and traditional name.

• The reaction arrow in single step reaction could not be copied using Ctrl+C, Ctrl+V.

IO

• CxSmiles string with extended part containing '(+)' string was not recognized as cxsmiles/cxsmarts format. CxSmiles string with extended part containing 'v5' string was not recognized as cxsmiles but as cxsmarts format.

Improvements:

Editing

• Invert selection (Ctrl+Shift+I ) has been added.

GUI

• Help has been revisited.

Bugfixes:

Editing

• Directed merge involving more than 2 atoms did not work properly.

• Aromatic circles were not visible (they were painted in black) when the background was set black.

Improvements:

Editing

• Rotate in 3D mouse mode has been eliminated.

Improvements:

Editing

• Reaction drawing has been revised. For more information see this chapter of the documentation.

• Analysis box has been introduced. For more information see this chapter of the documentation.

Bugfixes:

Editig:

• Recent color option did not work in Choose a color dialogue.

Improvements:

Editing

• Grid and guidedlines are added to the canvas to make easier the drawing.

Bugfixes:

Editig:

• Sometimes the position of commas separating superscipt numbers in IUPAC names was wrong.

• When the adamantane molecule was placed into the canvas from a template, the bond which was the back should have been in the front.

Improvements:

Document styles

• Documentum Style Settings window and functions have been revisited.

Charge painting

• Charge painting has been improved. Charge font settings change together with the atom label settings from now on. Parameters ChargeSize and ChargeFont have been deprecated.

Bugfixes

I/O

• Molconvert would sometimes print "error: null". It now prints the name of the relevant Exception.

• Exporting molecule with R-Group definition and scaffold gave a unscaled image.

Improvements

• MarvinSketch GUI

  • New functionality has been introduced for changing and formatting abbreviated groups, atom lists/ not lists, R-groups, alias and pseudo atoms. Documentation.

• Structure representation

  • When visibility option for R/S stereo labels is set, the undefined stereocenters are highlighted by (?).

• MarvinSketch Menu

  • Homology groups are sorted in alphabetical order in Advanced Tab of the Periodic Table.

• Molecule Representation

  • A warning is displayed when a user changes 2D canvas into 3D canvas, offering a clean method to preserve chirality.

Bugfixes

• Structure representation

  • Multiple groups were displayed as non-multiple in their expanded form.

  • It was possible to draw electron flow arrows in R group definitions.

• Editing

  • The square notation of `Stereo search` was wrongly positioned in case of double bonds.

  • Copy/Paste of formatted abbreviated group resulted in malformed label.

  • When using the Markush toolbar to add R-group attachement points to a structure, the order of attachment points was not assigned in R-group definitions.

  • MarvinSketch froze when an atom with its lone pairs displayed was overwritten by an abbreviated group.

  • Adding charge via toolbar or pop-up to a hetero atom in an aromatic ring gave different results in some cases.

• Image export

  • Font size of circled charge was not considered during image export.

  • When exporting a very small sized image, large atom labels were generated.

• Export/Import

  • Molfile import: some input strings having brackets in its first line were recognized as smarts.

Improvements

• Structure representation
  2D clean of certain cyclic structures and peptides has been improved.

Improvements

• MarvinSketch GUI

  • When eraser tool is active, its icon is displayed on mouse tip and the selection color is changed to red.

  • Abbreviated groups with valence error are underlined by red.

  • "Clean and arrange in 2D" option has been introduced (Short cut: SHIFT+CTRL+2).

• MarvinBeans

  • It is possible to set the bond length in pt in MolPrinter.

• Applet

  • The background can be set dynamically.

Bugfixes

• Painting

  • Atom and bond coloring in Markush enumeration were not consistent.

• Editing

  • When one typed map numbering as a short cut then dragged on the canvas a molecule was created without atoms. For example "Map:9-Map:9" molecule was created, with a bond between the "Map:9" numbers.

Bugfix

• Editing

The index of repeating unit polymers was not properly formatted.

Empty atom label could be created.

Attachement point(s) got erased upon placing an abbreviated group in its expanded form on the canvas.

• Import

MDL Molfile generated by Marvin JS could not be pasted into MarvinSketch.

• Structure representation

2D clean of certain atropisomers resulted in chirality change.

New feature

• Structure representation
  M/P atropisomer stereodescriptors are assigned to biaryl compounds having at least 3 (2+1) ortho substituents.

Bugfix

• Editing

Expanded amino acids got ungrouped when bond was drawn from one of their attachment point

Bugfix

• Export
  Hydrogen query properties of atoms within tetrahedral stereo configuration were not exported correctly to SMARTS.

New features and improvements

• Structure Representation

Alias, pseudo and abbreviated group labels are centered.

Bugfix

• Image I/O

The size of circled charge labels was not considered during image export.

New features and improvements

• Structure Representation

Atom numbers and atom query properties are rendered outside ring in cyclic structures.

• MarvinSketch GUI

Edit < Preferences < OLE Server was removed.

Bugfix

• Image import/export

Radical was displayed as electronpair after emf export.

InChi native libraries were not initialized on OSX systems since 14.7.21.

New features and improvements

• Structure Representation

Aromatic "wedge down" bond can be drawn.

Bugfixes

• Image I/O

Absolute label was partly missing from exported images.

Transparent png images were rendered with some artifact on java 7.

• Applet

Image generation in applet did not work.

• MarvinSketch GUI

Copy as dialog always opened on the centre of the primary screen in a multi-display environment.

• Editing

Joining points of graphical objects were considered even though one of them had been removed.

New features and improvements

• Structure Representation

  • Standalone ions are moved close to their counterion during Clean 2D.

  • Generated names (IUPAC/traditional) of compounds can be copied to a text editor using CTRL+C name box option

Bugfixes

• Structure Representation

  • End point of multicenter coordinated bond was moved out of the structure during 2 dimensional clean.

  • Decimal point was displayed at a wrong place and its relative place changed by zooming.

  • Dots representing electrons were displayed too far from the atom.

  • E/Z labels overlapped bonds.

  • Bonds were rendered incorrectly in "Ball and Stick" mode.

• Image I/O

  • Position of atom labels was not correct in exported images.

• MarvinSketch GUI

  • New template files could not be added to the default template.

New features and improvements

• MarvinSketch

  • The default MSketch window size has been increased.

Bugfixes

• Structure Representation

  • Ortho-periodic acid was not accepted by valence check.

• Image I/O

  • Exported PNG files could not be imported because the source was not attached to the png metadata.

• Editor

  • "Absolute" label disappeared when Data was attached.

  • Numbers in abbreviated groups were not displayed as subscripts.

• MarvinView

  • MarvinView printed an "a" on the console when it had been launched.

Improvements

• Structure Representation

  • Atomic masses and isotopic weights are updated to the 2013 standards and the isotope file format have changed.

  • Multiple S-group cannot be expanded if it contains one or more child S-group.

  • Pseudo labels are displayed centered.

• MarvinSketch

  • "Copy Special" dialog in the Edit menu is renamed to "Copy as".

• Image I/O

  • Images are exported with "fog effect" set by the user. Image export parameter "fogFactor" has been intoduced.

Bugfixes

• Import/Export

  • Parity was inverted during import of 0 dimensional CML files.

Improvements

• Editing

  • 'Alias' atoms cannot be sprouted.

Bugfixes

• Editing

  • Placing a graphical object (or a text box) on the canvas containing R-group definition, the position of the R group label changed as if the graphical object (or the text box) would be the part of the R-group definition.

• Import/Export

  • R-group members exported incorrectly SKC.

  • InChi I/O did not work on MacOS with Java 1.7 or higher.

  • Stereo care flag was lost during compressed MOL import.

• Image I/O

  • Position of subscript numbers in labels changed when zooming in.

  • There were patches around atom labels when EMF image was exported with transparent background.

• Stereochemistry

  • Retrieving parity information could change the result of the CIP stereo recognition.

Bugfixes

• Editing

  • R-group editing (such as connecting atoms in R-group definitions) froze MarvinSketch.

• Image I/O

  • Implicit H atoms and R/S stereo labels overlapped bonds on exported EMF images.

New features and improvements

• Molecule representation

  • New homology groups: "heteroSubstitutedAlkyl", "haloAlkyl" and "hydroxyalkyl" were introduced.

  • Invalid input is not accepted in the R-group logic definition field.

  • The terminal nucteotides are linked by bend bond in cleaned RNA/DNA sequences displayed in more than one row.

  • Text formatting options were introduced for abbreviated groups and alias atoms.

  • Validation was implemented for "Edit properties" dialog.

• Editing

  • Merging a contracted S-group while pressing shift button resulted in zero atom at the merging site.

  • S-group "Bracket style=Curved" was disabled.

  • In-hand contracted amino acid threw exception over an expanded amino acid.

  • vmn abbreviation groups are not supported.

• Clean 2D

  • Clean 2D was improved in order to keep the orientation of the molecule as much as possible.

  • Clean of sequences has been improved:

    • Sequences (even if they contain expanded residues) are aligned into a horizontal line and are broken into multiple lines after 20 residues. Each line is read from left to right.

    • Space is left for chemical parts connected to the third attachment of the residues, these attachments are aligned to the top of the residue. Attachments to expanded residues are also considered.

    • Chemical parts connected to the beginning and the end of the sequence are aligned to the left and to the right of the sequence.

    • Chains of sequences connected with chemical linkers are also handled: chemical linkers are aligned horizontally to the sequences to which they are connected and space is left for them between the lines of the sequences.

  • Default 2-dimensional clean of bicyclic molecules has been changed. The old behaviour can be switched back by selecting 'Bicyclics' on the Template Library GUI (Insert<Template) then ticking the 'Use molecules as template at 2D cleaning' option on the 'Properties' page.

• Import/Export

  • Picture format 'ppm' is not supported anymore.

  • New tag introduced in MRV file to store the atom properties of the abbreviation even if the Superatom S-group is expanded. Until now such properties were lost.

  • Default handling of bond lengths in the import of MDL formats has changed: bond lengths are rescaled to ChemAxon standard for 2D molecules not only for V2000 format input but also for V3000.

  • Character '.' which is the delimiter between atom property keys and values in CXMSMILES format is escaped, which allows the usage of '.' characters in property keys and values.

  • InChi improvement: import and export of axial chirality and not specified double bond stereo are now possible.

  • Atom properties set on the superatom of an abbreviation S-group can be exported to and imported from AbbrevGroup format (ChemAxon extension of smiles for abbreviated groups).

• MarvinSketch Menu

  • "Shapely" option was removed from View>Color menu.

  • "Quality" option was removed from View>Display menu.

  • "ChemAxon JChem Table format/JTF" was removed from the "Import As" dialog.

  • Edit<Copy as<IUPAC Name (ASCII) option was introduced.

• Calculator Plugins

  • Progress indication was introduced for Marvin Services.

• Applet

  • "Autocheckstructure" applet parameter is available.

• MolConverter

  • A new option "-f" was introduced in MolConvert in order to define import format and options even if the input files are defined with a wildcard.

Bugfixes

• MarvinSketch

  • If MarvinSketch was started with edit structure from MarvinView by double click on a structure NPE was thrown.

  • MarvinOLEServer process was stopped when multiple MarvinSketch windows had been opened and one was closed.

• MarvinGUI

  • The font size in Marvin was smaller than other commercial drawing programs and text editors (such as Word).

  • Font size was different on different screen resolutions.

• Editing

  • Abbreviated groups

    • In generic, component, monomer and mer type abbreviated groups charge was shown both on the atom and on the bracket.

    • When wedge bond(single down, single up, single up and down) was drawn between two contracted S-groups an overlay of a single and a wedge bond was created.

    • The Sgroup was not positioned correctly at contracting/expanding the group.

    • Sgroup label was not displayed in expanded form.

    • The "On atoms"/"On brackets" options were not available on the Edit Group dialog when the structure was imported.

    • Edited abbreviated group labels (except Sgroup labels) could not be saved.

• Import/Export

  • Import of MOL V3000 files containing aromatic wedge bonds threw MolFormatException.

  • MRV importer did not read molecule properties of R-group members.

  • SVG export threw exception.

  • When exporting graphical objects (e.g., brackets, arrows) into pdf and image formats part of the images was cut.

  • Extension ".properties" was not added atomatically to the 'File name' on the "Save style" dialog.

  • Bounding rectangle was calculated incorrectly for structures displayed in Ball&Stick view and this caused incorrect image export.

  • Attached data was lost upon export to png format.

• Elemental Analyzer

  • Molecule weight calculation could not read molecular formula with more than two dots.

• OLE

  • Opening OLE got into "Rotate in 3D" mode.

• Applet

  • Communication problem involving JavaScript was fixed.

Deprecated and Removed Methods

Deprecated or Removed Methods in version 14.7.7.0

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.

• 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.

  • 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.

• 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.

  • "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.

  • "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.

  • Stereo Analysis

    • Available via cxcalc and Chemical Terms.

  • Conformations

    • Advanced conformational search.

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.

• Image I/O

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

• 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.

August 1st, 2014: Marvin 6.2.4.

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.

May 12th, 2014: Marvin 6.2.3

No changes.

April 4th, 2014: Marvin 6.2.2

Bugfixes

• Clipboard handling

  • Compounds in a reaction could not be copied.

• Import/Export

  • Structure to Name (s2n)

    • Name generation failed on some compounds with a radical, such as oxidanyls with a cyclic substituent. The error manifested itself as a StackOverflowError wrapped in an IOException.

February 28th, 2014: Marvin 6.2.1

New features and improvements

• Clipboard handling

  • When the clipboard content is not recognized as a chemical object, the format chooser dialog is not displayed.

• MarvinView GUI

  • In MarvinView, the "Select" textbox was eliminated from the "Preview" tab of the "Open file" dialog.

• Import/Export

  • PDB

    • PDB import reads the following residue information of sequences: residue type, sequence number, atom ID in residue.

• Applet

  • Export of binary formats has become available from the applet API.

Bugfixes

• Editing

  • The toolbar buttons could not be used to add charge to single hydrogen atoms if there were other atoms on the canvas.

  • When drawing cycles and bridges in peptides, the blue feedback remained around the first bond.

  • When a repeating unit was created from one atom only and then the structure was selected, the content of the repeating unit changed.

  • Connecting a bond to an S-group which did not have any free attachment points changed the S-group to a carbon atom.

  • In some special cases, it was possible to overwirte an atom by just hovering the mouse over it with an active atom editing tool.

  • Rotating selected molecules in 3D changed the type of all bonds to single.

  • When a bond was connected to a multicenter, the whole molecule disappeared from the canvas.

• Molecule Representation

  • Valence Check

    • Tin atom with charge +2 had incorrect valence.

    • False valence error appeared on a sulfur atom having one negative charge and 5 or 6 bonds.

  • Clean 2D

    • Nucleic acid clean was not sensitive to arranging 5' to the left and 3' to the right end of the chain.

    • Two Dimensional Clean of Crown Ethers was ugly.

• Import/Export

  • MOL, SDF, RXN, RDF

    • Aromatic query property appeared after MDL MOL export and import on an aromatic atom having atom property.

  • SKC

    • Two single bonds of a cyclopropyl ring were read as coordinate bond.

  • CDX/CDXML

    • Some CDX files that contain atom or bond label formatting were not read.

• Calculations

  • Stereo Analysis

    • CIP convention issue has been fixed.

    • Imine type structures were not recognized.

  • pKa

    • Calculation for boron compounds has been fixed.

Known issue

• MarvinSketch Applet

  • External checker classes do not load if browser uses Java SE 6. Please, use Java SE 7 for successful checker class loading.

January 30th, 2014: Marvin 6.2.0

New features and improvements

• MarvinSketch GUI

  • R* is displayed on the canvas if R-logic is unspecified for an R-group and the "View > Advanced > R-logic" visibility option is switched on.

  • R-logic is always displayed even if it is set to the default value when the relevant visibility option is switched on.

  • When R-group attachments are added to fragments not belonging to an R-group, the attachment order begins with "1" on each fragment.

  • "R/S" stereo label is displayed on atoms which are stereocenters and have a "Single Up or Down" bond if the relevant visibility option (in "View > Stereo > R/S Labels") is switched on.

  • Crosslinking peptide bridges are colored automatically if the "View > Colors > Peptide Bridges" visibility option is switched on.

• MarvinSketch Dialog

  • Character encoding information has been added to the "About" dialog.

  • In dialog "R-logic", "unspecified" is displayed in the "Occurrence range" field if it is not specified for an R-group.

• Editing

  • Molecules are no longer checked by MarvinSketch whether the "Absolute Stereo (CHIRAL)" flag can be added to them.

  • Drawing wedge bonds on a 3D canvas has been disabled. These bond types are active only when the canvas is in 2D mode.

• MarvinView GUI

  • "Save image" option has been added to the contextual menu of MarvinView

• MarvinSpace GUI

  • Hydrogen visualization toolbar button added.

  • Display/drawing settings saved on exit.

• Import/Export

  • SMILES/SMARTS

    • SMILES import handles CACTVS-type representation of coordinate bonds ('|' character). Please note that the export does not handle it.

  • Sequences, FASTA

    • Terminal H and OH are added to nucleic acids by nucleic acid import.

  • Name to Structure (n2s)

    • CAS Registry Numbers® can be converted to structures even when they contain coordinate bonds¹.

    • Conversion of nitrogen-substituted acetohydrazides is now supported.

    • Elements with isotopes, such as (14)C, are converted in name to structure by default, and, optionally, they can be converted with document to structure using the "d2s:elements" format option.

    • Some OCR errors have been fixed in carbon ranges for homology groups, for example, "Ci_10 alkyl".

    • Generic structure names (such as "alkyl" in English) are supported in Chinese as well, for instance, N-???-4-??? and C1-C4-??.

    • Polyspiro names with a polycyclic component, such as dispiro[cyclohexane-1,2'-indene-1',2"-imidazole], are supported.

  • Document to Structure (d2s)

    • For enzymes with a substrate in their name, such as "serine protease", the substrate (serine) is not converted by default. A new format option, "d2s:substrates", enables the recognition of the substrate in such cases.

    • New format option "d2s:specific" has been added to convert only specific structures. This option excludes structures with R-groups from the conversion.

    • More OCR error correction is performed.

    • In the case of processing XML fragments not starting with "<?xml version="..."?>", it has become possible to specify that the input text is in XML format by using the "d2s:content-type=application/xml" format option.

    • Metadata is also extracted from older (since 2001) USPTO patents in XML format: the section where a name is found is recorded as metadata (title, abstract, description, or claim number). Furthermore, document metadata is extracted as well: patent title and ID, inventors, IPC categories.

    • OCR error correction has been added for Chinese names.

  • Structure to Name (s2n)

    • In fused ring systems with an atom being in a non-standard valence state, the generated name conforms to the IUPAC rules by using the lambda notation only in front of the fused names and not inside the component name.
      See for instance: 1H,3H-2λ⁴-naphtho[2,3-c]thiophen-2-one.

    • Name generation has become faster by about 10%.

• Molecule Representation

  • R-logic

    • Default value of R-logic range has been changed: instead of ">0", now it is an empty string which means "as drawn". ">0" value is handled as non-default and is exported in file formats where ChemAxon supports R-logic information (MRV, SKC, MOL). From now on, if a file does not contain R-logic range information, then it is interpreted with the new default value: "as drawn". Documentation

  • Stereochemistry

    • Cahn-Ingold-Prelog (CIP) stereo recognition has been extended and it has been added to the public API.

  • Elemental Analyzer

    • Molecular mass calculation is more accurate.

• Image I/O

  • Structures can be exported in image formats "TIFF" and "EPS".

  • S-group attachment point labels are not exported to image files (PNG, JPG, PPM, SVG, EPS, TIF, BMP). Exporting these labels to PDF files can be switched on/off using the "Edit > Preferences > Save/Load > Save/Load GUI Settings" checkbox.

  • During PDF export, text is also saved as image.

• Calculations

  • Stereo Analysis

    • New stereo analysis API.

  • 3D alignment

    • Hydrogens are taken into consideration during alignment process.

  • Conformers

    • New Generate3D documentation has been added.

• Structure Checker

  • "Overlapping Atoms Checker", "Overlapping Bonds Checker", and "Bond Length Checker" report correctly for molecules containing S-groups.

• API

  • IsotopesCompiler in isotopescomp.jar creates a UI in order to show error messages and information when it was not started from the console.

  • atomNumbersVisible parameter has been deprecated and has been replaced by the atomNumberingType parameter.

• Third-party applications

  • The Java COM Bridge (Jacob) version was updated from v1.15-M3 to v1-17.

Bugfixes

• MarvinSketch GUI

  • MSketchPane setPiece(Molecule) method did not work; it set the molecule on the canvas instead of putting it on the cursor.

  • Starting points of electron flow arrows drawn from radicals and/or lone pairs were changed when lone pair visibility was switched off and then on again.

  • R-logic label was not taken into account by zoom action even if visibility option "R-logic" was switched on.

• Painting

  • Electron flow arrows starting from an atom, a negative charge, or an automatically calculated lone pair disappeared when lone pair visibility was turned off and then turned on again.

• Editing

  • Menu option "Link Node" was not disabled when an atom had less than two bonds.

  • A contracted tripeptide disappeared from view when it was expanded, but 2D Clean brought it back.

  • It was not possible to draw an electron flow arrow from an atom to an incipient bond between this atom and an abbreviated group.

  • Erasing a structure without an R-group attachment left "1" on the canvas, which behaved as an atom.

  • When an atom was selected and the "R-group attachment" button of the Markush toolbar was used, the selected atom was changed to an R-group attachment point; however, a new R-group attachment should have been added to the selected atom in this case.

  • Dragging with the R-group attachment tool, a bond was created connecting two R-group attachments.

  • Using the R-group attachment tool, R-group attachments could be added to an existing R-group attachment.

• Load/Save handling in UI

  • Lone pairs were lost at "Copy As... > PDF" at Mac OS X.

  • PDF export did not use the color scheme setting.

• Clipboard handling

  • During PDF export, atom labels were turned upside down with some font types.

• MarvinView GUI

  • Pasting a SMILES string into MarvinView did not work.

• Import/Export

  • MRV/CML

    • After MRV export and reimport of a structure, its text box font color turned into the frame color of the text box and the font color turned to a not defined color (black).

  • Format recognition

    • '(S)-(-) Propanolol' was recognized as SMILES.

    • Chemical Registry Numbers® were recognized as MDL MOL format.

  • Name to Structure (n2s)

    • Automatic format recognition failed for names using unicode hyphens.

    • Names of some spiro compounds containing aromatic components were not converted. See, for instance, 6-(2, 5-dimethylphenyl)-5'-methylspiro[chroman-4,2'-imidazol]-4'-amine.

  • Document to Structure (d2s)

    • Some names containing a space character (for instance, "malonic acid") were not detected.

    • When using document to structure using the MRecordReader API, the MRecord.getMolString() method returned null.

    • The character position property of recognized names was sometimes wrong.

    • Spiro and fused ring system names were not recognized in HTML documents when the brackets were represented by HTML entities.

    • Processing an HTML document failed when the document was declared to be in XHTML format, but was not actually a valid XML (for instance, contained unclosed tags).

    • Processing a USPTO XML patent file in the current directory failed when it referred to CDX structures files.

    • Some structures embedded in Office documents were not extracted.

  • Structure to Name (s2n)

    • Names could not be generated for structures with lone pairs (MolAtom.LP).

    • The name generated for OH^- was "oxidanide" instead of the preferred form "hydroxide".

    • An extra locant was included in the name of cyclic structures with multiple hetero atoms with one of them having non-standard valence, for instance, 1λ⁶,4-thiomorpholine-1,1-dione instead of 1λ⁶-thiomorpholine-1,1-dione.

    • In cases where a cyclic substituent was connected indirectly to the parent through an ether, sometimes wrong names were generated.

    • Name generation failed for structures with a methanethione parent.

• Molecule Representation

  • S-groups

    • Flip property could be set on any polymer-type S-group resulting in structures with incorrect information. From now on, only ladder type polymer S-groups can have flip property, and it will disappear from invalid structures.

    • java.lang.ArrayIndexOutOfBoundsException was thrown when a multicenter atom being the only member of an S-group was removed.

  • Valence Check

    • Valence check did not accept chlorine and heavier halogens with 1 negative charge and with 2, 4 or 6 pieces of fluoride ligands.

  • Stereochemistry

    • Incorrect stereogenic center was found in some spiro compound.

  • Aromatization

    • General aromatization handled selenium differently than sulfur.

• Clean 2D

  • Cleaning of position variation bonds could make bonds overlap.

• Datatransfer

  • OLE

    • The buttons in the Periodic Table and on the Atoms toolbar were not rendered properly in Marvin OLE.

• Applet

  • Missing resources prevented successful name import of bridged structures in applets. For instance, template based cleaning and pasting names did not work in these cases.

• Image I/O

  • Lone pairs were painted only at the second call of painting.

  • R-logic label was not exported into images, although visibility option "R-logic" was switched on.

  • Circled charge font was not considered during image export.

  • During PDF export, stoichiometric numbers in subscript were placed wrongly.

Deprecated and removed methods

August 1st, 2014: Marvin 6.1.9.

Bugfixes

• Import/Export

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

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

Bugfixes

• Applet

  • Missing resources caused issues in applets with bridged structures. For instance, template based cleaning and pasting names did not work in these cases.

Bugfixes

• Java Webstart

  • Java Webstart did not run on Macintosh computers.

Bugfixes

• Applet

  • The mol property change event was not fired when an empty molecule was set initially for the MarvinSketch applet. This could cause misbehaviour in cases where the client JavaScript code relied on this marker to know when the applet was initialized.

Bugfixes

• MarvinSketch GUI

  • MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor.

• Import/Export

  • CXSMILES/CXSMARTS

    • CXSMARTS containing valence property information was recognized and read as SMARTS.

  • SKC

    • Some reaction was read as R-definition from SKC format.

New features and improvements

• MarvinSketch Dialog

  • 'Zoom to scaffold' checkbox option has been added to the "Preferences > Save/Load" tab.

• Structure Checker

  • External structure checker configuration file URL can be set via Java System Property.

Bugfixes

• Editing

  • Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure.

• Import/Export

  • MolInputStream and MolImporter could have different format options.

  • MolImporter did not close its inputstream when an exception was thrown in the constructor.

  • MOL, SDF, RXN, RDF

    • Molecule type property was allowed in SDF, CSSDF export.

    • The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.

  • CDX/CDXML

    • Color and text format of atom label is exported to CDX and imported from CDX and CDXML.

    • Graphical brackets were not imported from CDX files.

  • Gaussian Z-matrix input format

    • Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format.

• Clean 2D

  • Cleaning of position variation bonds could create overlapping bonds.

  • Cleaning of bridged systems could result in overlapping atoms.

• Calculations

  • Topology Analysis

    • Missing method has been added: TopologyAnalyserPlugin.getFsp3().

  • logD

    • New logD training documentation has been added.

• Structure Checker

  • Fixer options in MarvinSketch are updated with newly defined settings.

  • External checkers can be loaded from JAR file in case the JAR file contains a space.

New features and improvements

• MarvinSketch GUI

  • Peptide cycles and bridges can be drawn according to IUPAC recommendations.

  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Advanced > Atom Numbering > IUPAC Numbering" menu item.

  • Lone Pair (LP button) was removed from the "Special nodes" group of the "Periodic Table > Advanced" tab, so it cannot be reached from the GUI anymore.

• MarvinSketch Menu

  • The "Calculations > Predictor" menu option has been removed from the default Marvin menu.

• Painting

  • Drawing of electron flow arrows has been changed. Single electron flow arrows can now start either from a radical or from an electron of a lone pair. Electron pair flow arrows can only start from lone pairs.

  • Atom property values belonging to the same atom are now separated with semicolons instead of commas.

  • When lone pairs were displayed on a structure, the charge symbol was nearly invisible.

• Load/Save handling in UI

  • The same last-used folder is saved for the "File > Open" and the "File > Insert file" functions.

• Graphical object handling

  • Electron flow arrows can be started from or targeted to multicenter atoms.

• MarvinView GUI

  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Misc > Atom Numbers > IUPAC Numbering" menu item.

• Import/Export

  • MRV/CML

    • Namespace has been introduced to mrv format.

  • MOL, SDF, RXN, RDF

    • New export option, cc, is introduced to V2000 export in order to write absolute chiral flag if there are only ABS enhanced stereo labels in the molecule.

    • New import option, z, is introduced to MDL import that converts carbon atoms with "Z" label to R-group attachment points.

  • SMILES/SMARTS

    • [Z] is imported as R-group attachment point from SMILES.

  • CXSMILES/CXSMARTS

    • New export option, b, has been introduced to CXSMILES/CXSMARTS in order to turn off the export of bicyclostereo-information.

  • Name to Structure (n2s)

    • Name and corporate ID resolution webservice now supports NTLM authentication.

    • Names with a missing dash before the suffix locants are now recognized.

    • Non-standard IUPAC specification of stereochemistry inside suffix locants is supported.

    • Names with superscript locants of a bridged ring system numbering are denoted by spaces are now supported.

    • As a result of numerous improvements to the systematic name conversion algorithm, more names are converted by n2s and detected by d2s. The accuracy of structure generation has also increased. (For instance, 5% more names were detected and converted in a large, diverse set of patents.)

    • An example custom dictionary has been added to the documentation.

  • Document to Structure (d2s)

    • Chinese names are now detected in text documents using an approach which recognizes names in Chinese sentences without the spaces that separate words in English.

    • In addition to OSRA, the CLiDE and Imago Optical Structure Recognition tools (Chemical OCR) can be used to convert images to structures. These tools need to be installed separately from Marvin.

    • When processing USPTO patents in XML format, the section in which a name is found is recorded as metadata (title, abstract, citation, description, or claim number). Additionally, document metadata is extracted (patent title and ID, inventors and assignees, IPCR categories).

    • When processing a USPTO patent XML document, referenced CDX files are imported automatically if they are in the same directory as the XML file.

    • Processing of USPTO XML patents has become faster: an average 20% speed-up, more than ten times faster process for some patents.

    • PDF document pages with images in the JBIG2 format are now supported.

    • PDF documents generated by Adobe Acrobat Paper Capture Plug-In and ExperVision are now handled specially, since they contain both an original scanned image of text and the text resulting from OCR of the image. This allows much faster processing of such documents, and avoids double hits for the same text.

    • PDF documents with many small high-resolution images are now processed much faster, even when Optical Structure Recognition is used.

    • The document creation date property is stored as a java.util.Date object instead of string.

    • Structures returned by image recognition tools (OSRA, CLiDE, Imago) are better filtered to avoid false positives.

    • OCR processing for scanned texts can be disabled using the -ocr format option.

    • Processing of PDF documents with scanned black and white images (e.g., most non-searchable patent documents) has become approximately two times faster.

  • Structure to Name (s2n)

    • When retrieving a Chemical Registry Number® from , the InChiKey of the structure is used to search for the structure. This allows more structures to get a number in such cases where several different SMILES with chemically irrelevant differences are associated with the structure.

• Molecule Representation

  • New method, SelectionMolecule.addAtom(MolAtom, boolean), is introduced.

  • New methods, MolAtom.getBondArray() and Sgroup.getBondArray() are introduced.

• Calculations

  • NMR (CNMR, HNMR Prediction...)

    • Various phosphorus-proton spin-spin coupling parameters have been added to the predictor database.

  • Geometry (Topology Analysis, Geometrical Descriptors, PSA, MSA)

    • "Fsp3" option has been introduced in the Topology Analysis plugin for calculation of sp³ carbon atom fraction.

• Elemental Analyzer

  • Charge is taken into account in atomic mass calculation.

• Chemical Terms

  • Chemical Terms's (CT) Structure Checker functions accept XML configuration as string parameter, thus Structure Checker XML configurations can be used in JChem Cartridge via CT.

  • New checkErrorCount Chemical Terms function returns the number of errors/issues found by the checker(s) in the configuration.

• Structure Checker

  • Checker "substructure checker" has become available in Marvin Beans, so installing Marvin Beans will install the fully functional Structure Checker application.

  • Set Structure Checker configuration can be copied to the clipboard as action string from Structure Checker GUI and Structure Checker Editor.

  • The "excluded" list of Structure Checker's Abbreviated Group Checker accepts quotation marks in command-line. Possible definitions can be the following: "abbrevgroup:excluded=Ph,Ala,Gly", "abbrevgroup:excluded='Ph,Ala,Gly'" or "abbrevgroup:excluded="Ph,Ala,Gly"".

  • The checkers and fixers can be localized or customized according to individual requirements.

• Build/Installation

  • Mac OS X installer images were not digitally signed, and GateKeeper in newer OS X versions (10.7.5+) reported our installers as damaged and refused to install them.

Bugfixes

• MarvinSketch GUI

  • Aliphatic/Aromatic atom query property had three options ("a", "A", and "A,a") instead of the necessary two ("a" and "A").

• MarvinSketch Dialog

  • In case of long names, only a part of the whole name appeared on the naming panel.

• Editing

  • Deleting an atom having an R-group attachment did not delete the attachment.

  • The end of an arrow did not stick to the midpoint of an existing arrow.

• Load/Save handling in UI

  • In MarvinView, "File > Save All... > Advanced > Into SEPARATE FILES" did not save the last structure.

• History functions

  • When the "Stereo" atom property had been changed, Undo/Redo did not work properly and the IUPAC name was not updated.

• Graphical object handling

  • Labels written in text box were shifted when they were pasted either as an OLE object or as a PNG image.

• MarvinView GUI

  • When a structure which contained an R-group definition was opened from MarvinView for editing in MarvinSketch, the structure appeared with 0% zoom factor.

  • Text elements (atom labels, atom indices, text box contents, IUPAC name) were not resized in MarvinView while zooming the structure using the "View > Transform > Zoom" function.

• Printing in MarvinView

  • When choosing "Print > All Visible", the structures overlapped in the preview, and "Print > All Visible > Print to PDF" resulted in an empty file.

• MarvinSpace

  • A bug occuring at PDB import has been fixed.

  • The "Edit > Cut" menu option has been fixed in the MarvinSpace menubar.

• Import/Export

  • Aliphatic and aromatic query property, when they are used together, is not imported and exported any more. The "no property", no aromatic or aliphatic query property, has the same meaning.

  • Only lower case file extensions were recognized.

  • MRV/CML

    • MRV files that contained circular R-group references without attachment point information could not be imported.

  • MOL, SDF, RXN, RDF

    • Export of structures containing multicenter S-groups to format MOL V2000 resulted in a non-standard file.

    • Newline characters in molecule name were not escaped.

    • MDL MOL import did not use MDL valence model for non-charged metals.

    • Atom list embedded to atom list in MDL file formats resulted in invalid atom list elements after import.

  • CDX/CDXML

    • Reactions containing anonymous alternative groups were not imported from CDX format.

    • XML files with complex header could have been recognized as CDXML.

  • SMILES/SMARTS

    • Query Hydrogen atom with parity definition confused SMARTS import.

    • SMILES export did not throw exception when the molecule contained not supported reaction stereo information.

    • Newline characters in molecule name were not escaped.

    • SMILES import read Meitnerium atom (Mt) as any atom (*).

    • Strings containing valence property were recognized and imported as SMILES instead of SMARTS.

  • CXSMILES/CXSMARTS

    • Import of CXSMILES/CXSMARTS strings that describes the coordinates of atoms with option c added 'CIS OR TRANS' stereo information to double bonds in small rings.

    • Single or aromatic bonds could be lost during CXSMARTS export and import.

  • InChi/InChiKey

    • InChI was not recognized in MolConverter as one line molecular format that can be given as the argument of -s option without specifying the format.

  • PDF

    • Reactions could not be exported to PDF.

  • Name to structure (n2s)

    • Names with a cis- or trans-imine bond were failing to be converted to structures

    • Ions, such as "bismuth(3+)", were imported with valence property set to 0.

    • Ortho substitution on acetophenone generated wrong structures.

    • Some E/Z and R/S stereochemistry was missing in structures imported from names when the locant of the atom or bond with stereochemistry was not specified explicitly.

    • The "H^-" ion was missing from names containing "hydride", e.g., sodium hydride, they only had e.g., "Na⁺ instead of the correct NaH.

    • Names containing atoms with both a non-standard valence (λ) and a positive charge were converted to structures with an extra implicit hydrogen on that atom.

    • Primary and secondary amine oxides were represented as N-OH instead of [N⁺]-[O^-].

    • The "Name" format was not automatically recognized for names with XML/HTML character references, such as "&#946;" or "&alpha;".

    • In some cases, amino acids with α, β, and γ prefixes were not converted.

    • Using n2s in the applet required the downloading of an unnecessary component. This, in turn, made the first applet usage much slower.

  • Document to structure (d2s)

    • Some common words such as "DUST" or "crank", were recognized as names because, e.g., DUST is a rare acronym for a chemical structure. These words are now ignored.

    • The insideTag format option was not working for XML and XHTML documents.

    • Some uppercase words were mistakenly recognized as SMILES strings, such as "CISCO" or "ON-OFF".

    • Some embedded images were returned with 'PNG' type instead of 'OSR', and the usual OSRA options and properties (e.g., timeout, confidence filtering) were missing as well.

    • When d2s was interrupted (for instance, by a timeout), an OCR or OSR process could be left running in the background until it was completed. In similar cases such processes are now stopped immediately.

    • Extracted names sometimes contained some irrelevant characters at the end, such as "4-(trifluoromethyl)-2-((1H-1,2,4-triazol-1-yl)phenyl)-methanamine 2e" instead of "4-(trifluoromethyl)-2-((1H-1,2,4-triazol-1-yl)phenyl)-methanamine".

    • In some cases, single names separated by space were imported as if they were one compound, for instance, "2-hexanoyloxyethyl 1-formyloxypropyl".

    • Embedded structures in Office documents were always imported with the absolute chiral flag set.

  • Structure to name (s2n)

    • When generating names in parallel in multiple threads, some E/Z stereo bond modifiers were missing from the output.

    • Wrong names were generated for structures with multiple attachment points. These cases are now detected and no name is generated for them. Generating a name in this case will be implemented in the future.

• Molecule Representation

  • Valence Check

    • Valence check changed standalone Bi to BiH₃.

    • Valence error was not shown on a Carbon atom having a triple and an aromatic bond.

    • Valence Check accepted Stannane with any number of implicit hydrogens.

  • Implicit/Explicit Hydrogen Conversion

    • Stereoinformation was lost during explicit Hydrogen removal from stereocenter when all ligands of the stereocenter were also stereogenic.

    • Conversion of explicit Hydrogen to implicit one thrown exception when there is only a Hydrogen atom in an R-group definition or in a definition member.

• Image I/O

  • Text box contents, atom labels and atom attributes (e.g., atom indices, stereo labels), and IUPAC names were not exported to PDF as text. When the "Save/Load GUI settings" checkbox was checked in the Preferences dialog, text attributes (e.g., font type, size) were not exported either.

• Clean 2D

  • Clean removed stereo centers around the contracted superatom S-groups.

  • Clean2D got stuck and error message was thrown for some more complex molecules imported from SMILES.

• Stereochemistry

  • Cis-Trans stereoisomerizm was recognized on flexible Nitrogen atoms.

  • Stereo information could lost in symmetric bridged systems with explicit Hydrogen atoms.

• Calculations

  • Elemental Analysis

    • ElementalAnalyser.setMolecule(String) threw exception if the formula contained () brackets (e.g. C6H11N3.2(HCl)).

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • Minor bug has been fixed on the distribution chart.

  • Isomers (Tautomers, Stereoisomers)

    • Stereoisomers plugin failed to generate all stereoisomers for tricyclic compounds.

    • Generic tautomer generation threw exception on some molecules.

    • Some invalid 3D structures were not filtered out during stereoisomer generation although 3D-filter option was turned on.

    • Some cycloolefine stereoisomers were mistakenly filtered out as duplicates, so they were missing from the generated list of stereoisomers.

• Structure Checker

  • In Structure Checker GUI, the scroll bar was missing in the report tab if the report contained four to six structures.

  • When the Structure Checker configuration contained multiple substructure checkers, their order would change during structure checking process.

Deprecated and removed methods

• Deprecated and removed methods

November 25th, 2013: Marvin 6.0.6

Bugfixes

• Applet

  • The mol property change event was not fired when an empty molecule was set initially for the MarvinSketch applet. This could cause misbehaviour in cases where the client JavaScript code relied on this marker to know when the applet was initialized.

August 27th, 2013: Marvin 6.0.5

Bugfixes

• MarvinView GUI

  • Opening a structure for editing in MarvinView was opened with 0% zoom factor in the MarvinSketch window, when the structure contained an R-group.

August 6th, 2013: Marvin 6.0.4

• MarvinSpace

  • Transferring 3D molecules from MarvinSpace to MarvinSketch resulted in 2D structures in the sketcher.

July 23th, 2013: Marvin 6.0.3

No changes.

June 25th, 2013: Marvin 6.0.2

No changes.

June 21st, 2013: Marvin 6.0.1

New features and improvements

• Image I/O

  • The following file extensions were removed from the "Files of Type" list on the Import Image dialog: *.ps, *.pdf, and "All Files". PDF files can be imported through the "File > Open" menu.

• Calculations

  • Services

    • SOAP webservices:

      • SOAP version 1.2 webservices are supported.

Bugfixes

• Painting

  • R/S stereo labels were not displayed when there was an R-group on the canvas.

  • S-groups, created from structures containing a position variation bond, retained the grey patch of the position variation bond when the group was contracted.

• Editing

  • An atom of an expanded S-group could not be replaced with an S-group correctly

• Clipboard handling

  • On Mac OS X, copy-paste (from MarvinSketch to, e.g., TextEdit) did not transfer the atom colors.

• Graphical object handling

  • Formatting the head of a graphical arrow to a half-left arrow using the Document Style dialog crashed the display of the arrow.

• Import/Export

  • MRV/CML

    • MRV and CML export failed with the woodstock xml processor.

  • InChi/InChiKey

    • InChi export did not return standard InChi when the absolute stereo was not set in a non-chiral molecule.

  • Document to Structure

    • Documents with many consecutive names would lead to extremely long processing time (appeared as hanging, unless reaching the timeout).

• Molecule Representation

  • Implicit/Explicit Hydrogen Conversion

    • Adding explicit hydrogen to an atom being part of a Multicenter S-group added the hydrogen to the S-group as well.

• Clean 2D

  • Stereo clean created non-IUPAC standard depiction of certain tetrahedral configurations.

• Data Transfer

  • OLE

    • Redirecting ChemDraw OLE objects did not work.

• Applet

  • Applet parameter extraBonds did not work therefore the bond type menu appearance could not be changed.

• Image I/O

  • The xml header information was always included in the generated SVG content during image export. SVG export now has an option "headless" to exclude this information.

• Calculations

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • "Keep explicit hydrogen" option caused exception during pKa calculation.

  • NMR (HNMR, CNMR Prediction, ...)

    • When the mouse cursor was moved over an NMR peak on the chart, the relevant atom was not highlighted on NMR predictor molecule preview panel.

  • Services

    • SOAP webservices:

      • Parameters did not load from WSDL properly in SOAP version 1.1 webservices.

New features and improvements

• MarvinSketch GUI

  • The default tool in MarvinSketch is Rectangle Selection instead of Single Bond.

  • MarvinSketch GUI has been refreshed: Icon set has been changed in MarvinSketch. Menu items have been rearranged. Several dialogs, tooltips, menus has been renamed.

  • A new Marvin configuration has been added to MarvinSketch. Already existing Marvin configurations have been renamed.

  • MarvinSketch now starts with the native "Look & Feel" on Windows and on Mac OS X.

• MarvinSketch Dialog

  • At the first launch of MarvinSketch after installation, a dialog asks the user to select the desired skin for the GUI configuration.

  • The Open dialog has been modified. Selecting molecules to load from a multistructure file happens now directly on the Open dialog.

  • New dialog, called "Insert file", has been introduced into MarvinSketch for adding structures from new files to the canvas contents.

  • The Save dialog has been extended with an Advanced panel to set saving options.

• Painting

  • Drawing quality has been improved: join of single bonds has been refined.

  • Superatom S-group attachment points are denoted by numbers instead of asterisks.

• Editing

  • MarvinSketch GUI can handle unlimited number of attachment points on Superatom S-groups. There are new menu options for adding and removing attachment points in the Atom menu and in the contextual menu.

  • Bond length can be scaled. Bond length and size of other objects can be set by dragging the displayed corners of the bounding rectangle. Scaling is also available on the Document Style dialog. Scaling does not work when the structure has been rotated in 3D mode (with F7).

• Load/Save handling in UI

  • New loading mechanism has been introduced in MarvinSketch. New menu option, Insert file, has been added to the File menu; it appends the contents of the chosen file to the structure on the canvas.

  • New saving mechanism has been introduced in MarvinSketch.

  • New save mechanism has been introduced for MarvinView.

  • Reactions and structures containing R-group definitions cannot be saved either in separate files or separately in the same file.

• Clipboard handling

  • Images of chemical structures can be imported from the clipboard via the configured image import service or locally installed OSRA.

• Template Library

  • New template set, Organometallics, has been added to the Template Library.

  • New amino acid templates have been added (e.g., pyrrolysine, selenocysteine, "any/unknown/undetermined aminoacid").

  • The following amino acid templates have three attachment points: arginine, cysteine, histidine, lysine, selenocysteine, serine, threonine, tryptophan, tyrosine.

• Integration

  • The new Automapper has been introduced in MarvinSketch.

• MarvinSpace

  • Copy and Paste functions have been added to MarvinSpace.

  • 3D editor: Molecules can be edited in 2D in MarvinSketch, and aligned to the original 3D molecule.

• Import/Export

  • MRV/CML

    • Import and export of more than two Superatom S-group attachment points are supported.

  • MRV schema

    • New element, AttachmentPointArray, is introduced in format MRV to describe the new Superatom S-group attachment point representation.

  • MOL, SDF, RXN, RDF

    • The import of template based MDL MOL files is introduced.

    • Import and export of more than two Superatom S-group attachment points are supported from MDL MOL based formats.

  • SKC

    • Import and export of more than two Superatom S-group attachment points are supported. Superatom S-groups having at least one crossing bond are exported in their expanded form.

  • CDX/CDXML

    • Import and export of more than two Superatom S-group attachments point are supported.

    • Curved lines can be imported from CDX files.

  • CXSMILES/CXSMARTS

    • Generic, Polymer, and Mixture type S-groups are stored in CXSMILES/CXSMARTS format.

  • SMILES/SMARTS

    • In SMILES import, radicals are not added anymore to atoms with atomic number above chlorine, except for bromine and iodine. If implicit hydrogen can not be added to or removed from the atom (as it is in brackets in the SMILES definition), then a valence property is set to correct its valence if necessary.

  • Peptide

    • Amino acids: Cysteine, Aspartic acid, Glutamic acid, Histidine, Lysine, Asparagine, Glutamine, Arginine, Serine, Threonine, Selenocysteine, Tryptophane, and Tyrosine are imported with three attachment points from peptide format.

    • New 1-Letter and 3-letter amino acid codes were added: U and Sec for selenocysteine; O and Pyl for pyrrolysine; X and Xaa for "any/unknown/undetermined amino acid"; B and Asx for "Aspartic acid or Asparagine"; Z and Glx for "Glutamic acid or Glutamine"; J and Xle for "Leucine or Isoleucine".

  • FASTA

    • Peptide, DNA, and RNA import from FASTA format has been introduced.

  • Name to Structure (n2s)

    • Custom name-to-structure webservices can now be configured to receive the name in the middle of the URL, not just at the end, by using the [NAME] marker in the configuration URL.

    • More forms of ranged generic names are supported, such as "-C_1-6alkyl". These are found extensively as part of markush structures in patents.

  • Document to Structure (d2s)

    • Text document processing has become faster (around 20% speedup for typical texts with a small proportion of chemical names).

    • The context (surrounding text) in which names appear in the document is now available as a property of the returned structures.

    • The osraTimeout option has been added to configure the maximum time to wait for OSRA to convert an image to structure (the default is 20 seconds).

  • Structure to Name(s2n)

    • The new format option "cas#" allows the retrieval of Chemical Registry Numbers® from publicly available sources hosted by the U.S. National Institutes of Health (“NIH”) and the Wikimedia Foundation..

• Molecule Representation

  • S-groups

    • Any number of attachment points can be added to Superatom S-groups.

    • S-group attachment point information can be set only to atoms being part of a Superatom S-group.

  • Valence Check

    • Valence check does not deal with free attachment points.

    • New valence check option is introduced to allow/deny traditional forms of pentavalent Nitrogen.

• Calculations

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • log[%] vs. pH distribution chart is introduced in case of pKa calculation.

    • Major miscrospecies calculation is supported for molecules with coordinate bonds.

  • NMR (HNMR, CNMR Prediction, ...)

    • NMR predictor considers novel coupling types.

    • Updated trainingset has improved the NMR shift prediction accuracy in both 1H and 13C NMR predictors.

    • 1H NMR calculation has become faster as no 3D conformer generation is applied.

  • Geometry (Topology Analysis, Geometry, PSA, MSA)

    • Setting any ChemAxon supported aromatization method (general, basic, loose) is available in TopologyAnalyserPlugin which affects the result of many topology analyser calculations (e.g., aromatic atom/bond/ring count).

  • Chemical Terms

    • New sortableFormula() function is introduced. The generated sortable formula can be used to sort formulas in alphabetical order.

• cxcalc

  • pKa training library can be used without relying on user home. Use option --correctionlibrarypath to read custom training file.

  • New sortableFormula option is introduced. The generated sortable formula can be used to sort formulas in alphabetical order.

• cxtrain

  • New option, -p, has been introduced to save the training result to custom path.

• Automapper

  • New Automapper tool is introduced. It maps reactions more accurately.

  • Automapper tool requires Standardizer license.

• Structure Checker

  • "Traditional nitrogen representation allowed" option is available in Valence Error Checker.

  • External structure checker and fixer manager is integrated into Structure Checker GUI application. It is accessible from the preferences menu as "Checker/Fixer Manager".

Known issue

• MarvinSketch Applet

  • External checker classes do not load if browser uses Java SE 6. Please, use Java SE 7 for successful checker class loading.

Bugfixes

• MarvinSketch Menu

  • The "Recent Files" list was not updated with the new file name when the file contained multiple structures and more records were selected.

• Painting

  • There was a gap between the lines of the double bond and the single bonds when two single bonds connected to the same (non-visible) carbon atom on one end of a double bond.

  • Electron flow arrows partially hid lone pairs in some cases.

• Clipboard handling

  • When copying and pasting between Marvin applications in Linux, an exception was thrown which froze the application where the copy operation had been performed. The exception originated from the applied freehep library, which has been updated.

• MarvinSpace

  • 3D alignment: MCS mode is fixed to align molecules in 3D.

• Image I/O

  • Image export did not remember the last folder used for saving.

  • Molecule source was not saved in jpg, png, and svg files when "Save As Image" was selected.

• Import/Export

  • MOL, SDF, RXN, RDF

    • Structures that contained two S-groups with exactly the same atoms imported from MDL MOL format could cause java.lang.RuntimeException.

    • Property name was imported as its value from SDF file when the property name contained square brackets.

    • Exporting a peptide sequence containing bridge between two ungrouped amino acids to MOL format (V2000 or V3000), then importing it back, changed the coordinates of the contracted groups.

  • CDX/CDXML

    • CDX files created by ChemDraw 9.0.1 containing abbreviated groups with no attachment points was not imported.

    • ChemDraw CDX files containing textboxes with Chinese characters were not imported.

    • Chemical formula-like subscript of a Superatom S-group was read in reverse order from CDX when the group was to the left of the fragment.

    • Superatom S-groups not having crossing bonds were read as textbox from CDX files.

    • CDX files exported from ChemDraw 5.0 and containing contracted Superatom S-group was not imported.

    • CDX import read half headed arrows as full headed.

  • CXSMILES/CXSMARTS

    • CXSMARTS export did not keep CIS/TRANS information for symmetrical structures.

    • Extended part of CXSMARTS was not written correctly for any halogen query atoms.

  • SMILES/SMARTS

    • Unique SMILES string generation for a fragment could have differed depending on the fragment count of the molecule

  • Peptide

    • User defined custom amino acid dictionary caused wrong custom amino acid structure or java.lang.ArrayIndexOutOfBoundsException during peptide import.

  • Name to Structure (n2s)

    • When calling a custom name-to-structure webservice, names with special characters (including space) were not URL encoded, possibly resulting in failed conversions for such names.

    • Name containing fused rings and converted to all uppercase letters were not recognized.

    • Name to Structure could get stuck in a deadlock during the first usage when that occurred concurrently in several threads.

    • When using the "name converters" API, converters were not properly removed after using thread-local converters.

  • Document to Structure (d2s)

    • When interrupted while doing OCR or OSR, document to structure logged an exception about the interrupt. This caused in particular a warning dialog to appear in Instant JChem during a document import.

    • Names were not recognized when they contained a complex bracketed bond locant followed by a comma, such as "2(7)" in tricyclo[6.3.1.0^2,7]dodeca-2(7),3,5-triene.

    • Scrolling back in MarvinView could have caused failures for very large documents (more than 1000 structures) and names with non-ASCII characters.

  • Structure to Name(s2n)

    • name:source returned an empty name for empty structures instead of the actual stored name.

    • The name "perimidine" was not attributed to the right structure.

• Molecule Representation

  • Implicit/Explicit Hydrogen Conversion

    • Removing explicit hydrogens on some larger PubChem compounds caused infinite loop.

• Clean 2D

  • Partial clean misplaced the molecule when only one atom was fixed.

  • Clean 2D failed to preserve cis/trans stereo information in some cases.

• Calculations

  • NMR (HNMR, CNMR Prediction, ...)

    • PDF export of NMR spectra was failed when the generated new page contained a blank line only.

    • When displaying NMR spectra of selected tautomers, the background of the tautomer preview window was black in Linux OS.

Deprecation

• Deprecated methods

  • Molecule Representation

    • Valence Check: MoleculeGraph.VALENCE_CHECK_AMBIGUOUS, MoleculeGraph.ValenceCheckState, MoleculeGraph.setValenceCheckState(ValenceCheckState), MoleculeGraph.getValenceCheckState() MoleculeGraph.getPossibleAttachmentPoints(MolAtom)

    • S-groups: SuperatomSgroup.getAttachAtoms(), SuperatomSgroup.getLegalAttachAtoms(), SuperatomSgroup.getFreeLegalAttachAtoms(), SuperatomSgroup.isFreeLegalAttachAtom(MolAtom), SuperatomSgroup.isLegalAttachment(MolAtom), SuperatomSgroup.sortXBonds(), MolAtom.getAttach(), MolAtom.setAttach(int), MolAtom.setAttach(int, Sgroup)

    • Elemental Analysis: ElementalAnalyser.setMolecule(SMolecule)

    • Other deprecated methods Molecule.exportToFormat(String), Molecule.exportToBinFormat(String), Molecule exportToObject(String) throws java.lang.IOException.

  • Structure to Name (s2n)

    • The method chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.generateName(Molecule) , though not documented, was public for internal reasons, and used a non-thread-safe way to receive options. It is now deprecated in favor of chemaxon.formats.MolExporter(Molecule, String format) , where format can be for instance "name" for IUPAC name, "name:t" for traditional name.

  • Automapper

    • chemaxon.marvin.modules.AutoMapper

• Removed methods

  • Molecule Representation

    • MolAtom.setMassnoIfKnown(String), MolAtom.isNobleGas(), MolAtom.isArrowEnd(), MolAtom.valenceCheck(), MolAtom.getEdgeCount(), MolAtom.getEdge(int), MolAtom.getEdgeTo(MolAtom), MolAtom.haveSimilarEdges(MolAtom),

    • MolBond.ARROW(), MolBond.isCoordinative(), MolBond.isArrow(), MolBond.getNode1(), MolBond.getNode2(), MolBond.getOtherNode(MolAtom), MolBond.cloneEdge(MolAtom a1, MolAtom a2)

    • MoleculeGraph.AROM_CHEMAXON, MoleculeGraph.AROM_DAYLIGHT(), MoleculeGraph.setSetSeqs(int id), MoleculeGraph.getAromrings(), MoleculeGraph.getNonAromrings(), MoleculeGraph.getAromrings(int), MoleculeGraph.getNonAromrings(int), MoleculeGraph.mergeFrags(), MoleculeGraph.getFragIds(), MoleculeGraph.getfindFragById(int fragId, MoleculeGraph frag), MoleculeGraph.getNode(int), MoleculeGraph.setNode(int, MolAtom), MoleculeGraph.insertNode(int, MolAtom), MoleculeGraph.removeNode(MolAtom), MoleculeGraph.removeNode(MolAtom, int), MoleculeGraph.removeNodeVector(), MoleculeGraph.getEdgeCount(), MoleculeGraph.getEdge(int), MoleculeGraph.setEdge(int, MolBond), MoleculeGraph.insertEdge(int, MolBond), MoleculeGraph.insertEdgeInOrder(MolBond, MolBond[]), MoleculeGraph.replaceEdge(MolBond, MolBond), MoleculeGraph.removeEdge(MolBond), MoleculeGraph.getEdgeArray(), MoleculeGraph.getEdgeVector(), MoleculeGraph.getAllEdges(), MoleculeGraph.regenEdges(), MoleculeGraph.sortEdgesAccordingTo(MolBond[]), MoleculeGraph.mergeNodes(MolAtom that, MolAtom), MoleculeGraph.mergeFrags(int, int)

    • Molecule.mergeFrags()

    • RgMolecule.setAbsStereo(boolean, int, int), RgMolecule.createMol(String), RgMolecule.getBtab()

    • RxnMolecule.getBtab(), RxnMolecule.getStructureCount(int), RxnMolecule.getStructure(int, int), RxnMolecule.addStructure(Molecule, int), RxnMolecule.removeStructure(int, int)

    • CEdge, CNode, CGraph

    • MDocument.setGUIProperyContainer(MPropertyContainer)

Bugfixes

• Import/Export

  • MOL, SDF, RXN, RDF

    • Valid MOL file header was not recognized and therefore the file was not imported.

Bugfixes

• Import/Export

  • Name to Structure (n2s)

    • Names with ylium and uide suffixes are now supported.

• Calculations

  • NMR (HNMR, CNMR Prediction, ...)

    • Coupling of a nucleus with a group of magnetically equivalent nuclei was not handled properly.

    • NMR Predictor did not consider negative coupling constant values.

Bugfixes

• Molecule Representation

  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand.

• Import/Export

  • SMILES/SMARTS

    • Non ring bond information were imported as query strings from SMARTS.

    • After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.

New features and improvements

• Import/Export

  • CDX/CDXML

    • S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML.

Bugfixes

• Painting

  • Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off.

  • When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other.

  • The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.

• Editing

  • Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").

• Import/Export

  • MRV/CML

    • MRV and CML export wrote out characters incorrectly which are not supported by the character set.

  • MOL, SDF, RXN, RDF

    • SDF files having invalid header could not been imported.

    • Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL).

  • SMILES/SMARTS

    • MolExporter.exportToObject() added an extra newline to SMILES.

    • Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation.

  • InChi/InChiKey

    • Absolute stereo flag was missing during InChi export/import and InChiKey export.

• Molecule Representation

  • Valence check

    • Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.

• Calculations

  • Isomers (Tautomers, Stereoisomers)

    • After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases.

New features and improvements

• MarvinSketch GUI

  • Typing abbreviated group names is now case sensitive.

• MarvinSketch Dialog

  • "Cancel" button has been added to the "Customize" dialog.

• Painting

  • The font size and type of circled charge symbols can be modified on the "Display" tab of the "Preferences" dialog.

  • Position variation bond has been recolored for better visibility in a projected presentation.

• Clipboard handling

  • When pasting unrecognized format onto the canvas, "Import as" dialog appears, and the user can choose the correct format.

  • Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats.

• MarvinView GUI

  • Double-clicking on a molecule in MarvinView to open it in a separate window does not result in the disappearance of the original molecule from MarvinView while the separate window is open.

  • The original molecule does not disappear from MarvinView while it is edited in MarvinSketch.

• Applet

  • New applet parameter for specifying the URL of a name recognition and import service: namingWebServiceURL

• Import/Export

  • SKC

    • SKC import has been improved.

  • CDX/CDXML

    • Mapping of reaction agents can be imported.

  • Name to Structure (n2s)

    • Initial support for Chinese IUPAC and common names has been added, e.g., 2-??-4-????.

    • Names with extra closing brackets can be converted when OCR error correction mode is enabled.

    • Name to structure now also works when bridge and spiro numberings are represented by using unicode superscript numbers, such as: tetracyclo[12.4.0.0^2,6.0^7,12]octadecane.

    • Custom webservice to extend name to structure conversion - for instance using corporate IDs (e.g., ABC0001234) or common name dictionaries in addition to the default one - is supported.

    • Automatically fix and import spiro names where the superscript formatting has been lost, for instance, after copy-pasting. As an example, trispiro[2.2.2.29.26.23]pentadecane will be imported as if from the correct form, trispiro[2.2.2.2⁹.2⁶.2³]pentadecane.

    • Name to structure now works on names of bridged ring compounds where the superscript formatting of ring numbering is not present.

    • The custom dictionary can be encoded in UTF-8 - even if the system default encoding is not UTF-8 - providing a byte order mark (BOM) for the file. This can be used, for instance, to support dictionary in multiple languages on Windows OS.

  • Document to Structure (d2s)

    • Invalid hexadecimal character entities (e.g., "&#xblah") are now ignored instead of making the document processing fail.

    • Image to structure conversion using OSRA is working on Mac OS X.

    • Text OCR for scanned documents is now supported on Mac OS X.

    • Documents compressed in xml.bz2 and xml.xz formats can be processed directly.

    • The memory usage has been reduced when processing documents with several thousand hits. This improvement is in addition to the memory improvements already present in version 5.11.

    • Option "+/-groups" has been added to enable (+) or disable (-) the conversion of groups and fragments, such as "ethyl", "nitro", "phenoxy", etc.

    • OCR of scanned PDF documents has been improved on Windows OS thus reaching the same performance level as that of OCR on Mac OS X and Linux OSs.

  • Structure to Name(s2n)

    • The speed of batch conversion using a timeout (which is enabled by default) has been increased by about 15%; the earlier instability in case of timeout relying on the deprecated Thread.stop method has been avoided.

• Molecule Representation

  • The size of the Molecule object has been decreased.

• Data Transfer

  • OLE

    • New settings are available for both administrators and end-users (from the "Edit > Preferences > MarvinOLE" menu) to preset the displayed OLE document in a maximized child window.

    • MRV files are read and validated by DOM (document object model) in Marvin OLE.

• Clean 3D

  • MMFF94 forcefield has been added to Generate3D. Use option "[mmff94]" to switch it on; use "molconvert -H3D" for detailed help.

• Calculations

  • Isomers (Tautomers, Stereoisomers)

    • Performance improvement: Tautomerization will not apply "Clean2D" if the output result has no 2D coordinates.

    • Resonance structure is taken into account in dominant tautomer generation.

  • Conformation (Conformers, Molecular Dynamics, ...)

    • New MMFF94 forcefield implementation has been introduced in Conformer Plugin and Molecular Dynamics Plugin.

  • Services

    • Result structure of Marvin Services result panel can be copied to clipboard.

• Structure Checker

  • New checkers have been introduced:

    • Absolute Stereo Configuration

    • Chiral Flag

    • E/Z Double Bond

    • Multiple Stereocenter

    • Relative Stereo

    • Wiggly Bond

  • Fixer of checker "Query Atom": "Convert to Carbon" has been added.

  • Fixer of checker "Query Bond": "Convert to Single Bond" has been added.

  • Excluded list of abbreviated groups can be specified in "Abbreviated group" checker, i.e., checker will not find (and fix) abbreviated groups that are indicated in this list.

  • Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call.

  • Integration of external structure checkers and fixers into ChemAxon products has become easier via MarvinSketch GUI.

  • In case of more than one fixer, a logical order of priority has been preset.

  • New property change event to indicate when an editable MarvinView component is opened in MarvinSketch: sketchInView.

  • New property change event to indicate when a new MarvinSketch or MarvinView window is opened from the viewer: windowOpened.

  • New property change event to indicate when a MarvinSketch or MarvinView window, opened from the viewer, is being closed: windowClosed.

• Java Web Start

  • Name to Structure and Document to Structure are now available in the Java WebStart distribution of Marvin.

Bugfixes

• MarvinSketch did not deal with java property initialization bug.

• MarvinSketch GUI

  • When a group abbreviation differed from an atomic symbol only in upper and lower case letters (e.g., NO and No), the abbreviated group could not be reached by typing.

• MarvinSketch Dialog

  • Focus did not appear on the "Source" and "Import Name" dialogs with Java 7.

• Painting

  • The charge was not displayed in circle on the bracket of an S-group when the "Show charge in circle" was set on the "Preferences" panel.

  • Charge label masked the adjacent bond in several cases.

• Editing

  • Deleting "extra" explicit hydrogens from an atom with valence error resulted in the appearance of erroneous implicit hydrogens on this atom.

  • When there were several disconnected structures on the canvas, partial clean was very slow.

  • It was possible to create a molecule with R-group definition containing a single attachment point (and no other atoms or bonds).

  • Sprouting did not work for Alias atoms.

  • The two ways of deleting implicit hydrogens (with eraser directly or selecting them first then deleting) behaved differently.

• Load/Save handling in UI

  • "File > Open" dialog froze when an mrv file contained a dashed arrow and the preview pane was checked.

  • When opening a multi molecule file and selecting a range that is open ended, a false error message appeared, which stated that there were too many molecules selected to open.

  • IUPAC name with alpha or beta signs could not be imported.

  • MarvinView did not open when importing a file from command line failed.

  • It was not possible to append a name to an existing .name file in MarvinSketch.

• Clipboard handling

  • It was not possible to drag a structure from MarvinView in "Translate or Drag" mode.

  • Ctrl + V shortcut for pasting structures did not work in MarvinView in case of "Spreadsheet" view.

• Graphical object handling

  • MBracket object "BRACES" did not render correctly when the orientation was set as "SINGLE".

• Applet

  • After reloading an applet from the lifecycle cache, the propertyChange method was called in the javascript side regardless of the listenPropertyChange parameter.

• Image I/O

  • The source was not saved from MarvinView in png, jpg, and svg formats.

• Import/Export

  • Option -g of molconvert ignored only MolFormatException.

  • MRV, CML

    • MRV import could not handle contracted Superatom S-groups having less atoms than crossing bonds.

    • MRV export used operating system specific line ending, '\n'.

    • CML import failed on files that contained non-ASCII characters.

  • MOL, SDF, RXN, RDF

    • Superatom S-group brackets were imported from MDL files.

  • CXSMILES/CXSMARTS

    • CXSMARTS I/O lost the charge from generic metal atom.

  • CDX/CDXML

    • Reaction agent not having reactant and product (e.g., >CC1=CC=CC=C1>) was read as reactant from CDXML files.

  • Name to Structure (n2s)

    • RS - as the marker of racemates - was not converted properly, for instance in (2RS)-1-(Adamantan-1-ylamino)-3-phenoxypropan-2-ol.

    • Lower CamelCase chemical names (such as 2-cyclopropylPiperazine) were not converted to chemical structures.

    • Common names, which are also non-chemical names, were recognized as chemical names during automatic format recognition, e.g., "Royal Blue".

    • E/Z bonds were sometimes set to the opposite value (in cases of non-trivial CIP rules).

    • For some rare inputs, which are not valid names, n2s created invalid structures that could be exported to mol format but could not be opened.

    • Both "phenylene" and "phen-1,3-ylene" were wrongly converted to benzene. Now all forms convert to the correct structure with two attachment points, including "m-phenylene", "1,3-phenylene", and "phen-1,3-ylene" (similarly for the o-, p-, 1,2-, and 1,4- forms).

  • Document to Structure (d2s)

    • Processing of multiple XML documents in concurrent threads was slow and sometimes skipped some hits.

    • Names separated by the "non-breaking space" character were not recognized.

    • Some names split by extra spaces were not found.

    • English names were not recognized in Japanese documents when the ideographic comma character followed them.

    • SMILES with aromatic atom after non-aromatic ones ("Cc1...") and with triple(#) or explicit single(-) bonds were not recognized.

    • Text OCR failed when the images in PDF were encoded in a certain variant of the CMYK color space.

  • Structure to Name(s2n)

    • Some characteristic group names were missing when expressed as a prefix of a sulfonyl group, for instance, in "propanamidosulfonyl".

    • Names could not be generated for structures containing "-[N+]≡" substituent. They are now named using the "azaniumylidyne" IUPAC name component.

  • Peptide

    • During automatic format recognition, non-latin characters were recognized as peptide sequences.

• Molecule Representation

  • S-groups

    • Multiple S-group expanded incorrectly when it had an embedded S-group.

  • S-groups/R-groups

    • S-group creation was not possible for a structure within an R-group definition of a reaction; a warning message was given.

• Clean 2D

  • Wedge clean moved non-ring wedge bond between two rings into a ring.

• Calculations

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • Microspecies calculation of furan returned incorrect molecular formula at low pH.

  • Charge (Charge, Polarizability, ...)

    • Resonant charge calculation generated exception when the major form of the molecule is invoked with explicit hydrogen atoms.

  • NMR (HNMR, CNMR Prediction, ...)

    • Outdated HOSE database caused NullPointerException when predicting 1H NMR spectrum for some rare diastereotpic molecules.

  • Isomers (Tautomers, Stereoisomers)

    • D, T count in region labels of multifragment generic tautomers was computed incorrectly.

    • TautomerizationPlugin API did not clean the explicit hydrogens in the result molecule after tautomer generation which might have resulted in wrong stereo (R,S) specifiaction on chiral centers.

  • Geometry (Topology Analysis, Geometry, ...)

    • The result of topological polar surface area (TPSA) plugin depended on the call order of setMolecule() and setpH() methods.

• cxcalc

  • Calculation "ringcountofatom" returned only the ring count of atom number zero.

  • cxcalc returned irrelevant error message for calculations containing "ANY" bonds.

  • Thole polarizablility (tpol) calculation didn't interrupt when clean3D failed.

• Backend / Core

  • Removing explicit hydrogens on some large PubChem compounds caused infinite loop.

• Structure Checker

  • "Remove Stereo Care Box" was offered as fixer for results returned by "Query Bond Checker".

  • Fixer "Expand group" not only expanded but also ungrouped the abbreviated groups when using it via structurechecker command-line.

• API

  • The default value of parameters chargeWithCircle and lonePairsAsLine has been changed. The current default value of these parameters is "false". On the "Preferences" dialog, the "Restore default" button sets both parameters to "false", too.

Deprecation

• Structure Checker

  • Deprecated checker action strings: aromaticity, chiralflag, circularrgroup, missingrgroup, rare, reactionmap, unusedrgroup, valence, wedge.

  • Deprecated fixer action strings: clearabsstereo, aliastocarbon, crossedtowiggly, converttosingle.

  • Deprecated fixer class names: AbsentChiralFlagFixer, AbsoluteStereoFixer, CrossedDoubleBondFixer, CovalentCounterionFixer, ExplicitHydrogenFixer, IsotopeFixer, RgroupReferenceFixer, WigglyDoubleBondFixer.

Bugfixes

• Datatransfer

  • Structures copied from ChemDraw, Accelrys Draw, or Symyx Draw could not be pasted onto MarvinSketch.

New features and improvements

• Datatransfer

  • The imageImportServiceURL setting also affects the behavior of clipboard operations (drag and drop, paste).

Bugfixes

• Painting

  • Rounding error occurred in case of nearly 180 degree bond angle and it caused overflow error when resizing the structure.

• Import/Export

  • New export option, BOM, is introduced for non-binary chemical file formats in order to write out Byte Order Mark (BOM) if UTF-8 encoding is used.

  • Structure to Name (s2n)

    • Since 5.11.0, names generated for bridged cyclic structures with explicit bridge head hydrogen contained a spurious "hydrogenio" prefix.

• Clean 2D

  • Clean 2D got stuck in an infinite loop when fullerene-like molecules were cleaned.

• Calculations

  • Atom index issue might have occurred when molecule contained explicit hydrogen.

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • "averagemicrospeciescharge" calculation in cxcalc and "Isoelectric Point" calculation in MarvinSketch threw "ArrayIndexOutOfBoundsException" in the reported cases.

  • NMR (HNMR, CNMR Prediction, ...)

    • The calculated chemical shifts of equivalent atoms were not consistent in case of compounds with symmetric ring systems.

Bugfixes

• MView applet

  • Atom and Bond set coloring was not working properly when Marvin View Applet was called from JavaScript.

• Image I/O

  • When imageImportServiceURL startup option was not set for MarvinSketch, the same setting on the Preferences panel was lost. By default shortcuts and startup scripts do not specify this command line startup option.

• Java WebStart

  • chemaxon-core.jar, fontbox-1.7.1.jar and pdfbox1.7.1.jar were missing.

• Calculator Plugins

  • Tautomerization Plugin threw exception during generic tautomer generation if the input structure contained metal ions with valence error.

New features and improvements

• Image I/O

  • Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style).

• MarvinSketch GUI

  • A new "imageImportServiceURL=[URL]" program argument was added to the MarvinSketch application.

• MarvinSketch applet

  • A new "imageImportServiceURL" was added as an applet parameter.

• Graphical object handling

  • When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.

• Import/Export

  • Document to Structure (d2s)

    • Names broken over two lines with a hyphen (-) are now recognized.

    • Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin¹¹") are now recognized.

  • Name to Structure (n2s)

    • In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.

Bugfixes

• Painting

  • If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.

• Image I/O

  • Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.

• Import/Export

  • MOL, SDF, RXN, RDF

    • Aliphatic query properties of atoms with query string were not read from MDL formats.

    • After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.

    • Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.

    • SDF import returned structure with incorrect S-group embedding.

  • SMILES/SMARTS

    • SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.

• Molecule Representation

  • S-groups

    • Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.

  • Valence Check

    • Phosphorous atom in hexafluorophosphate was not accepted by Valence Check.

• Stereochemistry

  • Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.

• Clean 2D

  • Terminal methyl-group in phosphate-ester was cleaned incorrectly.

  • Clean2D could not handle condensed adamantane derivatives.

• Calculations

  • Other (HBDA, Huckel Analysis, ...)

    • The --pH command line option did not work in hydrogen bond acceptor-donor calculation.

• Structure Checker

  • If fixer action was not defined, default fixer was not applied in structurechecker command line tool.

New features and improvements

• Import/Export

  • Document to Structure (d2s)

    • Startup time of document to structure has been significantly reduced. This is especially important when processing very short text documents, such as a single sentence or paragraph. The speedup in such cases can be up to 10 times faster.

Bugfixes

• Calculations

  • NMR (HNMR, CNMR Prediction, ...)

    • NMR Prediction did not use the mixed prediction algorithm, so NMR shift predictions were less accurate.

• Chemical Terms

  • The -g (ignore error) option of evaluate did not work when -x (extract) option was used.

• Structure Checker

  • WedgeCleanFixer threw ArrayIndexOutOfBoundsException when the erroneous wedge bonds were located inside an S-group.

New features and improvements

• MarvinSketch GUI

  • Molecule properties like SDF fields can be added/edited/deleted in MarvinSketch GUI.

  • Bond properties can be added/edited/deleted in MarvinSketch GUI.

  • Lone pair can be displayed as a line. The option can be set from the "Preferences" panel.

  • Charge can be displayed in a circle. The option can be set from the "Preferences" panel.

  • An aromatic benzene template has been added to the Generic templates.

• Data transfer

  • Clipboard handling

    • Java wrapper for CXNSharedAddin library has been introduced to handle tabular data transfer from/to Microsoft Office applications.

• Import/Export

  • CDX/CDXML

    • Graphical arrows "retrosynthetic" and "equilibrium" are imported from CDX and CDXML files.

  • Name to Structure (n2s)

    • Names, such as "methyl ether", are used either to denote a group (CH3-O-*) or the dimethyl ether compound (CH3-O-CH3), as well. The default behavior still is to generate the complete compound, but a new name option "expectGroup" has been added to get the group instead.

    • A name converter can now prevent a name from being converted (even by other lower-priority converters). See the API of the chemaxon.naming.NameConverter class.

  • Document to Structure (d2s)

    • Peptide 3 letter abbreviations are now recognized in documents, for instance ValGlySerAla or Val-Gly-Ser-Ala.

    • A new option has been added to control the maximum time allowed for processing a document: format option "d2s:timeout=60" to allow a maximum of 60 seconds. Default is 0 meaning infinite timeout.

    • A new option has been added to disable the extraction of OLE embedded structures from Office documents (option name: "d2s:-ole").

    • Structures imported from the custom name dictionary now have the "Type" property set to "custom" instead of "common".

    • Memory usage has been significantly reduced when processing large PDF documents (for instance hundreds of scanned pages).

    • Structure image conversion by OSRA has become faster, resulting in more structures converted when previously a timeout was reached.

    • CAS Registry Numbers® (which typically include commas) are not converted by default by d2s anymore (they are still converted by n2s). The old behavior can be activated by using the "d2s:CASnames" format option.

    • The unwanted interpretation of some common words as chemical names, that are frequent especially in patents, has been avoided. For example, the 'amino' group when used in the phrase 'amino acid', or 'Ser' when it is not the abbreviation of Serine but 'Ser. No.' for 'serial number'.

  • Structure to Name(s2n)

    • Multiple name generation tasks can now be run in parallel at full speed to make use of multiple CPUs and cores.

    • Multiple name import tasks now run faster, as partial locking is no longer required and has been removed.

    • Generated names now use unicode characters when needed, for instance, 6λ⁴-thiadispiro[5.2.5⁹.2⁶]hexadecane instead of 6$l^{4}-thiadispiro[5.2.5^{9}.2^{6}]hexadecane. The pure ASCII output can be generated using the "name:ascii" format option.

  • Image I/O

    • New parameter imageImportServiceURL has been added to the image importer module. The URL can be set on the "Preferences" dialog or as an import option.

  • VMN import

    • VMNs of type "display" are now read.

    • VMN abbreviated group list has been extended: carbon chains up to 50 members have been added.

    • AV (abnormal valence) property is now stored in atom property and not set as atom valence. The VMN valence representation will be revised in a later version.

    • Deuterium and tritium count property is handled properly in VMN (added as D and T ligands for non-homology atoms). D and T are transposed during the import in comparison to the VMN, as this represents the correct information in the majority of the MMS database.

    • Correcting incorrect atom types in VMNs: C0 is transformed to CHK; C1 is transformed to C; homology groups in ring are transformed to XX

    • Attachment bond type is set to parent R-atom bond type if different.

    • VMN import option is available for switching off corrections:

• Molecule Representation

  • New option, MolAtom.BRIDGEATOM_H, is added to Hydrogenize.removeHAtoms(MoleculeGraph, int) method to remove hydrogens connected to bridgehead atoms.

  • Valence Check

    • Local valence check has been introduced, which calculates the valence by considering only the neighboring atoms. Although the new valence check is the default, the old one is also available.

  • S-groups

    • ElementalAnalizerPlugin calculates Polymer Formula for molecules containing SRU or RepeatingUnit S-groups.

• Calculations

  • Charge (Charge, Polarizability, ...)

    • Dipole Moment Calculation plugin: calculates the net molecular polarity.

  • NMR (CNMR Prediction, HNMR Prediction)

    • New, mixed HOSE code/CXN model has been introduced, which results in more accurate NMR shift prediction.

    • C-F and H-F couplings are considered during NMR shift calculation.

    • Diastereotopic protons are supported in HNMR Prediction.

    • The tautomers of the predicted molecule are accessible via the Options > Select Tautomers... option of the NMR GUI. The spectra of the selected tautomers with defined percent composition are added to the predicted spectrum.

  • Chemical Terms

    • "molString" and "molFormat" Chemical Terms functions are accessible under the name "molConvert" as well.

• Structure Checker

  • New Structure Checker GUI has been introduced. Besides the redesigned GUI, new features are also available:

    • Profile management;

    • Filters in Report view.

  • Structure Checker is going to be moved to the MarvinBeans package. Until it is done, the new Structure Checker GUI is available in both JChem and MarvinBeans packages as Structure Checker JChem and Structure Checker, respectively.

  • Substructure Checker feature is accessible only in Structure Checker JChem until the complete relocation of Structure Checker.

  • Improved R-group Attachment Error Checker detects R-group definitions having incorrect R-group attachment orders. Fixer is not available for this feature yet.

  • New Explicit Hydrogen Checker options are ready for use.

  • Checkers that are not recognized as internal or external checker are called: "Invalid Checkers". Invalid Checkers cannot be used in valid Structure Checker configurations; they need to be removed to perform proper working behavior.

• Build/Installation

  • Marvin Beans and JChem installers - for Linux - bundled with Java 1.6.0_33 have been introduced.

Bugfixes

• MarvinSketch GUI

  • The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.

  • Several mnemonics were duplicated or missing in the menu of MarvinSketch.

• Painting

  • Bond topology representation was not visible in R-groups.

• Dialogs

  • Periodic table view 'Blocks' showed Helium color coded as a part of 'p block' instead of the correct 's block'.

• Import/Export

  • Load/Save handling in UI

    • MarvinSketch did not overwrite the former PDF file when changes were made and it was saved as a PDF again with the same file name.

  • MRV, CML

    • The string value of a query property was imported as element.

  • MOL, SDF, RXN, RDF

    • Registry number of a molecule that is a property of an other molecule was not imported from RD file.

  • SMILES/SMARTS

    • Cis/Trans information was not exported for bonds being in two rings.

  • CXSMILES/CXSMARTS

    • Query pseudo atoms represented by CXSMARTS lost their valence property during import.

    • R-group definition of an Rg-molecule described in CXSMARTS was imported as CXSMILES.

  • CDX/CDXML

    • Reaction agent was not possible to read from CDXML file.

    • From CDXML file containing only a product of a reaction, the product was imported as reactant.

  • Name to Structure (n2s)

    • Names ending with "group", such as: "cyclohexyl group" were not imported.

    • Chirality specified without locant was sometimes not included in the generated structure, for instance in (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate.

  • Document to Structure (d2s)

    • Several names separated by a comma were sometimes wrongly recognized as a single name.

    • Document to structure was leaking some memory in a way that was problematic for extremely large documents (tens of thousands of structures in a single document).

    • When using the d2s API, waiting threads could be left behind when large documents were converted but the structures were not read until the end. This is now fixed, provided the client calls MolImporter.close().

    • Document to structure was not processing text from PDFs with non-standard fonts, for instance English text encoded in Japanese fonts.

    • Certain images in PDFs were not processed correctly by OSRA during optional image-to-structure conversion.

    • Names found in documents may have included unwanted trailing characters when the next word started with an open bracket, for instance, "cholesterol [28]" instead of "cholesterol".

  • Structure to Name(s2n)

    • The group "[NH3+]-" was given traditional name "aminio", instead of the correct "ammonio".

    • Names were generated for structures with link nodes, as if the link nodes had been absent.

    • Incorrect names were generated for structures with one attachment point.

• Molecule Representation

  • Meitnerium appeared at a wrong position in the periodic table of MarvinSketch.

  • Explicit hydrogen that connects to an atom having more than one wedge bond was not converted to implicit one.

  • S-groups

    • When an expanded SuperAtom-Sgroup was inside an other S-group, its attachment points had invalid implicit hydrogen count.

  • Stereochemistry

    • Stereoinformation were not recognized on cyclohexane-1,3,5-triol.

• Clean 2D

  • Calling clean 2D on a 3D molecule resulted in short bond length between a Hydrogen and an other atom

  • Clean 2D inserted wiggly bond into a Kekule form of a 0 dimensional aromatic molecule.

• Aromatization/Dearomatization

  • Basic aromatization method aromatized rings containing sulfur atom that have four ligands.

  • Basic aromatization method aromatized rings with -S= substructure.

• Calculations

  • Isomers (Tautomer, Stereoisomers)

    • Cross bond was not handled correctly by canonical tautomer generator.

• Structure Checker

  • Abbreviated Group checker options did not work as expected: checker recognized both expanded and contracted groups regardless of the selected option.

• Build/Installation

  • Desktop icons were missing from the Marvin Beans for Linux installer.

New features and improvements

• Applet

  Class reorganization for more efficient applet loading.

New features and improvements

• Import/Export

  • MDocSource implements Iterable<Molecule>.

  • MOL, SDF, RXN, RDF

    • New option for MDL MOL format import, Fsg, has been introduced to ungroup superatom s-groups with more than two attachment points.

Bugfixes

• Import/Export

  • MRV

    • The string value of the query property was imported as element.

New features and improvements

• MarvinView Printing

  • Resolution of PDF printing has been increased.

• Datatransfer

  • Legacy MRV '\n\ header (5.7) format is supported in Marvin OLE.

New features and improvements

• Import/Export

  • MOL, SDF, RXN, RDF

    • Coordination bond is written and read from extended MOL file.

  • Name to Structure (n2S)

    • More extensive support for the retrieval of CAS Registry Numbers® from publicly available sources hosted by the U.S. National Institutes of Health (“NIH”) and the Wikimedia Foundation.

• Clean 2D

  • New clean option, Toff, is introduced to ignore template based cleaning.

  • Coordinate bond length has been increased for a better view of its arrow representation between atom labels.

Bugfixes

• MarvinView

  • MarvinView did not display the SD file property if no property values were attributed to the first entries.

• Painting

  • The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.

• Editing

  • Transfer button did not appear on the "Sketch new substituent..." popup window when the 'Insert>New Substituent' menu item was selected.

• Import/Export

  • Byte Order Mark (BOM) was not written out during the export.

  • Default line separator was not unique in MolExporter.

  • CDX/CDXML

    • Empty CDX and CDXML files could not been imported.

• Molecule Representation

  • S-groups

    • Contracted Superatom S-groups drawn to MarvinSketch and having only one crossing bond had no attachment point information.

  • Stereochemistry

    • Absolute chiral flag calculation terminated with "java.lang.OutOfMemoryException" for large, symmetric molecules, e.g., fullerene derivatives.

• Calculations

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • Major microspecies calculation threw "ArrayIndexOutOfBoundsException" in the reported case.

New features and improvements

• Import/Export

  • MOL, SDF, RXN, RDF

    • The template based coding of amino acids in MOL V3000 files are read as pseudo atoms. However, the template based structure of peptides cannot be read.

    • Method MolFileHandler.collectFileInfo() returns molecule and reaction identifiers $MFMT $MIREG, $MFMT $MEREG, $RFMT $RIREG, $RFMT $REREG, $MIREG, $MEREG, $RIREG, $REREG as well.

• Clean 2D

  • An option is introduced to set explicit C-H bond length to 1.0 instead of 1.54 in case of two dimensional cleaning.

• Calculations

  • "Keep explicit hydrogens" option has been added to pKa plugin, Major Microspecies plugin, and Isoelectric Point plugin.

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • The speed of major microspecies calculation has been improved when "Take major tautomeric form" option is used.

  • NMR

    • The accuracy of the NMR predictor has been improved.

Bugfixes

• Painting

  • "Absolute" label was not visible when only contracted Sgroups contained stereo information and the "Absolute" stereo flag was set on the Molecule.

  • Joining two product structures of a reaction erased both structures.

  • Joining aromatic rings drawn in Kekule form sometimes caused their aromatization.

• Editing

  • Atom labels could disappear when the structure was cleaned in 3D, rotated then cleaned in 2D.

• Import/Export

  • Byte Order Mark (BOM) was not written out during the export.

  • MRV/CML

    • Molconverter could not convert files containing multiple molecules to separate MRV/CML files.

    • Encoding could not been set during MRV and CML export.

  • MOL, SDF, RXN, RDF

    • Bond length of a molecule imported from MOL V3000 file was short, therefore the atoms overlapped.

    • RD file records written after an empty structure were not read correctly.

  • CDX

    • CDX files containing labels without chemical structures were not read. Now, these labels are read in text boxes.

  • SKC

    • SKC import put an R-group attachment point to Superatom S-groups.

    • Stereo information was lost at importing a peptide from an SKC file.

    • Wedge bond information of a contracted S-group was lost during the SKC import.

• Molecule Representation

  • Valence check

    • Valence check allowed any number of bonds on carbon atoms having implicit hydrogens.

  • R-groups

    • Method RgMolecule.fuse() resulted inconsistent molecule when it was invoked on RgMolecules having SuperAtom S-group in its definition.

  • Stereochemistry

    • Nitrogen being one of the fusion points of ring systems was detected as chiral when the carbon atom at the other fusion point had four explicit ligands.

• Aromatization/dearomatization

  • Dearomatization failed for porphyrin-like ring systems.

• Calculations

  • Charge (Charge, Polarizability, Orbital Electronegativity)

    • Charge calculation was not consistent on fragmented molecules.

  • Isomers (Tautomers, Stereoisomers)

    • Different rational canonical tautomers were generated for some molecules when they came from different sources (e.g., InChi and SMILES).

    • Tautomer distribution was not calculated for various porphyrin-like structures.

  • Geometry (Topology Analysis, Geometry, PSA, MSA)

    • Negative or zero Van der Waals and Solvent Accessible molecular surface area values were generated for molecules with inconsistent chemical structures.

• Structure Checker

  • Abbreviated group checker did not identify expanded and contracted groups correctly.

  • "substructre" action string did not work in command line.