Bug fixes:
No changes.
Bug fixes:
Bug fixes:
Gallium 1 has been released based on Frequent Release 20.19.0.
Bug fixes:
No changes.
Improvements
New features
No changes.
New features
Improvements
Bugfixes
No changes.
Improvements
Bugfixes
Improvements
Bugfixes
No changes.
No changes.
Bugfixes
Bugfixes
Improvements
Bugfixes
Known Issue
Improvements
Bugfixes
No changes.
Fermium 1 has been released based on Frequent Release 20.8.
No changes.
No changes.
No changes.
Bugfixes
Improvements
Bugfixes
Bugfixes
Improvements
Installer
Bugfixes
Bugfixes
Improvements
Toolbar
Menu
Bugfixes
Improvements
Drawing
Bugfixes
No changes.
Improvements
Installer
Bugfixes
Export InChIKey
Known issues:
Improvements
Applet
Installer
Known issues
No changes.
Improvements
Checkers
Bugfixes
Image generation
No changes.
Europium 1 has been released based on Frequent Release 19.21.
Bugfixes
View
Bugfixes
View
Mac OS
Improvement
Abbreviated Groups
User interface
No changes.
No changes.
Bugfixes
I/O
Importing CAS Registry Numbers®
Bugfixes
I/O
Bugfixes
Editing
Importing CAS Registry Numbers®
Improvement
Search
No changes.
Bugfixes
Editing
No changes.
Known issues:
Bugfix
I/O
No changes.
No changes.
Bugfixes
Editing
I\O
OSX
Sizing of Save As dialog was miscalculated.
Improvement
Stereocalculation
A new method for calculation of optical isomerism has been introduced.
No changes .
Bugfixes
Editing
Dot disconnected formula with charges did not work in the Analysis box.
MarvinSketch had a performance problem in case of large structures with enabled M/P labels calculation.
When symbol characters were inserted, the textbox did not resize automatically.
Text from the Naming window could not be pasted into a MarvinSketch's textbox.
Background, outline, alignment settings are lost when a textbox was copied.
GUI
No feedback was displayed for the selected tool on Mac OS.
In some cases, the selected Save>Folder changed when the user modified the file format.
The context menu item was missing when contracting more expanded groups at the same time.
I\O
TROPOS mol2 file was not saved correctly from GUI.
HCOUNT import and export didn't work in MOL v3000 format.
In some cases, a part of the grey background of position variation bond was cut from images.
Improvements
GUI
MDL Mol V3000 format has been added to the Copy As... options
Stereocalculation
A new method for calculation of Cis – trans isomerism has been introduced.
No changes .
No changes .
Deuterium 1 has been released based on Frequent Release 19.7.
Improvement
Analysis Box
The formula in Analysis Box is displayed without charged molecular species .
GUI
ChemDraw, ISIS like, Marvin 1-5, Marvin5 presets are not available anymore.
Bugfixes
Editing
The simple text could not be pasted into a textbox.
Bugfixes
Editing
The label of atoms with implicit Hydrogens displayed on the top of the atom was misplaced
The arrow tool did not snip the target atom while mapping reactions.
Molprinter
In some cases, MolPrinter did not render reaction signs.
No changes .
Bugfixes
Editing
The label of data S-group was misplaced.
No changes .
Bugfixes
Editing
The retention/inversion flags were not displayed correctly.
Colored lone pairs were painted using the monochrome view.
OpenJDK11 bundled installer for Windows, OSX, and Redhat platform has been released.
Bugfixes
I/O
There was a significant slowdown in the import of SMILES of some molecules with a huge ring system.
Improvement
I/O
D ocuments larger than A4 are exported as poster in .CDX file format.
Bugfixes
Editing
API
In certain cases the coordinates of textbox were miscalculated.
I/O
There was a significant slowdown in the import of SMILES of some molecules with huge ring system.
Wrong bond spacing values were exported in .CDX file format.
No changes.
Improvements
GUI
Structure to Name and About dialog has been revisited.
No changes.
Bugfix
Molprinter
Improvements
GUI
Improvements
Editing
Improvements
I\O
Bond length, bond thickness, bold bond width, bond spacing hash spacing and margin are imported from .CDX and .CDXML formats.
Text font size are corrected in .MRV files created before version 18.22.0.
GUI
Structure to Name and About dialogs have been revisited.
MolPrinter
The performance of MolPrinter has been improved.
Bugfixes
Editing
Analysis box was not displayed when a selected structure contained abbreviated group.
The reactants and products were copied with the reaction arrow.
Removal of selected atoms/bonds switched to erase mode.
Bugfixes
Editing
Expanding abbreviated groups gave distorted structure.
View port changed for a different Journal were applied.
The feedback of Lasso selection tool didn't work for single-step reactions.
MacOS Mojave is not supported.
Improvements
Editing
Copy from Analysis box has been introduced.
Textbox handling has been revisited.
Bugfixes
Editing
Analysis box was not erased when the molecule was deleted.
Empty analysis box was added when a product/reactant was deleted next to a merged product/reactant.
Carbon 1 has been released based on Frequent Release 18.22.
Bugfixes
Editing
Chain drawing didn't mirror the mouse movement.
The fontsize in textboxes wasn't independent of bondlength.
Textbox handling has been revisited.
Analysis box
Clipboard
Improvements
Editing
Help
Bugfixes
Editing
The viewport changed when 'Esc' was pressed or was clicked into a textbox.
No changes.
No changes.
No changes.
Bugfixes
Editing
Brackets in multiple S-groups were not selected by double-clicking.
Analysis box
Values for multiple groups were miscalculated.
Clipboard
Image generation
No changes.
No changes.
Improvements
Naming
CAS Registry Numbers® can be retrieved from from the U.S. National Institutes of Health (NIH) and the Wikimedia Foundation via Structure >Name submenu.
Mac OS
Copy as .PDF option has been removed.
Bugfixes
Printing
Atom numbers were not shown on printed picture.
## MarvinView **
If marvin.properties file contained deprecated property "wireknobs", MarvinView did not start.
"Save?" dialog did not appear when MarvinView was closed after modifying a file.
Improvements
Editing
Basic template bar has been changed.
Bugfixes
Editing
First and second merge points weren't indicated with same size patches.
No changes.
Bugfixes
Editing
"All" zoom option didn't handle atom labels correctly when Journal Style is applied.
Preferences menu didn't not open under JAVA 10.
Scale/Zoom factor were omitted upon copy.
Marvin View didn't open structures via double click on files on Mac OS.
Image generation
The label of abbreviated groups sometimes was cut.
Improvements
Editing
Ctrl+D shortcut and new Edit menu item have been added for Copy as OLE.
Bugfixes
Editing
NPE was thrown on the console when atom formatting was done.
User defined properties were lost when a new bond was attached to a homology atom.
Molconvert
*.mol was not found .
No changes.
Barium 1 has been released based on Frequent Release 18.8.
Improvements
Default minimum heap size has been changed to 512MB.
Option for selecting MDL Molfile v2000 and v3000 has been introduced into Save as and Source dialogs.
OLE format has been removed from the transferable list of Ctrl+c.
{warning} From this version on OLE format can be copied using the Copy as... (Ctrl+K) option.
API
'strict' option has been introduced for MDL Molfile conversions. When it is applied, the output strictly follows the CTFile format specification i.e. names longer than 80 characters are omitted.
Improvements
I/O
The order has became flexible in the in AttachmentPointArray block of .MRV files.
Data S group import from .CDX and .CDXML files has been improved.
Editing
Structures were not centralized correctly when the window was resized.
Printing
Printing didn't work using JAVA 9 in Windows.
Bugfixes
Editing
Atomsets could not be discarded when changing the document style.
I/O
Upon import of SGroup data from ChemDraw file the data was added as textbox.
Bugfixes
Editing
Copy as .MRV did not work when Save/Load GUI Settings option was disabled.
Pasting rich text the sub/superscript formatting was lost.
Structures were not displayed in Marvin Services result window.
I/O
The font size of textboxes was not kept during .CDX, .CDXML file import.
The font size of textboxes was not kept during .SKC file import.
I/O
MRV import of abbreviated group failed if the file did not contain AttachmentPointArray.
OLE
Dimensions of EMF image was recalculated during generation in MarvinOLEPanel.
Improvements
Editing
Stereocalculation
In some cases higher order stereo detection incorrectly returned WIGGLY result instead of UNKNOWN.
I/O
NPE was thrown during the import of some tetrahedral stereo molecules containing explicit Hydrogens on the stereo centers.
When CDX/CDXML file was imported, the font size of text was smaller than the original one.
Installer
MarvinSketch could not be launched by clicking its icon on MAC OSX.
No changes.
Upon import unnecessary cleaning was performed.
I/O
NPE was thrown during the import of some tetrahedral stereo molecules containing explicit Hydrogens on the stereo centers.
Improvements
Editing
Shortcuts Alt+↑ and Alt+↓ for super- and subscript has been introduced for textbox.
Shortcuts Alt+↑ and Alt+↓ for super- and subscript has been introduced for Atom Label Editor.
Editing
Structure cannot be seen in Marvin Services result window.
Zoom scale changed when a R group attachment point was added
Upon rich text pasting sub/superscript formatting was lost.
Escaping did not work for DataSGroup.
Copy as .MRV didn't work when Save/Load GUI Settings option was disabled.
I\O
The plus signs of the reaction imported from SMILES was painted in wrong position in MarvinView.
No changes.
No changes.
Bugfixes
No changes.
Editing
Clean and arrange duplicated the arrow in reactions when the automatic plus sign calculation was disabled.
Pasting to a newly opened window didn't work.
Improvements
Editing
Aryl Heteroaryl Heteroalicyclyl Fusedheteroaryl, Fusedheteroalicyclyl is added to the Homology groups.
Analysis box handles pseudo formulas.
The size of textbox follows the changing in font type/size.
Stereo calculations
Assignment of quaternary stereocenters aligns with the IUPAC recommendations.
OLE
Editing
Charges were missing from the chemical formula in Analysis Box.
Copy of a reactant of a reaction threw null pointer exception in some cases.
Opening new MarvinSketch window deleted the clipboard.
In some cases the bounding box of text box was active even in unselected state.
Image IO
Image export options for (de)aromatization were not considered.
IO
Extra plus signs were added when exporting reactions to SKC format.
SKC export transforms the coordinates in a way that the molecules will be rendered in the middle of the canvas.
Names longer than 80 characters were saved in MOL v2000 files.
Editing
Improvements
Speed of editing (dragging/rotating) big molecules decreased.
Abbreviations NBoc and OBoc have been introduced.
Aromatic ring templates have been added to the template library.
Editing
When rotating structure containing aromatic ring in 3D, the aromatic ring was painted in a wrong position in few cases.
The blue feedback of a selected molecule changed its position when the user moved the mouse.
Send to back context menu of graphical objects did not work.
When trying to create an R-group definition in a reaction, the drawing pane stopped refreshing, and the response time increased.
MarvinSketch mirrored the rectangle object which was created by MarvinJS.
Text box
Exception was thrown when pressing space key in one character long text box.
When a user copied a text which was a name of a chemical compound into an empty text box, the structure was displayed.
The molecule was not centralized on printouts, resulted that some part of the structure was cut.
In Macintosh computers, structure printouts did not include colored bonds.
Image IO
Quality of generated EMF was low when .Net libraries were not installed on the user`s computer.
I\O
Editing
In some cases the selection wasn't disabled by 'Esc'.
The definition of Markush structures was lost when a reaction arrow was drawn.
I\O
Atom numbers weren't considered during molecule bound calculation.
No changes .
No changes.
Bugfixes
Editing
Copy/pasting structures having M/P label froze Marvin.
Atropisomerism for agents wasn't calculated.
In some cases aromatic rings were drawn incorrectly after canvas have been got increased
OS
Copy/pasting as PDF to/from Sketch and Office didn't work properly.
Installer
Marvinbeans.jar was missing from 'MarvinSketch Installer with OLE Support'.
I/O
SMARTS import of some porphyrin-like molecular structures failed with IndexOutOfBoundException.
Print to pdf using 'All option' gave warning..
High usage of CPU was observed upon scrolling.
Bugfixes
GUI
Editing
When changing Journal style the structure disappeared.
Atom font could not be set when "Apply for selection only" was selected.
Marvin crashed when MP stereo visibility option was on and a single arrow was placed on the canvas.
In some cases the removal of explicit hydrogen atoms resulted in an error.
I\O
Bond coloring did not work in SVG export.
2D Clean
No changes.
2D clean
In some cases the double bond stereo information changed during 2D coordinate generation.
In some cases Printing to PDF using 'All visible option' generated structures with missing heteroatoms.
Images could not not be exported from MView.
No changes.
Editing
Wirefame with knobs view option has been eliminated
.
I\O
GroupId property has been intoduced to .CDX format.
sketchRendering2d=wireknobs option has been deprecated.
Bugfixes
Editing
Upon resizing the display was not centered.
Editing
Editing
Multiselection (Shift+selection) didn't work.
In certain cases when a large file was opened, it was not centered.
No changes.
Editing
Curved arrows imported from MRV file that was created by Marvin before version 16.5.2. were malformed.
In few cases of directed merge, merging two compounds transformed isolated bonds into aromatic bonds.
No changes.
Coordinates of the feedback of abbrev groups were positioned imperfectly.
Only the atoms were highligted when colored bonds were selected.
Merge feedback was indicated when bond tool was in hand.
When MarvinSketch was installed to computers with single CPU exception was thrown.
Molecules weren't resized when window size changed.
Editing
Analysis box uses the user defined text format (from Edit>Preferences).
I\O
Mol import 'z' option has been enchanced.
Property of merged agent is saved in MRV.
Bugfixes
Editing
Editing
The head of coordinate bond resizes with the length.
New R-group hit detection feedback has been introduced.
Stereo labels are not included in the selected structure.
Bugfixes
Editing
The values of "Bond thickness" on "Document styles settings" and "Format" panels were different.
When there was a selected molecule on the canvas and the user pressed Ctrl+C, the molecule slightly shifted.
Editing
Zooming has been removed from Undo/Redo history.
Viewport does not change when zooming.
Editing
Color of text could not be set from Preferences dialog.
Textboxes could not be recolored using the Format option.
Cleaning option were disabled when Templates were reopened.
Disabled wedge bond tools after turning to 2D mode from 3D.
Mouse mode>Reset View was not synchronized with Zoom panel.
Dragging a structure replaced the structure in the center of the canvas.
Molecule was not centralized when changing the size of the editor.
Display
Fog effect was not visible.
I/O
Rich text from .SKC files in the canvas could not be modified.
Changing the text color in an imported .cdx file did not work from the Format panel.
Image generation
Export of some molecules created invalid SVG images.
In some cases when a coordinate bond was drawn from a multicenter bond in a molecule the image generated was cut.
No changes.
No changes.
Editing
Editing
Insert character by typing it to the unicode table didn't work.
R-group attachment points were not painted in selected structures
Molconvert
Molconvert did not take into account the colored atoms/bond.
Image generation
An invalid XML character was inserted into the generated SVG.
Editing
New icons have been added to Mirror and Flip functions.
I/O
CDX/CDXML fragment object attributes are imported as molecule properties in MRV.
CDX/CDXML fragment IDs are imported as molecule properties in MRV.
Molecule properties are exported as CDX fragment object attributes.
Editing
Link to Chemicalize was broken.
Display
If imported MRV file contained atom and bond unique IDs, they were visible on the canvas.
I/O
Forced SMILES export for molecule fragments with attachment point fixed.
Scale factor was not saved when the user saved the content of the canvas to the clipboard in MRV format.
Editing
Atom number position has been revisited in case of structures having implicit hydrogens.
Editing
Overwriting an atom with the keyboard did not refreshed the analysis box.
Naming - Name to Structure
CAS Register Number® retrieval from publicly available sources hosted by the U.S. National Institutes of Health (NIH) and the Wikimedia Foundation. didn't work in Java versions lower than 8.
No changes.
No changes.
Editing
Merging two molecules on the canvas by dragging failed, however feedback indicated the merge.
Merge did not work after rotation.
Merge feedback indicated, but merge does not happen in case of chain tool.
Single bond turned into triple bond on a single click if previously a double bond has been drawn with the single bond tool.
Shift button did not expand the abbreviated group.
Editing
Some Linux environment the last file open location was not remembered.
No changes.
Editing
Marvin froze when one tried to aromatize a three-membered ring or imported this kind of structure.
Direct copy of EMF image in other applications resulted in poor quality picture.
Editing
Position of implicit hydrogens have been revisited.
Template icons has been improved.
API for image export parameters of Journal styles has been introduced.
Editing
Atom mapping visibility option was disabled.
Second arrow appeared when there is a reaction on the canvas, and the user deleted something then reverted the deleted item with UNDO.
Editing
Editing
"Place analysis box" option did not work if the whole canvas whole cleared before during the editing.
Copy/Paste
Only MRV and MDLSK formats were available on the clipboard after copying two fragments with two attachment points from Marvin Sketch.
OLE
I/O
When a picture of a reaction was exported via API from SMILES string, the plus signs were missing.
No changes.
MarvinSpace development is discontinued. MarvinSpace is not part of the Marvin suite and MarvinSketch installer anymore.
A separate installer can be downloaded from here.
Core
Editing
MolPrinter option for S-group attachment visibility has been implemented.
Atom map and atom number positioning has been revisited.
The highlight of valance error has been changed to a red patch.
Editing
Map numbers visibility was bad in exported png images for middle sized structures..
R/S label position did not take into account bold bond thickness.
Atom mapping numbers were positioned badly in some cases.
Aromatic rings could not be seen in selected structures.
I/O
Scale factor was not saved when the user saved the content of the canvas to the clipboard in MRV format.
No changes.
Editing
Editing
Distribute and/or Align messes up position of polymer brackets.
When a picture of a reaction is exported via Marvin API, the plus signs were missing.
Deleting an arrow from empty canvas threw a NPE.
Unmerge reactant/product deleting another component.
Text from Firefox, Google Chrome and some text editing application could not be pasted to text box in MarvinSketch.
No changes.
No changes.
Bugfixes
Editing
Selection has been revisited.
Clicking on the canvas with the Atom assigning tool during directed merge painted a reaction +.
Editing
The last used template was not preserved in template library.
Services
"Calculate automatically" was not fully synchronized with the modification of the canvas.
Editing
Plus sign was not added in reaction when creating two structures from one via bond deletion.
Problems with historization of reaction drawing were eliminated.
Auto + sign cold be be deleted using the Eraser tool.
Plus signs in a reaction remained after deleting the arrow in reactions.
" +" symbol were not drawn automatically when adding a diatomic molecule to a reaction.
I/O
R-group attachment points were not imported properly from MDL Molfile.
Editing
Duplicated graphical elements were drawn (rectangle, electronflow arrows) in reaction.
Plus signs did not appear between reactants (products) during SMILES import.
Plus sign were not deleted when two components got connected in reactions.
I/O
No changes.
Editing
Reaction arrows snap every7.5 degree.
Dragging and Pressing 'Shift' enables the free rotation of reaction arrows.
Editing
No electron flow arrow could not be drawn from a lone pair.
In some cases analysis box could be called for a selected part of a molecule.
Feedback of attachment points were painted too close to the atom label.
In some case Analysis box was not updated properly when the molecule had been graphically formatted.
Editing
Merging agents in reaction threw a NPE.
Analysis box was not updated properly if it had been replaced before the modification.
OSRA
OSRA import did not work for CopyPaste and DragN'Drop.
Import/export
2D Clean
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.
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.
Editing
Editing:
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.
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.
I O
Editing
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.
Editing
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.
Editig:
Editing
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.
Editing
In some cases the selection feedback was not colored for homology groups.
Selection of multiple S-groups sometimes caused exception.
Rendering
Atom labels became much smaller using MolPrinter.
Implicit hydrogen atoms were added to isotopic carbon atoms when the carbon visibility was switch off.
GUI
Editing
I/O
cxsmiles:u was not unique in case of coordinate bonds
Editing
Circles in aromatic compounds was too small when the bond length was relatively short.
I\O
Number of explicit hydrogens of metals is exported in MRV format.
Editing:
I/O
Editing
Editing
Text box is copied with all its formatting and not as simple text in MarvinSketch.
I\O
Charge position is considered when importing CDX files.
Bold double bond is imported and exported from/to CDX and CDXML files.
Export to SVG files has been revisited (Batik library has been updated).
Editing
Atom < Label Editor menu item did not work.
Aromatization was eliminated in rings containing three consecutive atoms adding two electrons to the aromatic system like O-P-O.
I/O
Bold bond width was not saved in MRV files.
I/O
Editing
Editing
Editing
I/O
Editing
IUPAC atom numbering was not shown.
Known issue:
I/O
Regression related to SMARTS export option was partly fixed.
Editing
Visibility option in the View<Advanced submenu for S-group attachment points has been added.
When carbon labels are not drawn in a structure a green patches are displayed if they are selected.
Clipboard
Coordinate bonds were replaced with solid bonds when copying as pdf from MarvinSketch to Pages in Macintosh computers.
Editing
Electron flow arrows could not be drawn.
Image export
PNG export with molSource failed when molSource contained non-latin-1 characters.
Applet
Base64 encoded strings as value of the mol parameter were handled as URL.
2D Cleaning
Editing
OLE
I/O
The import of Mol files containing sequences with ungrouped structures generated wrong molecules.
Editing
Charges of polymers were displayed both on the atom label and the bracket.
The atom list label was sometimes cut upon selection.
Changing bond type using the Bond< Type menu generated different structure than the Bond tool.
Image export
Circled charges were cut from images when no margin was set .
Installation
No structure
Editing
Editing
The result of Elemental Analysis remains formatted when it is copied to into a MS Office or in a MarvinSketch textbox.
Aromatic rings were lost when the document was printed into .pdf file.
Textbox
.NET
It was not possible to copy using Ctrl+K in binary file formats (ie: SKC, CDX) from Marvin .NET.
2DClean
Templates
'Conformers' template has been added to the default library.
'Organometallics' have been revised.
The former 'Amino acids' template has been renamed to 'Peptide building blocks' and 'Amino acids' containing the 22 proteinogenic amino acid has been added.
Abbreviated groups
Customization
Default selection tool can be set.
Editing
After deleting an alias or pseudo atoms the original atom (i.e, R,A ) are kept.
2D Cleaning
The Ctrl+2 cleaning did not centralize the molecule.
Customization
When a system level setting was overridden by a non default value, then the default value could not be reapplied.
Pop -up dialogues did not work on Mac.
Typing in the Insert Abbreviated Group window's textbox froze the application.
Editing
Journal styles
2D Cleaning
I/O
CXSMILES
R-atoms with alias strings are supported.
Charge painting
Charge painting has been revised.
Customization
New, general way to apply system level settings in MarvinSketch.
Painting
Red/blue pKa value painting did not work correctly.
Saving
Save/Load zoom factor in MRV format did not work
2D Cleaning
Wedged bonds were lost when reactions involving ionpairs were cleaned.
Import
Editing
S-group containing S-groups imported from a molfile was lost on selecting or clicking on the canvas.
Bounding rectangle was too big around certain S-groups.
Import
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.
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.
Journal styles
Editing
No changes.
Improvement
Editing
Document style handling has been improved and style properties files ha been changed.
Improvement
Improvement
Painting performance has been improved due to revised caching.
Bug
Memory limits (128MB) on Mac OSX could cause serious slowdown.
Editing
Aromatic rings within R-groups were drawn with aromatic bond.
API
Setting a rectangle with x and y coordinates other then zero lead to loss the upper and left part of the created image, when MolPrinter.paint(Graphics2D, Rectangle) method call was used.
Bug
Editing
On Turkish locale since 15.2.9 MarvinSketch and MarvinView was unable to start due to a Java character conversion issue in Java
When molecules were saved separetely and load them again bonds sets were lost.
I/O
Exported SVG files could not be read.
Export of Sgroup with attached data into v3000 molfile failed in some cases.
Improvement
Improvement
Editing
Position variation bond drawing from aromatic rings has been improved.
Naming
Display specific conversion error message.
Measurement unit : % of bond length has been added to the "Document style" dialog.
The end of a wedge bold has been changed to 1.5 times the bold bond width.
Bugfixes
Editing
2D clean of peptides in some cases resulted in temporary loss of bridges.
Peptide drawing: delete and re-draw a non-side connection in an amino acid having side-connection caused switch of the attachment points.
Graphical objects were lost during Paste when there was no chemical structure on the canvas.
Improvement
Editing
The alignment of isotopes and implicit H on the same atom has been improved.
Position variation bond drawing in symmetrical structures has been improved.
Coordinate bond drawing has been improved.
I\O
Inner reference ids are unified in individual SVG files. This prevents id collision when multiple SVG files are embedded into one HTML page.
"Document style" dialog is added to the File menu.
Circle Charge font type dialogue offers only the applicable font types.
Naming
IUPAC name for structures in reaction has been improved.
Bugfixes
Editing
Abbreviated group did not get ungrouped when an atom was overwritten.
Abbreviated group did not get ungrouped when a chirality center was changed.
Applet
Improvements
Editing
The alignment of isotopes and implicit H on the same atom has been improved.
I\O
Margins size parameter has been introduced.
Header of MDL Molfiles has been changed and now contains the version of the software generated it. The format is YYmDD where YY is the last two digits of the current year, m is the month in hexadecimal format (from 1 to c) and YY is the day of the month the software was released.
GUI options are saved in MRV file by default. (This can be switched off on the Load/Save Tab of the Preference dialog.)
Bugfixes
Editing
The reason of name generation failures was displayed on the canvas.
I/O
Improvement
Editing
Bold width parameter has been introduced.
Format dialog has been revised.
Wire thickness parameter on Preferences panel is displayed with 2 digit precision.
Bugfixes
Editing
2D clean of large molecules failed.
Selected Reacting Center properties became unrecognizable.
I/O
Valence property set on Sn, Tl and Te were lost in Molfile import-export.
Images with reaction arrow were exported incorrectly.
OLE
Improvement
Editing
Alignment of the double bonds can be changed. See documentation.
Customizable hash bond spacing has been introduced.
Stereo search desciptors are always displayed in black.
Bond spacing parameter is applied for triple bods as well.The "Double bond spacing" option in Preferences<Display has been renamed to "Bond spacing".
"Document Style" menu item has been renamed to "Format... " and moved to the Edit menu.
The measurement unit of bond thickness has been changed to pt.
"Circled charge label" has been renamed to "Charge label" and the setting is applied for all charge display options.
I/O
MOL file import:
Brackets of repeating unit are drawn even when the coordinates are not indicated in the MOL file.
Bugfixes
Editing
Abbreviated groups did not get expanded upon sprouting with Shift modifier key.
In several cases "value" overlapped with atom label.
Atom number, atom map, atom property, atom query property values are displayed in the same row separated by semicolon.
I/O
MOL file import:
2D clean of large MOL files ( i.e large peptides) failed with error.
Improvement
"Open Marvin Space" menu item was removed from the Edit menu.
Bugfix
Zooming did not work properly on MacPro.
Editing
Atom Labels having "^" characters at the last position threw exception.
Numbers in attached data were displayed as subscript.
I/O
MRV
Bugfix
Stereo calculation
Unnecessary E/Z stereo was calculated in rings.
Editing
Abbreviated groups did not get ungrouped when an extra bond was drawn from one of their attachment points.
Image export
Improvements
Editing
Bugfix
Editing
Improvements
Bugfixes
Naming
Bugfixes
Molecule representation
S-groups
Painting
Improvements
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).
Applet
Bugfixes
Painting
Editing
Improvements
Improvements
Pt has been introduced as measure unit for bond length and atom size.
Bond length can be set on Preferences dialog and in marvin.properties file. This property is kept during image export. Applet parameter: bondLength and image export parameter bondl are also introduced.
Valence check has been improved for negatively charged polyhalogen ions.
Bugfixes
Editing
Improvements
Bugfixes
Editing
It was not possible to draw a bond from an amino acid which is connected to a side chain of an other amino acid.
It was not possible to delete a structure with electron flow arrow using erase tool.
Export
| Improvements |
|---|
Import/Export
CDX import has been improved: special characters in textbox, empty S-groups, abbreviated group with left-name can be imported
.skc import has been improved: reactions (agents/arrows/mapping) can be imported
Bugfixes
Editing
The centre of the multi-center bond was not the geometric center of the atoms.
Numbers in visual feedback of data fields were displayed as subscript.
More icons of the General Toolbar could be enabled at the same time.
952
MarvinSketch GUI
Structure representation
MarvinSketch Menu
Molecule Representation
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
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
Applet
Painting
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.
MDL Molfile generated by Marvin JS could not be pasted into MarvinSketch.
2D clean of certain atropisomers resulted in chirality change.
Structure representation
M/P atropisomer stereodescriptors are assigned to biaryl compounds having at least 3 (2+1) ortho substituents.
Expanded amino acids got ungrouped when bond was drawn from one of their attachment point
Export
Hydrogen query properties of atoms within tetrahedral stereo configuration were not exported correctly to SMARTS.
Alias, pseudo and abbreviated group labels are centered.
The size of circled charge labels was not considered during image export.
Atom numbers and atom query properties are rendered outside ring in cyclic structures.
Edit < Preferences < OLE Server was removed.
Radical was displayed as electronpair after emf export.
InChi native libraries were not initialized on OSX systems since 14.7.21.
Aromatic "wedge down" bond can be drawn.
Bugfixes
Absolute label was partly missing from exported images.
Transparent png images were rendered with some artifact on java 7.
Image generation in applet did not work.
Copy as dialog always opened on the centre of the primary screen in a multi-display environment.
Joining points of graphical objects were considered even though one of them had been removed.
Bugfixes
Special query atoms M, MH, X, XH were given too much space during clean 2D.
New feature
Abbreviation groups have been revisited and formatted according to the IUPAC recommendation.
Bugfixes
H_hetero option in the Pdf export did not work.
Atom extra lables such as numbers, mapping, query properties etc. were displayed relatively far.
Bugfixes
Formatted text import was improved from SKC format.
Molecule properties with quotation marks and whitespaces were lost during export to Smiles/Smarts.
Chorene dioxide had false valence error.
New Features and Improvements
Class chemaxon.struc.Sgroup.MulticenterSgroup is now public.
Bugfixes
Applet parameter "extraBonds" disabled the chain tool if the "Any bond" parameter was not set.
Structure Representation
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
MarvinSketch GUI
Structure Representation
Image I/O
Editor
"Absolute" label disappeared when Data was attached.
Numbers in abbreviated groups were not displayed as subscripts.
MarvinView
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
Image I/O
Editing
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
Editing
Image I/O
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
Applet
MolConverter
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
OLE
Applet
Deprecated or Removed Methods in version 14.7.7.0
Import/Export
Image I/O
Import/Export
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
S-groups
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)
Painting
Clipboard handling
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
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
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)
Molecule Representation
Method chemaxon.struc.MolBond.equals()compares the bonds by reference and not by the end points.
Clean 2D
Applet
Licensing
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
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
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
Import/Export
MRV, CML
java.lang.ArrayIndexOutOfBoundsException when reading parallel bonds atoms. Now chemaxon.formats.MolFormatExceptionis thrown instead.SMILES, SMARTS
CXSMILES, CXSMARTS
InChi, InChiKey
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
Implicit/Explicit Hydrogen Conversion
Image I/O
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
Structure Checker
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.
No changes.
Bugfixes
Clipboard handling
Import/Export
Structure to Name (s2n)
StackOverflowError wrapped in an IOException.New features and improvements
Clipboard handling
Import/Export
PDB
Applet
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.
I mport/Export
MOL, SDF, RXN, RDF
SKC
CDX/CDXML
Calculations
MarvinSketch Applet
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
MarvinSpace GUI
Hydrogen visualization toolbar button added.
Display/drawing settings saved on exit.
Import/Export
SMILES/SMARTS
Sequences, FASTA
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
Stereochemistry
Elemental Analyzer
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
3D alignment
Conformers
Structure Checker
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
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
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
MarvinView GUI
Import/Export
MRV/CML
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
Stereochemistry
Aromatization
Clean 2D
Datatransfer
OLE
Applet
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
Bugfixes
Import/Export
Applet
Applet
MarvinSketch GUI
setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor.Import/Export
MarvinSketch Dialog
Structure Checker
Editing
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
Clean 2D
Cleaning of position variation bonds could create overlapping bonds.
Cleaning of bridged systems could result in overlapping atoms.
Calculations
Topology Analysis
logD
Structure Checker
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
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
Graphical object handling
MarvinView GUI
Import/Export
MRV/CML
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
CXSMILES/CXSMARTS
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)
Molecule Representation
New method, SelectionMolecule.addAtom(MolAtom, boolean), is introduced.
New methods, MolAtom.getBondArray() and Sgroup.getBondArray() are introduced.
Calculations
NMR (CNMR, HNMR Prediction...)
Geometry (Topology Analysis, Geometrical Descriptors, PSA, MSA)
Elemental Analyzer
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
MarvinSketch GUI
MarvinSketch Dialog
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
History functions
Graphical object handling
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
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
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
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 "β" or "α".
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
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
Protonation (pKa, Major Microspecies, Isoelectric Point)
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
Bugfixes
Applet
Bugfixes
MarvinView GUI
MarvinSpace
No changes.
No changes.
New features and improvements
Image I/O
Calculations
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
Clipboard handling
Graphical object handling
Import/Export
MRV/CML
InChi/InChiKey
Document to Structure
Molecule Representation
Implicit/Explicit Hydrogen Conversion
Clean 2D
Data Transfer
OLE
Applet
extraBonds did not work therefore the bond type menu appearance could not be changed.Image I/O
Calculations
Protonation (pKa, Major Microspecies, Isoelectric Point)
NMR (HNMR, CNMR Prediction, ...)
Services
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
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
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
MRV schema
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
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
SMILES/SMARTS
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
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 "-C1-6alkyl". 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)
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)
Chemical Terms
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
-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
MarvinSketch Applet
MarvinSketch Menu
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
MarvinSpace
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
Peptide
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[6.3.1.02,7]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
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
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)
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.AutoMapperRemoved 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
Import/Export
Import/Export
Name to Structure (n2s)
Calculations
Molecule Representation
Import/Export
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
Import/Export
MRV/CML
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
Molecule Representation
Valence check
Calculations
MarvinSketch GUI
MarvinSketch 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
Import/Export
SKC
CDX/CDXML
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[12.4.0.02,6.07,12]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., "lah") 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)
Molecule Representation
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
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, ...)
Services
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
MarvinSketch did not deal with java property initialization bug.
MarvinSketch GUI
MarvinSketch Dialog
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
Applet
Image I/O
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
CXSMILES/CXSMARTS
CDX/CDXML
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
Molecule Representation
S-groups
S-groups/R-groups
Clean 2D
Calculations
Protonation (pKa, Major Microspecies, Isoelectric Point)
Charge (Charge, Polarizability, ...)
NMR (HNMR, CNMR Prediction, ...)
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, ...)
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
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
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.
Datatransfer
Datatransfer
Painting
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)
Clean 2D
Calculations
Atom index issue might have occurred when molecule contained explicit hydrogen.
Protonation (pKa, Major Microspecies, Isoelectric Point)
cxcalc and "Isoelectric Point" calculation in MarvinSketch threw "ArrayIndexOutOfBoundsException" in the reported cases.NMR (HNMR, CNMR Prediction, ...)
MView applet
Image I/O
Java WebStart
Calculator Plugins
Image I/O
MarvinSketch GUI
MarvinSketch applet
Graphical object handling
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)
Painting
Image I/O
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
Molecule Representation
S-groups
java.lang.IllegalStateException is thrown.Valence Check
Stereochemistry
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, ...)
--pH command line option did not work in hydrogen bond acceptor-donor calculation.Structure Checker
Import/Export
Calculations
NMR (HNMR, CNMR Prediction, ...)
Chemical Terms
-g (ignore error) option of evaluate did not work when -x (extract) option was used.Structure Checker
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
CXNSharedAddin library has been introduced to handle tabular data transfer from/to Microsoft Office applications.Import/Export
CDX/CDXML
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
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
S-groups
Calculations
Charge (Charge, Polarizability, ...)
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
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
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
Dialogs
Import/Export
Load/Save handling in UI
MRV, CML
MOL, SDF, RXN, RDF
SMILES/SMARTS
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
Stereochemistry
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)
Structure Checker
Build/Installation
Import/Export
MarvinView Printing
Datatransfer
Import/Export
MOL, SDF, RXN, RDF
Name to Structure (n2S)
Clean 2D
MarvinView
Painting
Editing
Import/Export
Byte Order Mark (BOM) was not written out during the export.
Default line separator was not unique in MolExporter.
CDX/CDXML
Molecule Representation
S-groups
Stereochemistry
Calculations
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
Calculations
"Keep explicit hydrogens" option has been added to pKa plugin, Major Microspecies plugin, and Isoelectric Point plugin.
Protonation (pKa, Major Microspecies, Isoelectric Point)
NMR
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
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
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
R-groups
RgMolecule.fuse() resulted inconsistent molecule when it was invoked on RgMolecules having SuperAtom S-group in its definition.Stereochemistry
Aromatization/dearomatization
Calculations
Charge (Charge, Polarizability, Orbital Electronegativity)
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)
Structure Checker
MarvinSketch GUI
New graphical arrows: equilibrium arrow, curved arrow, dashed arrow, and crossed arrow has been introduced.
The built-in abbreviated groups can be easily extended and overridden with custom abbreviated group definitions.
New display option has been introduced: peptide sequence can be visualized in 1-letter form besides the original 3-letter form.
Cleaning preset is added to template sets. It can be controlled on the Template library dialog.
When opening an item of the Recent File list fails, the entry is deleted.
All query atoms and query properties are available from menu and toolbar by customization.
Names of homology groups on "Advanced" tab of "Periodic System Dialog" and in "Template Library" have been updated.
The elements of the Advanced tab on the Periodic System dialog are now available from MarvinSketch by typing as shortcuts.
The picture of custom defined template appears at the mouse tooltip when the name of the structure is unknown.
The name of reaction arrow: "Resonance" and graphical arrow "Two-Headed Arrow" have been changed.
MarvinSketch Printing
Import/Export
Load/Save handling in UI
Disconnected molecules can be saved separately in MarvinSketch.
When saving a document opened by d2s in MView, MRV is offered as default format.
Structure to Name (s2n)
Extended and updated structure to common name dictionary.
L-amino acid structures are all converted to L- traditional name.
Name to Structure (n2s)
Improved conversion of systematic names, notably names expressed as amides of acids, such as "pyridine-4-carboxylic acid (2-methoxy-ethyl)-methyl-amide".
Extended and updated common name to structure dictionary.
All peptide abbreviations are now consistently converted to the L- stereo form structure.
Possibility to set custom name converter plugins for n2s and d2s (e.g., converting internal company compound IDs) specific to a single conversion in a thread-safe way has been introduced (see API of the new method: chemaxon.naming.NameConverters.addThreadLocal).
Fragments names such as phenyl can be converted with attachment points *C1=CC=CC=C1 |$_AP1|, using the "name:+rgroups" format option.
Document to Structure (d2s)
Document to Structure can be instructed to process only a subset of pages in a document using the new startPage and endPage format options.
The custom dictionary format option (dict=...) is available in Document to Structure.
Possibility to set custom name converter plugins for n2s and d2s (e.g., converting internal company compound IDs) specific to a single conversion in a thread-safe way has been introduced (see API of the new method: chemaxon.naming.NameConverters.addThreadLocal).
Acronyms such as BBC are not converted anymore (as BromoBenzyl Cyanide) since they most often have a non-chemical meaning. Conversion of acronyms can be enabled if desired by using the "d2s:+acronyms" format option.
Fragments names such as phenyl are converted with attachment points, such as *C1=CC=CC=C1 |$_AP1|.
DNA/RNA
Molecule Representation
Molecule/atom/bond properties
Similarly to MolAtom, general properties are possible to be added to MolBond.
New, simple way is provided to replace isotopes.data and elements.zip used in PeriodicSystem.java.
S-groups
R-groups
Calculations
Isomers (tautomer., reson.)
Rational tautomer generation option has been introduced. Generation of All tautomers and Canonical tautomer can take this new option into consideration.
Improved generic tautomer generation in case of aromatic molecules.
NMR Predictor
Services
Structure Checker
New checker: Absent Chiral Flag checker; when the molecule is chiral and all stereo centers are precisely marked, absolute chiral flag can be applied to the molecule.
R-group Reference Error Checker is deprecated and has been split into three separate checkers:
Circular R-group Reference Checker;
Missing R-group Checker;
Unused R-group Checker.
Partial clean fixer is available for certain structure checkers: it can fix the erroneous part of the molecule exclusively.
Stereochemistry
API
MarvinSketch
When MarvinSketch was launched from command line with -h or --help option, the application was not terminated after printing of help message.
When using MarvinSketchPane from an application, and pop it up as a modal dialog, its children could disappear behind the main application (e.g., DialogLauncher example).
MarvinSketch GUI
Scaling bug occured on the button of the template toolbar if there was a contracted group displayed on the button.
"Calculations" menu did not appear in ISIS/Draw-like configuration.
MarvinView GUI
MarvinSpace
Applet
Although a valid URL was given in sketchHelp applet parameter, Marvin applet loaded the default help by selecting Help->Help Content instead of the given URL.
"My templates" became unavailable in applet after modifying it from template library.
Painting
Chemical Structure Painting
Datatransfer
Clipboard handling
Import/Export
MOL, SDF, RXN, RDF
The subscript information of the S-group generic bracket was not exported to MOL V3000 and V2000 formats.
Export of compressed MOL files allowed too large coordinate values, which caused distortion in the molecule after importing it.
After importing an RDfile that contains an empty S-group, its brackets didn't appear.
SDF
SMILES, SMARTS
CXSMILES, CXSMARTS
CXSMILES import added radicals to atoms that have coordinate bond to a central, metal atom.
I/O of atom alias "," was not working in CXSMILES format.
CML, MRV
Format mrv had missing closing tags at the end of the generic S-group lines.
MolExporter exported to MRV format using operating system specific line ending, '\n'.
CDX
Standalone list atoms and labels were read as text boxes from CDX files.
Component grouping was not recognized during CDX import.
SKC
CDX/SKC
Structure to Name (s2n)
There were extraneous numbers in generated names for structures containing atom values.
Generation of IUPAC names for large structures might have stopped before the timeout.
Name to Structure (n2s)
The n2s import option to specify the location of the custom dictionary was not thread-safe, and was not accessible in d2s.
Name to structure failed to return a result on some very long names (several hundreds of characters).
Document to Structure (d2s)
Non-chemical data in embedded structures, for instance text labels, were not extracted from embedded documents.
Some embedded structures were not extracted from office documents.
Reactions embedded in documents were not extracted.
Some uppercase strings were wrongly interpreted as smiles, for instance "BOUCHON".
When OSRA was called by Document to Structure, it could run even after Marvin is stopped (on Windows only).
OSRA was not working on PDFs containing monochrome images.
Molconvert
Molecule Representation
Valence Check
Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
False positive valence error was on aromatic rings which have sulfur ligand that is part of a ring.
Removing explicit hydrogen atoms from LiH, CaH2, SH4, PH5, PbH2, PbH4 did not keep the original hydrogen count.
Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
S-groups
Bracket positioning did not take the implicit hydrogen atoms into account.
If data were added as "relative", the cleaning or arrange methods did not take them along with the fragment/component/molecule.
The chirality of expanded S-group's atom changed, when there wasn't enough space in the canvas for the expanded S-group.
After expanding S-groups, atoms of the molecule could overlap.
Removal of explicit hydrogen being the only atom of an S-group was unsuccessful. New flag, SGROUP_H, has been introduced, for remove such hydrogens.
Exception was occurred when an abbreviated group was copied then pasted.
Method MulticenterTransform.transformMulticenters(Molecule mol)and MulticenterTransform.restoreMulticenters(Molecule mol)changed the number of implicit hydrogens of atoms.
R-groups
Clean 2D
Aromatization/dearomatization
int[] getSSSRBondSet(), was removed and, instead, BitSet getSSSRBondSet() was introduced.Calculations
Protonation (pKa, reson.)
Isomers (tautomer., reson.)
Tautomer generation was very slow on proteins.
Some deuterium atoms were removed during tautomer generation.
The structure of the generated tautomer was not cleaned if the input molecule contained abbreviated group(s).
Conformation
Structure Checker
Clean Wedge fixer of Wedge Error checker had no effect in case of wedge bond between two chiral centers.
Atoms and bonds inside S-groups were not handled correctly by certain checkers.
Elemental Analyzer
Calculations
Backend / Core
Import/Export
Structure Checker
Molecule representations
S-groups
Import/Export
Aromatization/dearomatization
Import/Export
CXSMILES import/export handles every special atom available in the Periodic System dialog window in MarvinSketch.
DNA/RNA sequences are imported in their acidic form (i.e., instead of negative charge, an implicit hydrogen is added to the phosphoric acid ester group).
Calculations
MarvinSketch GUI
Painting
Import/Export
CDX/CDXML
Coordinates of graphical objects were incorrectly imported from CDX files. Currently, imported "Anonymous Alternative Groups" are placed next to the imported molecule; "Anonymous Alternative Groups" with no bonds are imported as textboxes.
MRV attributes that contain line breaks were not exported correctly: \n , \r , \r\n were not escaped.
SKC
Atom and bond colors, font types, and bond thickness in SKC import and export were incorrect.
SKC import was failing on some structures containing built-in abbreviations.
PDB
VMN
Document to Structure (d2s)
Reactions embedded in documents were not extracted.
When OSRA was installed, a failure of OSRA prevented the rest of the document to be processed.
Peptide
DNA sequence import resulted in RNA sequence representation because of ambiguous one letter abbreviations. Currently, abbreviations dA, dC, dG, and dT are used to import DNA, while A, C, G, and U are used to import RNA sequences.
A peptide sequence containing custom amino acids was only imported when the custom amino acid was the last one in the sequence.
Aromatization/dearomatization
Calculations
Protonation (pKa, etc.)
Isomers (tautomer., reson.)
Wiggly bonds were changed to single bonds during standard canonical tautomer generation.
Resonance structure calculation of nitrogen containing molecules has been reconsidered: 10 valence electrons around a nitrogen are only allowed for nitro groups.
Backend / Core
MarvinSketch GUI
MarvinView GUI
Import/Export
CML, MRV
Name to Structure (n2s)
Conversion of systematic names has been increased by about 5%, and increased accuracy of the generated structures.
Prefix "nor" has been implemented (e.g., 17-Hydroxy-19-norpregn-4-ene).
Name with stereo-markers "r" or "s" where such stereoconfiguration cannot be present are now interpreted as "R" or "S". This allows names that have been completely lowercased to be converted correctly.
Document to Structure (d2s)
Document to Structure supports the following common office document formats: doc, docx, ppt, pptx, xls, xls, odt in addition to pdf, xml, html and txt.
Format options have been added to d2s, to specify what input formats should be converted (for CAS Registry Number®, SMILES and InChi). Format option "insideTag=<tag>" to restrict conversions to the content of a specific tag (for instance in HTML).
The type of source text used for the conversion is included in generated structures. Possibly values: systematic, generic, common (for names), smiles, InChI, CAS Registry Numbers® (for text formats), cdx, mrv, symyx (for embedded structures in office documents).
Processing speed has been increased: doubled on typical documents including chemical names, and tripled on documents with few chemical names.
Molecule Representation
Molecule/atom/bond properties
Valence Check
Calculations
Isomers (tautomer., reson.)
NMR Predictor Beta
cxcalc
Structure Checker
Chiral flag error checker options have been improved.
Custom fixers use annotations replacing property files. Backward compatibility is ensured for both custom checkers and fixers.
Pattern based report file generation is available as a new option in structurecheck commandline.
MarvinSpace
MarvinSketch GUI
Applet
Painting
The query properties were wrongly painted in some cases and covered the atom labels.
3D rotate action activated automatically when joining a structure in hand to a bond of a 2D structure on the canvas.
Double bond was not painted in centered position in case of terminal bonds when the label of the connected atom was displayed or both of the atom labels were displayed.
Single arrow type brackets were not painted.
The orientation of explicit hydrogens was incorrect when explicit hydrogens were added to the (selected) upper methylene C atom of a cyclohexane.
Import/Export
MOL, SDF, RXN, RDF
Handling of special characters (-, ", space) in extended MDL MOL format IO was wrong.
RDF file exported by Instant JChem was not imported correctly to ISIS/Base.
SMILES, SMARTS
CML, MRV
VMN
Image I/O
The molecule source was generated in unnecessary cases.
javax.imageio left temp files open if the ImageOutputStream was not closed properly.
Structure to Name (s2n)
The generated names for bridged and spiro ring systems were missing E/Z stereodescriptors for double bonds in large rings.
Some unconventional names were generated with suffixes such as amido, sulfonyl, carbonyl, ... mentioned as prefixes. For instance 2-[(2-chlorophenyl)amido]benzoate for [O-]C(=O)C1=C(NC(=O)C2=C(Cl)C=CC=C2)C=CC=C1. The generated names is now 2-(2-chlorobenzamido)benzoate.
Name to Structure (n2s)
Stereochemistry was not indicated in the displayed structure when cis or trans is used to specify the configuration of the two substituents of a ring system.
Cycloalkane substituents of fused ring systems were aromatized.
The stereochemistry of chiral atoms in subsitutents was sometimes inverted.
Name to Structure was blocked on some very long names with unbalanced parentheses.
Document to Structure (d2s)
Peptide
Molecule Representation
Molecule/atom/bond properties
ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
Molecule.implicitizeHydrogens() threw "java.lang.IndexOutOfBoundsException" after fragmentation if the molecule contained information in MDocument field.
Valence Check
Structure Checker
Structure Checker
Stereochemistry
Structure Checker
MarvinSketch GUI
Import/Export
Molconvert has a new option, :D, which is important if the molecule has parity information and has 0 dimension. By default during the export, a clean method is invoked on the structure and the generated coordinates and wedge information are exported into MRV format but NOT the parity information. However, using this option coordinates and wedge information are not generated but parity information is exported.
Mrv files can be validated by using the XSD schema containing the description of the mrv format.
Export options of cml and mrv formats can be used in molconverter application.
MarvinSketch GUI
Import/Export
MarvinSketch GUI
Dialogs
Import/Export
MOL, SDF, RXN, RDF
CML, MRV
Molecule Representation
Valence Check
The aromatic nitrogen handling in case of pyridine-oxide was incorrect.
In release 5.8, all amino acids of an amino acid chain were detected to have valence error if it was imported from the Edit > Source menu of MarvinSketch.
S-Groups
Data Transfer
OLE
Calculations
Structure Checker
MarvinSketch GUI
Group types on "group creation" dialog can be configured.
The icon of manual atom mapping has been changed.
A new radical electron setting and the corresponding toolbar icon group has been introduced, solely for educational purposes: Up to four radical electrons can be defined for an atom, and it is arranged evenly in the empty space around the atom label.
Recent file list length has been increased up to 50. (The default is 25.)
MarvinView GUI
Import/Export
Structure to Name (s2n)
Name to Structure (n2s)
n2s handles stereochemistry of cyclic monosaccharides.
Extended support for common names: n2s can convert 123 thousand common names – including synonyms – corresponding to 34 thousand structures instead of the previous 63 and 28 thousand, respectively.
Document to Structure (d2s)
MRV
The information on the selected atoms and bonds can be stored in MRV format.
MRV format has been changed: there is no indentation, there are line-breaks only after the header and after the documents. The original format (including line-breaks and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications.
SMARTS
CML
CML bondStereo implementation has been completed with atom references.
CML format has been changed: there is no indentation, there are line-breaks only after the molecules and after the header. The original format (including line-breaks and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications.
Calculator Plugins
New integrated component: NMR Predictor Beta has been implemented.
"Consider tautomerization" option has been renamed to "Consider tautomerization/resonance" in logP and logD calculator plugins.
"Tools" menu content has been moved to "Calculations" menu.
Data transfer
Native PDF format as the default image pasteboard format is used on MAC systems. It allows the user to copy a structure (which was originally created by either Marvin or ChemDraw) from a Microsoft Office 2011 document and to paste it to Marvin.
More verbose logging from OLE .NET panel (catching managed bridge exceptions via COM) has been introduced.
MarvinView
Sometimes molecules were lost when switching from "Spreadsheet mode" (Table>Options>Table Type) to "Molecule matrix" mode.
When a zero length structure file was opened, the content of the previous file remained in the viewer until the first repainting.
Scrolling up and down increased the number of molecules and changed their orders.
Painting
Import/Export
Structure to Name (s2n)
Incorrect name was generated for chiral allenes, for instance: (2M)-1,3-dichloropropa-1,2-diene, the correct is 1M. (The locant was previously in the middle of the cumulated double bond system, but is now at the beginning of it, as prescribed by IUPAC.)
Fixed generation of names in the case where a radical marker "yl" was missing, for instance "...(4-methylbenzene)sulfonyl..." instead of the correct form "...(4-methylphenyl)sulfonyl..."
Name generation was sometimes failing on fused ring systems with a spiro connections or adjacent fusion bonds. Conversion rate of fused ring systems goes up from 99.83% to 99.95% on the NCI database set.
The numbering of fused ring systems was incorrect in about 1% of the cases both in s2n and n2s.
Name to Structure (n2s)
Automatic name format recognition failed for names containing unicode prime characters.
CAS Registrx Number® cache could get corrupted and created failures.
Document to Structure (d2s)
SMILES
CXSMILES IO error due to non-escaped characters appeared.
The name imported from SMILES format was wrong in rare cases, when special characters (e.g., |) were in the fields part of the extended SMILES.
Calculator Plugins
Molecule Painting
Calculator Plugins
Build/Installation
MarvinSketch GUI
New bond type: "Hashed bond" has been introduced.
"Coordinate" Bond Line Style – in the Edit>Preferences>Bonds menu – allows changing the type of coordinate bonds between the default ones (arrow for single atom and hashed for multicenter) and solid.
Selected structures can be aligned or distributed relative to each other horizontally or vertically. The Align&Distribute function aligns and distribute the objects at the same time.
New chain drawing tool: Curved chain tool. Instead of creating a straight chain it modifies the direction of the last bond of the chain based on the mouse movement. Curved chains or macrocycles can be created that way.
The chain drawing direction is mirrored based on the direction of the mouse movements.
Selection can be moved in greater units with SHIFT + arrow keys.
Import/Export
Structure to Name
Name to Structure
"Name to structure" converter supports more systematic names (6% to 50% measured on various sets of names extracted from patents). For instance, names representing esterification with locants (e.g., 1,4-di-tert-butyl piperazine-1,4-dicarboxylate).
Optional support for CAS Registry Numbers® in Document2Structure.
Faster loading of PDFs by Document to Structure (from 25% to 75% speedup in most cases). Names can be extracted from more types of PDFs.
CDX/CDXML
Clean 3D/optimization
Data transfer
Native pasteboard for Macintosh has been implemented. It solves general copy/paste issues, e.g., copy/paste between Marvin and other chemical sketcher programs (e.g., ChemDraw).
Marvin supports conversion of other Vendors (currently ISIS and Symys) embedded OLE objects to Marvin OLE.
Structure Checker
New checkers are available:
R-atom Checker: detects R-atoms (all, disconnected, generic, linker, nested).
R-group Attachment Error Checker: detects attachment differences between R-atoms and R-group members. A new fixer corrects the attachment bond types and adds missing attachments in unambiguous cases.
R-group Reference Error Checker: detects missing R-atoms, missing R-groups, self or circular references of nested R-atoms.
Checker and fixer classes implemented by the user are loaded from given jar file.
API
MarvinSketch
MarvinSketch GUI
Scrolling with mousewheel or arrow keys enlarged Marvin Sketch canvas.
Moving selection with arrow keys could not be undone.
Attachment points were not highlighted by green when they were selected.
Sugar templates: D-furanoses had S label on carbon 5.
Double click selection did not work when it pointed to an atom.
MarvinView
MarvinView printing
Painting
Molecule Painting
Import/Export
Structure to Name
Inchi Key
SMILES/SMARTS
A molfile or sketch is carrying an 'rb*' flag on any atom(s) was translated incorrectly to SMARTS ('x' atomic primitive).
cxsmiles IO of Data sgroup was incorrect.
mol format from smarts which contained "[C,!N]" (representing "Carbon , not Nitrogen") was converted incorrectly.
Molecule representation
Stereochemistry
Aromatization/dearomatization
Elemental analysis
Import/Export
Import/Export
Import/Export
MarvinSketch GUI
New mouse cursors have been introduced.
New structure templates have been added (Alpha D sugars, Beta D sugars, Deoxynucleosides, Flavonoids, Nucleobases, Nucleosides, Protoalkaloids, True Alkaloids, Vitamins, Functional Groups).
MarvinView GUI
Applet
New parameters have been introduced:
onError
alertError
Import/Export
Str2Name
New option has been added to generate all common names for a structure, e.g.: molconvert "name:common,all" -s viagra.
Less brackets are generated in names in traditional mode. For instance, instead of "{1-[(tert-butoxy)carbonyl]-1H-indol-2-yl}boronic acid" the generated traditional name is now "1-(tert-butoxycarbonyl)indol-2-ylboronic acid".
Name2Str
MolImporter can now process a PDF file as input and convert the chemical names in the text into structures. Structure images are also converted if OSRA is installed on the computer.
Increased support for name to structure conversion (measured between 6% and 30% on certain datasets).
Calculator Plugins
"Marvin Services" has been introduced: Web/local services client, which provides seamless integration of third-party calculations into Marvin Sketch, cxcalc, and via Chemical Terms into Instant JChem or JChem for Excel. Industrial standard solutions like SOAP with WSDL are supported, along with the more lightweight XML-RPC or JSON-RPC protocols. Java based calculations can be called without server, directly from the jar file.
A new type of fragmentation has been implemented where the fragments contained in the same S-group are not separated. Fragmentation methods now have fragmentation type as parameter. The three types of fragmentation are:
Basic: no S-groups are considered, fragments are separated even if they are in one S-group. Broken S-groups are not added to the fragments.
Keeping multicenters: multicenter S-groups are kept in one fragment, other types of S-groups that contain more than one fragment are not added to the fragments, those fragments are separated.
Keeping S-groups: all S-groups are kept, fragments in the same S-group are not separated.
Previous fragmenting methods which did not indicate the type of fragmentation are deprecated; they do the same as before (keep multicenters), but now – correctly – without generating inconsistent molecules with broken S-groups. These methods will be removed in later releases.
Markush enumeration
Structure Checker
New checkers are available:
Unbalanced Reaction Checker: reports if there is difference in the total number of atoms or atom types on the two sides of the reaction arrow.
Atom Query Property Checker: detects atoms having query properties. A new fixer can remove the identified query properties.
New feature: "3D checker" detected issues can be fixed by "Remove Z-Coordinate Fixer". It flattens molecules by setting the z-coordinates of atoms to zero.
Structure Checker command line application has greatly improved.
Improvements in substructure checker: multifragment molecule handling, implicit hydrogen handling, improved command line access. "Transform" fixer for substructure errors: modifies substructures.
API
MarvinSketch GUI
MarvinView GUI
MarvinView printing
When multiple structures were printed in PDF with molecule matrix rendering, structures with crossing bonds in the second or further cells were just partially drawn.
Applet
Marvin Applet failed to load changes in a file if the same file url was loaded before and applet started from the legacy cache.
Legacy_lfecycle related initialization (parameter loading, event listening, etc.) was fixed in applets.
Molecule Painting
The shadow painting of the sprout drawing feature removed the error highlight of Structure Checker.
Atom label was shifted in case of terminal double/aromatic bonds at the end of chains. Double bond was not painted in the centered position when there were no substituents on either sides.
Import/Export
MOL and SDF files including pipe character in the first line were recognized as Chemaxon Extended SMILES.
MOLFiles including a caret symbol in the Alias or Sgroup label fields were displayed incorrectly (the caret symbol was not hidden).
MOL/SDF files starting with "BM" characters in the first line were recognized as BMP file.
SMILES/SMARTS
Data transfer
Copy/paste of Marvin OLE objects from MSOffice applications back to Marvin did not work.
OLE image was not updated consistently after editing structure in MsOffice applications on 64 bit environment.
2D clean
Aromatization/dearomatization
Calculator Plugin
logP calculation threw ArrayIndexOutOfBoundsException in some cases.
There were incorrect systematic names generated in case of sulfur-based groups with non-standard valence (for instance dihydroxy-lambda6-sulfanone).
FindAllRings failed with OutOfMemory error.
Structure Checker
StructureCheck command line application did not generate report field in output if checker options are set (e.g. "explicith:isotopic=true").
Build/Installation
Marvin Beans installer could not start with 64bit Java 1.6 under OS X 10.5.
Import/Export
molconvert: The -T option works with pipes using the fields of the first molecule.
Name to structure: Document to Structure also extracts smiles and InChI from the text.
CML: CML files now passes the validator at http://validator.xml-cml.org.
MarvinSketch
Chemical structure painting
Bond coloring was wrong in 2D if the colors of the neighboring atoms were different.
Quick rotation of the 3D view of 2D structures sometimes resulted in the disappearance of the structure.
The Java beans and applet parameters for switching the valence property visibility OFF was missing.
Import/Export
MOL/SDF: The coordinate bonds in R-group definitions were wrongly exported.
Name to structure: Traditional naming export failed in applet.
Name to structure: Document to Structure failed to extract names from PDF documents .
Calculator Plugins
Calculator Plugins
Structure Checker
Marvin Sketch
Bold Tool is intended to be used for graphical presentations of molecules. Activate the tool, click on a bond and it will be changed to bold. Bold Tool is located in the Bond Menu, Tools toolbar, and bond PopUp menu by default.
The explicit valence setting display (v#) can be switched off.
Ctrl + Mouse Wheel zooms in and out on the canvas, while the geometric center of the zoom is defined by the current position of the mouse pointer.
To scroll the canvas you can use the mouse wheel or the arrow keys on the keyboard.
If there is a selection on the canvas, you can either move the selected object using the arrow keys or move the canvas with Ctrl + Arrow Keys.
MarvinSketch canvas is centered to the scaffold after opening R-Group molecules.
Atom List and Atom Not List can be entered by simple typing (without opening the Periodic Table).
Symbols can be inserted into textboxes. An Insert Symbol dialog with recent symbol list is accessible from the Textbox toolbar.
Error messages, warnings, warning details, and error stack trace can be copied to the clipboard.
Version and Copyright info can be found in Marvin splash screen.
Marvin View
Printing the molecule matrix view of a multirecord file containing data fields has been improved:
Instead of cropping the content of the data fields when the cell is too narrow, they are wrapped into multi-line texts automatically.
A minimal size is provided for the molecule structure, so it is visible even if the data fields want to occupy more space than the cell size.
The explicit valence setting display (v#) can be switched off.
Molecule matrix view is scrollable with mouse wheel.
R-groups are visible in MarvinView by default.
Marvin Space
Compatibility
Data Transfer
Chemical structure painting
Drawing 2D projected views of 3D aromatic rings.
Aromatic rings have ellipses in 3D view as well.
Bold bonds and Aromatic Up bonds can be displayed.
The display quality of the junctions of Bold and Up bonds with other bonds has been improved.
The electron flow arrow display has been improved: Radicals, lone pairs, and negative charges are considered now. If the source is an atom, the electron flow automatically starts from the lone pair, the radical or the charge when they are displayed.
The automatic attachment point placement in R-group lists has been improved.
Electron flow arrow
Import/Export
Image Export:
JPG, SVG and PNG formats contain the molecule source, so when opening or pasting these images, the molecule source is used (instead of trying to convert the image using OSRA).
PNG image color-depth can be specified as bitrate: 1-, 2-, 4-, 8-, 24- and 32-bit PNG image can be created.
Syn/Anti and Endo/Exo stereoisomer information is exported into ChemAxonExtended SMILES and SMARTS format.
Data fields are exported into SMILES format.
Improved SMART representation of generic query atoms (Q, QH, X, XH, etc.).
IUPAC Name
Major rewrite of the name to structure converter. Higher precision (around 50% improvement) and support for additional names.
Import of sulfide has been improved in Name To Structure.
Dictionary format improvement in IUPAC naming.
Name To Structure supports Alpha and Beta sign in names.
Automatic format recognition for CAS Registry Numbers®.
IUPAC InChI
Inchi converter now uses the IUPAC software API via the jni-inchi instead of the executable. Now it can handle stereochemistry information in 0D.
Marvin now uses inchi 1.03.
The conversion is much faster now.
InChI export does not clean in 0d any more.
2D clean / aromatization
Keep stereo information at aromatization.
Query aromatization considers single/aromatic and double/aromatic.
Converting to aromatic form keeps the Bold property of the bond.
Stereochemistry
Syn/Anti and Endo/Exo stereoisomers are recognized.
Proper chirality detection in case of topographical differences.
Define chirality for adamantane structures.
New standardizer action: add implicit parities of bridged systems.
NEMA features: atrop isomers, allenes.
Structure Checker
New Checkers:
SubstructureChecker detects user defined substructures (requires JChem);
RacemateChecker detects tetrahedral stereo centers without specific stereochemistry defined.
Improvements:
Tooltip improvements.
Checker status bar indicator can display warning and error icon as well.
Rename of specific checkers is supported (affects SubstructureChecker).
Calculator Plugins
Molecular volume calculator plugin has been introduced.
Generic tautomer generation ignores all options except "Protect all tetrahedral stereo centers".
Preserve exocyclic groups in BMF.
Chemical Terms
Improving initialization speed of Chemical Terms Editor.
Enhanced integration of BMF in Chemical Terms.
New Chemical Terms function: markushLibrarySize(), markushLibrarySizeAsString(), markushLibraryMagnitude(), matchFirst(), booleanToNumber().
Automapping
API
Marvin Sketch
A bond to the second attachment point of an Sgroup could not be drawn if it was created by changing a terminal atom of a previously drawn structure.
The BzOM group has to be renamed to PhOMe, and its left name should be MeOPh.
Selecting every atom and using the "Ungroup" function from the menu caused ArrayInedOutOfBoundsException.
Edit source dialog could not be opened after importing SKC.
After setting of "Save/Load-default location - Startup directory" in Preferences dialog, Marvin did not navigate to the Startup directory by saving or loading a molecule.
The canvas was not scrollable with mouse wheel.
When Ala was ungrouped in the R1 definition, the attachment point (which was both an Sgroup and an Rgroup attachment) disappeared.
When a reagent was placed over the reaction arrow in abbreviated form, Marvin Sketch became unresponsive.
When drawing electron flows to multicenter, Marvin stopped doing anything.
Electron flows could cross double and triple bonds when starting from bond.
The exception frame was not scrollable when the message was too long.
Atoms from periodic table modified bond length when the atom in hand was attached to the end of a bond on the canvas.
The aromatization/dearomatization did not run during Directed Merge, therefore if the double bonds were not located at the appropriate positions in case of two aromatizable rings, 5-valence carbon atoms were created.
Marvin View
Scrolling and cleaning 2D in the same time caused CuncurrentModificationException.
After clean 2D, Marvin View cells in molecule matrix view were not repainted automatically. You had to click on each cell to refresh them.
OLE support
Molecule representation
QueryBond cloning did not preserve bond type.
Exception related to expanding Sgroups in RgMolecules
SuperatomSgroup.attachAtoms was not set automatically during SuperatomSgroup creation.
Chemical Structure Painting
3D rotation of fragments started to wrong direction.
Valence count displayed ugly: on the top of the atom label.
The COCl group was not connected through the Carbon label when it was on the left side of a structure.
Import/Export
Smiles did not set arrow for reaction because of it RXNMolecule threw NullPointerException.
Molecule.toFormat("smarts") changed the state of Molecule: getAtomCount(), getBondCount() and the unifiedStructure properties of query were null value.
Certain MRV files could not be imported where tag included a line break.
R-group queries could not be exported to SMARTS as recursive SMARTS in 5.4.x.
ArrayIndexOutOfBoundsException was written on System.out by parsing SMILES.
IUPAC Name
By parsing 2-(o-Toluidino)ethanol IUPAC name, the 'o' was ignored.
IUPAC name import did not support correctly poly spiro in the simple case (numbers, not structures).
Those IUPAC name could not be parsed from HTML where an preceded the name.
By importing certain IUPAC names, the stereo center missed on the created molecule.
All IUPAC names with "hydrazon" were wrongly imported.
dicarbonimidic diamide and imidodicarbonimidic diamide were not supported.
Generate correct name for hydrides of elements in group 1 to 12, for instance "sodium hydride".
IUPAC InChi
There was a memory leak in the native call, now in the jni-inchi interface it is resolved.
InChI failed to export stereochemistry on 0D molecules.
Certain CDX files that included graphical arrows and dashed rectangles could not import properly.
2D cleaning / Aromatization
General aromatization put single-or-aromatic and double-or-aromatic bonds when it shouldn't.
Molecule.partialClean(int, int[], String) removed stereo info from molecule when the input was in mrv format.
At first attempt, the aromatization did not work after creating a ring with bold double bonds in it.
The 2D clean of a molecule with position variation bond caused an error dialog: "Error in module Clean2D".
Five membered rings were not converted to aromatic form with single_or_aromatic and double_or_aromatic bonds respectively.
StereoChemistry
Superfluous wedges appeared by importing of certain SMILES.
The Phosphorus in phosphines was not recognized as stereo center.
3D alignment
Calculator Plugins
Elemental Analyser result window did not display text fields in single fragment mode.
In Naming Plugin result window, the IUPAC name disappeared after scroll down and scroll up by those compounds whose name included special characters (like lambda).
Chemical Terms
API
Molecule.getBondTable() threw exception when a bond with atom index higher than atom count was get.
MoleculeGraph.getFormula getMass and getExactMass were not thread-safe.
When a new bond with a new end-atom was added to a SelectionMolecule, it was not cloned properly.
Serialization threw an EOFException when it was used from MolImporter/MolExporter.
Marvin Sketch
MarvinSketch
New features and improvements
MarvinSketch
Public database search in chemicalize.com.
Possibility to change ligand order in MarvinSketch.
Molecule Painting
Fog-effect can be controlled in various ways:
There is a slider on the Display tab of the Preferences dialog in the Sketch/View GUI to set the strength of the fog-effect and a checkbox to switch off the automatic fog-effect.
Applet and beans parameters are introduced: fogFactor, automaticFogEnabled.
Molecule Representation
Attaching to a group attachment point does not automatically ungroup the Sgroup anymore.
Determination of S-group content: multiple and generic S-groups have to contain the whole subgraph between the bonds crossing the brackets.
Update of S-group content if bracket positions change: either brackets or the structure is moved.
S-group embedding and overlap are checked at molecule consistency checks.
Import/Export
SMARTS import supports aliphatic carbons with double bond.
SMILES import/export supports allenes.
IUPAC name
Generate traditional name for fragments inside a larger compound (e.g. "dextromethorphan hydrobromide").
Support for retrieval of CAS Registry Numbers® from publicly available sources hosted by the U.S. National Institutes of Health (“NIH”) and the Wikimedia Foundation.
Improved OCR error correction in DocumentExtractor (missing commas, misrecognized parenthesis type, extra spaces, ...).
Document Extractor on PDF documents now gives the page number of hits.
Improved support for common names in structure-to-name and name-to-structure. The general support for name import increased by around 5% for common and 10% for systematic names. Conversion speed is increased by about 20%.
Installers
Calculator Plugins
Markush Enumeration
Halogen can have more than one connection during enumeration.
Aromatic bonds are considered during calculating the number of double bonds for homology property checking.
API
MarvinSketch
Name box was not updated after group creation because creating a group did not increase graph invariant change count.
MarvinSketch application did not understand "-{name}" command line parameter.
When the Structure > Find structure online menu was invoked under Linux, the default browser could not be detected to display result.
Applet
Molecule Painting
Graphical objects were not displayed in the Geometry Plugin result window.
On the electron-flow arrow, the blue box for highlighting was missed.
Ligand order was not displayed on the scaffold if the definitions were deleted, even if the "Always" display option was set for "Ligand Orders" on the preferences dialog.
Import/Export
Index of the multicenter atom became corrupt after exporting into MDL Mol format if it was connected to an R-group.
Arrow stuck to rectangles was damaged during Mrv import/export.
Import of 1-letter peptide failed at a single Histidine.
Implicit hydrogens were missing by importing from skc.
Null property value of MolAtom was not exported/imported in Mrv format.
By importing certain SMARTS, wrong bond type was determined instead of single or aromatic bond.
Certain brackets imported from Cdx files drawn in ChemDraw were displayed in the wrong direction.
SMARTS export: 1-atom single bond neighbor of an aromatic ring was exported as single bond instead of single/aromatic .
Exporting queries with link node and R-groups in SMARTS format were incorrect.
The H atom handling was ambiguous in SMARTS expressions.
Mol file comment field import failed.
Importing of certain SMILES was wrong.
Clean 2D
Molecule Representation
The Fine with Hydrogenize option of Clean3D did not ungroup S-groups automatically.
Molecule.contractSgroups() messed up the molecule coordinates.
Stereochemistry
Calculator Plugins
Markush Enumeration
Structure Checker
Incorrect charge count after applying CovalentCounterion fixer.
The log output format of StructureChecker command line differed from output format of the wizard.
ChiralFlagErrorChecker did not handle chirality correctly. Instead of calculating chirality from parity data, it used an implementation based on the isChiral method of TopologyAnalyser.
MarvinSketch
Applet
Import/Export
MDL MOL and SDF
SKC
CDX
Calculator Plugins
Tautomer calculation
Generic tautomer was not unique enough in some cases. Due to the fix, the generic tautomer is provided aromatic form.
Canoncical tautomer calculation has been improved due to the fix of dearomatization.
cxcalc
Certain structures with explicit hydrogens connected with wedge bond gave an exception during generic tautomerization.
Volume calculation was missing from cxcalc.
Structure Checker
API
MarvinSketch GUI
Multiple, ordered R-group attachment points in Markush structures. It is possible to define bond types on the ligands, and change the order of the attachment points as well.
PubChem substructure search from Marvin.
New 3D transformation options: rotate around various axes, group rotation, horizontal/vertical/group Flip, horizontal/vertical/canvas/group Mirror, and Inversion.
3D Plane option: upon three selected atoms it rotates the structure to have the selected atoms in the drawing plane.
Directed Merge option: It merges a fragment (Substituent) to another (Template or Scaffold) based on atom pairs assigned by the Atom Assigner tool.
New Substituent option: Opens a separate MarvinSketch window to sketch a new fragment, and transfers it back to the main window.
Context based, configurable attached data editing
Delete actions have been uniformized, and the Delete tool work differently on terminal atoms when holding the Alt key. The default behavior of delete can be configured on the Preferences dialog.
Atom editing procedures have been improved, so the "feature" that automatically deleted a bond when an atom was dragged over it has been removed.
Applet
New parameters have been introduced:
disablePluginsLookup
defaultDatatransferPolicy
isMyTemplatesEnabled
Molecule Painting
Aromatic and double bond display improvements: now it follows the IUPAC recommendation in each case.
Ellipses are drawn in asymmetric aromatic rings in 2D.
The R-group attachment point display has been changed to follow the IUPAC recommendation. The order of the attachment points is visualized both at the Scaffold and the substituents.
R-logic can optionally be displayed on the sketch.
The degree of rotation is displayed during rotations having specified axis.
Molecule Representation
S-groups are validated at creation based on the selected (sub)structure: only the chemically meaningful types can be created.The option can be switched off on the Preferences dialog.
R-group attachment point representation has been redesigned.
Import/Export
IUPAC Naming
Major upgrade of Name To Structure. Reduces wrong conversions by 50% to 70%, and supports about 10% more names.
Significant speedup (around 100%) in structure to name generation.
Local relative stereo (R and S) is supported in name to structure.
Pseudo-asymmetric stereo descriptors (r) and (s) are generated.
The generated names for salts have been improved.
Name generation detects new cases of very complex structures and aborts quickly instead of timing out or locking. All known cases are handled well now.
MRV
MOL/SDF
The S-group and the R-group storage has been separated: the APO tag stores only the R-group attachment points, and the SAP tag is used for storing the S-group attachment points. The new storage format is not imported properly by older versions of Marvin.
A new option, called "skipAtomValues" has been introduced in MolImporter and molconvert to avoid importing lines containing atom values.
SDFiles (incorrectly) having an empty line between the CTAB block and the properties block are accepted at import.
SMILES/SMARTS
CDX/CDXML
Datatransfer
Configurable clipboard handling in applets: the file formats available for copy and paste can be customized.
Marvin OLE object: 64-bit support for windows natives (OLE, EMF generator).
Traditional name has been added to the Copy as dialog formats.
Stereochemistry
Graph invariant calculation uses local parity instead of local chirality.
Improved stereochemistry (r, s, M, P descriptors).
Aromatization
New aromatization option for ambiguous 5-membered rings.
Query aromatization changes single bonds to single_or_aromatic, double bonds to double_or_aromatic in a ring which contains _or_aromatic bond.
Calculator Plugins
logP and logD plugins support multiple logP training parameter files.
pKa and logD plugins support multiple pKa correction library files.
Fused output option on Markush enumerator GUI
Industry standard MMFF94 forcefield options in Conformer Generator and 3D Molecular Properties.
Atrop isomers are detected during conformer generation.
Canonic tauotomer generation was improved.
Performance and accuracy improvements of 3D molecular alignment.
Structure Checker functions in Chemical Terms.
Chemical Terms uses a new file format for storing predefined molecules. The new format contains also the R-group representation of the molecules, which can be used for visualization.
Training and Prediction
A new plugin called Predictor enables to train and run the users' own molecular property prediction.
A command line trainer tool has been introduced, called cxtrain.
LogP and General (Atomic Contribution Based) Training and Prediction has been refactored (performance improvement and structural changes).
Structure Checker
New checkers are available:
Empty Structure Checker
Explicit Lone Pair Checker
Star Atom Checker
Metallocene Checker
Covalent Counterion Checker
OCR Error Checker
Ring Strain Error Checker
A command line tool called structurecheck is available for checking files in batch mode.
Application based structure checker configuration support has been added to the API. It is also available in the applications that are integrating Structure Checker.
Several improvements have been made in the Overlapping Atoms and the Overlapping Bonds checkers: The accuracy of the overlap detection has been improved to avoid fault warnings.
Licenses
Installer
MarvinSketch GUI
Delete action sometimes had undesired effect from atom context menu.
On Mac OS X, Drag and Drop of names to the canvas did not work.
Marvin Space GUI
The screen flickered and an empty canvas was displayed sometimes.
There was a frame closing problem when MarvinSpace was launched for MarvinSketch.
The pull-down menus were not displayed properly.
Applet
Molecule Painting
Charges disappeared on carbon atoms if carbon labels were hidden and lone pair painting was turned off.
Certain MEflow object disappeared when display properties were changed.
The second data attached to the same selection using absolute placement overlapped with the first one.
Molecule Representation
RgMolecule.addRgroup(int rl, Molecule m) did not change the grinvCC, therefore the graph union was not updated and had not contained the newly added Rgroup.
The bond table representation of the MoleculeGraph has been changed to avoid OutOfMemoryError.
There were a few S-groups related bugs: in creating a reaction from a molecule with S-groups, in creating S-groups in reactions, and in merge/unmerge of reaction components containing S-groups.
When deleting multiple groups, n-1 occurrences of its content remained.
Import/Export
0D molfiles can not contain stereo information, therefore Marvin applications apply a 2D clean to 0D molfiles in the future.
SMILES/SMARTS
Certain SMARTS was imported wrongly.
Explicit bond appeared where it was not needed in SMARTS.
Datatransfer
Stereochemistry
If only one explicit Hydrogen is attached to one side of the double bond, then it incorrectly got E/Z stereo information.
The calculation of chirality/parity for phosphanes was incorrect in some cases.
Remove explicit hydrogen removing some stereochemistry.
Clean 2D
Calculator Plugins
MarvinSketch
Lone pair placement wrong in some case.
Simple arrows could not be deleted at enpoints.
Import/Export
Applet
Molecule representation
Painting
When a reactant contained Sgroup, reaction arrow was not drawn.
If an Sgroup was a single reactant in a reaction, it could not be ungrouped.
Data transfer
Clipboard operation hanged with an error in ExecutorService if legacy_lifecycle was off and two applets were started in the same JVM.
OLE copy fail-over mechanism did not work.
Calculator Plugins
Molecule representation
Calculator Plugins
Import/Export
IUPAC Name
Name generation has been improved and handles more traditional names.
Shorter names are generated in more cases, for instance "pentamethylhydrazinium" instead of "1,1,1,2,2-pentamethylhydrazinium".
Name generation for large structures succeeds with a systematic, Von Baeyer name instead of failing with a timeout.
MarvinSketch
MarvinSpace
MSpace did not start on various platforms or OS versions: the installation of native OpenGL libraries failed in some cases.
MSpace menus were displayed behind the canvas.
Editing
When trying to open the Format dialog from contextual menu over the corner point of a bracket, the Format dialog was empty.
Uniformization and bug fixes in delete actions.
Painting
Import/Export
MDL MOL import of incorrect bracket information caused AIOB.
InChI failed to export stereochemistry on 0D molecules.
InChI export silently ignored unknown options.
SRU was read as repeating group with repetition ranges.
ReaxysGenerics were not imported from Extended MOLFile.
In IUPAC Name export, generation of E/Z stereo descriptors was missed in certain cases.
Molecule representation
The implicit H was not correct after importing cxSmarts string with radical information.
Changing group type to MultipleSgroup produced inconsistent molecule.
Changeing a type of a non-expandable s-group to SRU didn't change bracket type from double to single.
MarvinSketch had a problem with valence calculation after removing explicit hydrogens.
Rubber tool was not working for attached data.
On terminal groups the Repeating unit with repetition ranges group type had only a single bracket.
MarvinSketch GUI
Setting "Automatic Lone Pair Calculation" off does not work after restarting MarvinSketch.
The Save as image menu action did not update the save directory.
Applet
Marvin Applets could not load-in resources from out of jars.
Improve Java Plugin detecting mechanism in marvin.js to print warning when required Java is missing.
Import/Export
IUPAC Name2Structure
Marvin OLE support
MarvinSketch
Loading predifined styles in format dialog threw an exception.
Structure checker dialog was displayed behind the main sketcher window in OS X.
Applet
There was a false request to download chemaxon/marvin/dict.class.
Template files that were out of jars could not be accessed.
In the student examination example, newer Java Plugins (1.6.0_19 or higher) could not load resource bundles of customization.xml from outside jar.
RejectedExecutionException was thrown by module loading.
IUPAC name recognition system could not load functional groups dictionary in case of newer Java Plugins (1.6.0_19 or higher).
Compatibility
In Safari, under OS X 10.6, the default value of "legacy_lifecycle" applet parameter has been changed (to false) to avoid hanging by concurrent applet loading and insufficent delay at the closing of applet pages.
In the default configuration of Marvin applets, the "codebase_lookup" Java Plugin parameter has been set to false to avoid insufficent search of certain localization files in applet codebase.
Import/Export
Molecule Representation
Calculator plugins
API
Periodic system modality problem inside MSketchPane on a dialog or frame.
The Periodic System dialog was not displayed properly in Instant JChem.
Structure Checker dialog stuck under MSketchPane when it was in a modal dialog under Mac OS X.
chemaxon.util.ImageExportUtil did not calculate the size of the image properly in certain cases.
ChiralityFlagErrorChecker got wrong result when molecule contained a stereo with no enhanced stereo property.
MarvinSketch
Applet
A message dialog containing a progress bar is displayed if the loading of a module takes more than 100 milliseconds, which automatically disappears when the module is loaded.
New applet parameters ahve been introduced to control pre-loading of modules: preload,bgloadEnabled and bgloadPriority.
Molecule representation
Calculator Plugins
Tautomers: dominant tautomers are returned by default, instead of all tautomers (cxcalc, Chemical Terms, GUI).
Markush enumeration: New homology example definitions are used, which are based on matching statistics from a large data base.
TPSA: Sulfur and Phosphorus atoms optionally can be excluded from calculation.
MarvinSketch
The "extraBonds" parameter value was missing for Single Bold Bond, therefore the Bold Single Type could not be removed from the Bond menu.
Joining two multicenters threw an exception in some cases.
MarvinView
Applet
Painting
Import/Export
Mrv: Reaction arrow parameters exported into Mrv files with Marvin 4.1.13 or older versions were not imported properly.
Name to Structure: The stero information was lost during the conversion of Name to some other formats (inchi, mol, sdf, ...).
Molecule representation
Deleting atoms in reactions raised exception, did not ungroup the superatom s-group and could split content of one s-group into several reaction components.
During setting bond array in Sgroup constructor, an exception was thrown when calling mol.clonecopy(int[], MoleculeGraph).
The attachment point information was missing when creating abbreviated group in MarvinSketch.
Markush enumeration failed on repeating unit with repetition ranges.
Calculator Plugins
StereoisomerPlugin returned wrong stereoisomer count via API.
Random Markush enumeration was very slow for highly complex Markush structures.
Chemical Terms
MarvinSketch
New parameter "abbrevgroupsAllowed" is introduced to be able to disable abbreviated groups on key types.
New parameter "toolbarFloatable" is introduced that can be used to make the toolbars immovable.
Changes in the Structure > Aromatization menu of MarvinSketch: renaming menu elements, the default aromatization method is changed to Basic.
Change in the behavior of the Custom Property buttons on the Periodic System dialog window. (The buttons are not toggled automatically any more. If the Value cannot be represented in the given Type, the Value text field is highlighted.)
Import/Export
ISIS (Symyx) sketch file (skc) format import and export.
CDXML import.
InChI is now available on windows 64 bit.
Licenses
Arbitrary license file names are supported under the user's home directory.
It is possible to define multiple license file locations using environment variables or Java system properties.
Calculator Plugins
ElementalAnalyser and ElementalAnalyserPlugin can accept molecular formula input, so mass, atom count, etc. calculations can be performed on molecular formula.
New option for excluding halogens from acceptors in HBDAPlugin. Halogens are excluded from acceptors by default.
Molecular volume calculation.
Projected surface area calculation: new implementation, speedup and enhanced accuracy.
The import of traditional names supports greek letters, salts, sulfonamides and bi/tri/... phenyl groups.
Name import supports mixture names with proportions, for instance 'Methanol, bismuth(3+) salt (3:1)'.
API
MarvinSketch
After adding a Multicenter to a structure, the menu item did not become disabled, and a second invocation threw an AIOOB exception.
Sometimes an NPE was thrown at initialization of Abbreviated groups.
Switching from 3D to 2D mode using the button on the statusbar caused loosing stereo information.
It was impossible to resize a textbox created by mouse-click.
It was impossible to create ladder-type repeating unit with repeatition ranges in sketcher.
Adding bonds in bond drawing mode sometimes damaged the molecule.
It was possible to create too small textboxes by drag-drawing; a minimum size was intorduced for graphic objects to avoid that.
The hydrogen number was not updated after creating position variation bond.
MarvinView
The MarvinView parameter "tabScale" did not work properly.
Unnecessary hourglass cursor was displayed in MarvinView's spreadsheet view when selecting a structure.
MarvinView did not display associtated file in OS X. Dragging molecule file into MarvinView did not work either.
MarvinSpace
Import/Export
Mol2 export did not export fragment count properly and there was a multifragment charge problem.
There were OSRA errors on some Linux and Macs machines.
IJC and JCman crashed when using inchi chemical terms expressions.
Molecule Representation
Bold bond type remained set when changing the bond type to single/double/triple from menu.
Mrv import of two contracted embedded abbreviated S-groups was not working.
There was an endless loop in MolSearch on a structure having a Multicenter S-group.
The E/Z stereo information was incorrectly displayed after S-group expansion.
Attachment points were mixed after copy and then paste or export and then import.
Ungroup function of Sketcher didn't remove the empty S-groups.
Template Handling
Template parameters (tmpls, ttmpls) did not work properly.
Moving template sets up or down in the Template Library did not have affect on the toolbar.
Calculator Plugins
Molecule with homology atoms and undefined R-atoms threw ExpansionException during markush enumeration.
JavaDoc on MarkushEnumerationPlugin.setEnumerateHomology and setMolecule order dependency was not up-to-date.
Markush enumeration was not working on ladder-type repeating unit with repeatition ranges structures.
The MarvinView result window of the 3D Aligment calculation in MarvinSketch contained the coordinate info of the removed Hydrogen atoms, which sometimes resulted in not enough space for the display of the aligned structures.
MarvinSketch
Manual mapping did not work.
The bond between the two atoms of the multicenter part of a position variation bond was deleted when a new bond was added to the position variation bond by click drawing
Applet
Calculator Plugins
MarvinSpace
Applet
API
Marvin OLE
Documentation
Installer
Marvin Sketch
Applets
MarvinSketch GUI
Structure Checker add-on, a tool for detecting molecule features or drawing errors is integrated.
The Template Library is redesigned. It allows hierarchic template structure and custom locations to be set in the library. Templates are loaded dynamically.
OLE anti-aliasing is improved: enhanced embedded object quality in MS Office documents.
"Sprout" drawing: attaching templates and abbreviated groups by automatically inserting a bond. Using the SHIFT button the rings are attached as spiro, while the abbreviated groups are attached in expanded form. Rotation by 15 degrees is possible before releasing the mouse button.
Bracket drawing tool: simple group creation without the need of preselection; the targeted substructure just have to rounded by the bracket tool.
Bracket editing: group type can be changed in Edit > Group (no need for recreation of group).
Data can be attached to brackets.
Possibility to load up to 100 molecules from multirecord files to the canvas. Ranges can be defined during the opening process.
Importing images by converting them to structures (using OSRA in the background).
The Copy As dialog is redesigned to contain explicit formats. At the same time, the Copy tab of the Edit > Preferences dialog has been removed.
Copy/Paste: single line text formats (name, inchi, ...) can be pasted even if they contain extra newlines.
New bond type: bold bond.
Ellipse drawing and circle drawing.
Rectangle with rounded corners drawing. Square drawing.
Direct structure search in public database: ChemSpider.
Web links are detected in attached data, and opened in browser by Ctrl-click.
The layout of the Attach Data dialog is improved, new data types are introduced and listed by default in "Name" field: [DUP], REAGENT.
Copying Marvin Objects to MS Office documents is sped up.
CDX format is placed on the clipboard by default copy action and automatically recognized during paste.
MarvinView GUI
Text search in molecule tables.
Marvin View can now open name files even when not all names are supported.
Save layout in MarvinView.
MolConverter
Marvin Space
3D molecular alignment is integrated into Marvin Space.
Save structure in Marvin Space.
Applets
Chemical Structure Painting
Molecule Representation
Annotating with URLs.
New bond type: bold bond.
Atoms with three similar wedge had no parity value.
A bracket button for S-group bracket drawing.
Valence check of alkali metals has been changed. (Alkali metals are not imported as alkali hydrides: Na is imported without implicit hydrogen atom instead of NaH.)
Import/Export
Concurrent processing in molecule import/export.
CDX Export.
VMN file import.
Usage of S-group bracket coordinate info (BRKXYZ tags) and style info (SBT) in MDL MOL formats.
Import and paste images via OSRA.
SMILES/SMARTS
Aliphatic explicit H is written as [H] instead of [#1A]
SMILES export default behavior to check graph invariants at CIS TRANS export.
IUPAC Name
Concise names generated for acyl-CoA (coenzyme A) derivatives.
Dictionary of common and traditional names have vastly improved and augmented.
Structure to name generates many more common names with the "traditional" option.
Clean 2D
Use the template wedges in PartialClean.
Clean of adamantane structures is nicer.
3D Alignment
Alignment by pharmacophore types.
Alignment by Maximum common substructure.
Calculator Plugins
Tooltips with help messages are displayed on Calculator Plugins options panels.
Some Calculator Plugin options panels have been redesigned, to fit small resolution displays.
Tautomerization Plugin: ester groups are not considered as tautomerizable region by default but you can switch it on.
In HBDA Plugin, sulfur atoms are not hydrogen bond acceptors by default (optional).
Documentation
Licenses
API
MarvinSketch
Fixing compatibility problem of structure templates with a file named custom.t .
Some of the tooltips in the Reaxys Generics dialog were mixed.
Undoing the deletion of a reaction arrow was not working in case of there was nothing more on the canvas.
Anti-aliasing was not working in OLE objects if atom labels were present in the structure.
The multipage function buttons were missing on statusbar.
NullPointerException in Marvin Sketch when opening a recent file.
E/Z labels display option was not saved in MarvinSketch.
Applet
URL of java download pages in marvin.jar have been modified.
Security errors in applet when it called from JavaScript.
Import/Export
SMILES/SMARTS
Clean2D not called from molconvert cxsmiles:+c
SMILES export: elements in the "organic subset" is considered more seriously.
SMILES export without stereo info.
IUPAC Name
Clean2D
Stereochemistry error during 2D clean.
Badly cleaned molecules in JWS example.
Improvement of multicenter bonds' 2D cleaning.
The Hydrogenize Chiral Center option in 2D clean changed the stereochemistry.
Clean2D threw exception for graph containing only hydrogen atoms.
Generate 3D
3D coordinate generation stereo critieria handling has been improved.
Bugfix in clean 3D parallel execution.
General improvement in conformer generation.
Forcefield (Dreiding) patch: correct geometry fo hydrazine (CNNC) like substructures.
ChemAxon force-field enhancement: planar geometry of aniline nitrogen is ensured.
Molecule Representation
StereoChemistry: CIS TRANS interpretation fix.
Add explicit H should not move the original atoms.
Chirality fix for symmetrical molecules.
Installer
Batch files failed if its path was C:\Program Files (x86)\ChemAxon.
Installer did not upgrade the previously installed OLE server to newer version.
API
Import/Export:
Structures can be saved in InChiKey format from the GUI. InChiKey can also be selected in the Edit > Source window.
Support rel- relative stereo names in name import.
Support of nucleosides and nucleotides in name import.
Better support for traditional names in name import (over 15% more names supported from NCI database).
Better support of stereo descriptors in name import: cis-, trans- is supported.
Documentation
API
New getter and setter methods in MolPrinter API for trancparency, ballRadius, stickThickness, wireThickness, lonePairsAutoCalculated, carbonVisibility, boundingRectangle.
Name to structure extraction from text and html documents API has been added to the name-to-structure infrastructure (see the api documentation of chemaxon.naming.DocumentExtractor.
Custom name conversion plugin API has been added to the name-to-structure infrastructure (see the api documentation of chemaxon.naming.NameConverters). This allows for instance the integration of a large in-house structure dictionary (including names) stored in a local or remote database into name-to-structure and document-to-structure conversions.
Deprecated asynchronous molecule setting methods in MViewPane API: setM(int, String), setM(int, String, String) and setM(int, File, String).
.NET integration
MarvinView
Import/Export
Aliphatic property was not added to aliphatic C with doublebond and any bond during SMARTS.
MarvinView and MarvinSketch sometimes crashed when bad InChI was imported.
Chemical Structure Painting
Clean 2D
Explicit H atoms having parity were improperly added with the Clean option.
2D cleaning of a bridged ring having another ring as neighbor was wrong.
Licenses
MarvinSketch
New icon is added to the "Add Attachment Point" action.
New keyboard shortcuts: 5 - Single Up, 6 - Single Down, 7 - Wiggly bond.
Molecule representation
MarvinSketch
MarvinView
Licenses
Applet
Import/Export
Molecule representation
Nitrogen with double bond and explicit H gets stereo value.
Bug was in setDim method in RgMolecule.
Chemical Structure Painting
Calculator Plugins
API
MarvinSketch
Calculator Plugins
MarvinSketch
Import/Export
Partial charges are saved in mol2 file format based on the calculation result of the charge plugin (charge license required; if it is not found then the mol2 file is created without charges).
Relative stereo descriptors (using enhanced stereo OR groups) is supported in name export.
Amino acid recognition in Name import has been improved: substituents are recognized, D/L configuration is supported.
Importing non standard names is more flexible: more freedom at numbering, bracers and dashes.
Cis/trans releated information is supported in name import.
Clean 2D
Applet
The loading of MSketch Applet is sped up: the total size of the files downloaded during the first initialization has been reduced by 14% compared to the previous version.
The value of the "legacy_lifecycle" parameter is true in default in Marvin applets if you use marvin.js..
New methods have been introduced in marvin.js, which return with the generated applet source instead of writing it into the html source: msketch_end_to_string() , mview_end_to_string() and mspace_end_to_string() .
A new applet parameter has been introduced ("appletid") to identify applet in the propertychange event notification sent to JavaScript.
The marvin.js uses ID attribute instead of NAME to refer to the applet.
Chemical Terms
New Chemical Terms functions have been introduced:
importMol()
isMarkush()
whereIsValenceError()
hasAromatizationError()
Calculator plugins
MarvinSketch
The 'Recent file list' contained two separate (and incorrect) items if the filename contained a comma character (divided at the comma).
OLE failed with some repaint events when the canvas was in the background of other java components.
Applet
The JVM version in the EMBED and the OBJECT tag in the marvin.js generated code was not up-to-date. In addition to the update the NAME attribute was changed to ID.
The "viewCarbonVisibility" applet parameter did not work.
Import/Export
Some R/S and E/Z stereo descriptors were missing in generated names.
Failing on name generation of very complex structures was not handled too gracefully.
cxsmarts:h failed.
MOLFiles with incorrect spaces at the end of the new type of Atom list definition lines can now be imported without error.
CDX import failed at some reaction mapping.
Molecule representation
There was a NullPointerException in aromatization.
Copy/paste and import/export of a molecule in mrv format having an S-Group with only one atom did not work.
The getAromaticAndAliphaticRings method threw NullPointerException.
Calculator plugins
The exceptions of the Structural Frameworks plugin were sometimes improper (now it throws PluginException on error).
Projected surface area prediction produced inconsistent values.
Template handling
Installation
Licenses
New features and improvements
MarvinSketch:
The Clear Atom List button is added to the Periodic System dialog window.
Icon for Reaxys Generics is added.
MolConverter:
Applet:
Import/Export:
InChi 1.02 version has been integrated.
InChiKey can be exported. New export option: inchi:key
Calculator Plugins:
Documentation:
API:
Named constants for applet and bean parameters are available in the API: chemaxon.marvin.common.ParameterConstants.
New MolRenderer API available: chemaxon.marvin.beans.MolRenderer.
Deprecated methods in chemaxon.formats.MolImporter : parameterless constructor, setOptions(String) , setFileName(String) .
Bugfixes
MarvinSketch:
Undo sets viewport to lower-right corner/Undo-Redo scaling.
Number of missing from menu label AND1 and AND2 in Atom > Stereo > Enhanced menu.
MarvinView:
Import/Export:
Pseudoatom export bug in MDL Molfile export.
Chiral center had wrong connectivity at atom.
chemaxon.util.MolHandler threw ClassCastException by SMILES.
Unique SMILES export bugs.
ClassCastException threw by endless loop for invalid SMILES import.
Reaction arrow was not visible by creating JPEG reaction images.
MRV import failed for polymer in abbreviated S-group.
IUPAC name import bug by certain structures.
Molecule representation:
Chemical structure and graphical object painting:
NullPointerException in a MolPrinter example.
The Get Sketch Image button on Marvin Beans example ( examples/beans/sketch-images/SketchImages ) generated misplaced drawing.
Calculator Plugins:
3D flexible alignment throws NullPointerException if molecules are too dissimilar to align.
Timelimit setting added to 3D flexible alignment API.
Licenses:
New features and improvements
MarvinSketch
Copy actions run in background thread.
Speed up OLE copy: MarvinOLEServer running in the background permanently.
Applet
Import/Export
Allows aromatic boron in cxsmiles.
cxsmarts format stores attachment point data.
Support for atom values in cxsmiles.
Keep wedge arrangement in cxsmiles.
Calculator Plugins
Structural frameworks plugin is moved to Other plugin group, 3D Alignment plugin is moved to Conformation plugin group.
Added stereoDoubleBondCount calculation to TopologyAnalyserPlugin.
Licenses
API
Bugfixes
MarvinSketch
The first alteration of the structure couldn't be undone in MarvinSketch opened through MarvinView.
The .H+/.H- buttons could not be used in some cases.
Do not show carbon atoms when charge is on bracket.
Bold font is used for superscripts in case of charge for better visibility.
Missing bond problem after OLE copy: reimplementing bond-crossing drawing.
Missing bond crossing visualization when crossing a bond with a bond vertically.
The Insert > Groups dialog contained some empty elements.
MarvinView
MarvinView hid the right side of text boxes.
MarvinView did not display SD file property when first entries are missing the value.
MarvinView freezing when molecule subset start index set to invalid value.
MarvinSpace
Import/Export
Rdf conversion lost the reaction number.
Fixed fusion bridge wrong lettering in name export.
Molecule Representation
Ungrouping of multilevel S-groups with Molecule.DEFAULT_UNGROUP caused NPE.
Empty DataSgroup-s are removed if an S-group gets empty (API, GUI).
Merge Brackets popup menu item was not available in some cases.
Rings were not cleaned perfectly.
Calculator Plugins
Licenses
API
MolImporter.getRecordCount returned 2* the expected number.
First (record number) column displays the value returned by MDocSource.getDocLabel.
New features and improvements
Compatibility
MarvinSketch
Truly transparent structure painting method: higher quality drawings at crossing bonds and atom labels.
Vector graphics (EMF) copy place transparent picture to the clipboard.
New color schema options on the Periodic System dialog.
Charge can be assigned to the S-group and displayed on the molecule bracket.
Drawing attachment points outside S-groups.
Homology group drawing.
MarvinView
Copy/Paste transfers molecule properties.
"Go To" option in Table menu.
New values of edited data fields and molecules are stored permanently in memory even in case of large (cached) viewer tables.
Import/Export
Extended support for the generation of fused names (from 75% to 80%) in IUPAC name export.
CAS naming and simple fused systems supported in name import.
Transparent background in image export (EMF, SVG, PNG).
Molecule representation
Calculator Plugins
New plugin: Flexible 3D alignment of multiple molecule structures to each other.
New plugin: structural framework calculation including Bemis-Murcko.
Markush enumeration:
Enumeration of homology groups.
Enumeration of X pseudo atoms [F,Cl,Br,I].
pKa calculator is trainable.
Total charge calculation in cxcalc ("totalcharge").
"Take major tautomeric form" option in MajorMicrospeciesPlugin.
23 new ring related functions in TopologyAnalyser.
Resonance Plugin was moved to "Other" plugin group, and it can be used without license key (free).
Chemical Terms
Flexible plugin parameter setting in Evaluator: "name1:value1 name2:value2 ...". (Example: markushEnumerations('random:true id:true', '1,2', 5).)
hasRadical(), radicalCount(), and hasIsotope() functions in Chemical Terms.
fragments() function in Chemical Terms.
CT Editor is available in Marvin API.
API
Transfer button: optional button to send the molecule to the specified target after closing MarvinSketch window.
Specify own background color separately for each cell in MarvinView via (applet) parameter.
New metal types can be specified in Periodic system.
Structure checker core classes and functions are implemented.
MViewPane enhanced table support.
PluginFactory creates new plugin and display instances for each getPlugin() and getDisplay() call in case of multimol display; added MOLECULES result domain type and canRepeat() in CalculatorPlugin
Bugfixes
MarvinSketch
Disabled tooltips in menus.
The copied and generated structure with Data S-group is much bigger than needed.
MarvinView
Print All displayed only the first row on each page.
Multi-line SDF properties seem to be truncated in the cells until somone clicks on them (then a scrollbar appears).
Page Up/Page Down not working in spreadsheet view.
NullPointerException in empty mview when the "Show Fields" option was selected.
Import/export
Cis Trans info defined by aromatic bonds in SMART / SMILES import.
SMILES export of SuperAtom S-group in SuperAtom S-group did not work.
Molecule representation
Calculator Plugins
Double bond stereoisomers of molecules containing wiggly type double bonds are generated correctly.
Ungrouping grouped molecules before calculating functions in ElementalAnalyser.
cxcalc in concurrent mode always used ReusableInputProducer and hence plugin objects are always re-set in the working units.
New features and improvements
MarvinSketch
Customizable behavior of the "Close" option of Sketcher window.
The isotope list can be modified by the user.
Applet
Bugfixes
Import/Export
New features and improvements
MarvinSketch
Import/Export
Applet
A java splash screen ("Applet is loading...") is displayed while the applet is loading.
Load on-demand modules in background thread.
Display wait icon when loading on-demand modules.
New features and improvements
MarvinSketch
MarvinView
Applet
celli_jand the possibility to escape characters.Import/Export
Installer
API
Save/load MSketchPane toolbar and menu configuration : reset active configuration fix.
New method in MolAtom (getLonePairCount()) that returns the same value as MoleculeGraph().getLonePairCount(int i) is implemented.
Bugfixes
MarvinSketch
MarvinView
Print All accessed only cached molecules from the table.
Save As did not save all molecules.
Applet
Width of HTML label components fixed in MarvinView applet.
Marvin applets did not accepted inline CML/MRV files that were given in applet parameter.
Calculator Plugins
New features and improvements
MarvinSketch
Arrows group is restructured in the toolbar and in the menubar.
The Insert > Groups menu is replaced by a more convenient dialog.
Import/Export
Calculator Plugins
Unique Markush code can be generated for each enumerated structure.
logP and logD calculations are significantly faster.
API
New methods in chemaxon.beans.MViewPane : isViewWindowOpened(int) , isSketchWindowOpened(int) and closeSketcher(int) .
PDBReader and related classes were moved from chemaxon.modules to chemaxon.marvin.io.formats.pdb .
MacroMolecule and related classes were moved from chemaxon.modules to chemaxon.struc .
MarvinSketch
The layout of the Copy As... dialog is polished.
Periodic System button remained pressed on the toolbar even after the dialog was closed.
The Atom > Stereo > Enhanced, Atom > Charge, Atom > Map, Atom > R-group menus are replaced by more convenient dialogs.
Ctrl+Del in MarvinSketch did not delete properties.
Licenses
Calculator Plugins
When using Calculator Plugins, the result window of a previous calculation sometimes reappeared.
Huckel Analysis Plugin threw exception if the input molecule contained explicit hydrogens.
Bugfixes
MarvinView
Thread conflict while scrolling in huge SDfiles.
ArithmeticException in progress monitor.
Import/Export
The implicit hydrogen setting option did not work in image generation.
Molfile import bug: pseudoatom names in atom block were not trimmed.
New Features and Improvements
MarvinSketch
MarvinView
New helper API (chemaxon.marvin.beans.MViewParams) that generates the value to the molecule table parameters of MarvinView.
Support MDLCT format in OLE Object.
Licenses
Import/Export
Encoding detection when the default system encoding is not suitable for the input file. It tries to recognize UTF-8, UTF-16, EUC-JP and Shift_JIS. If all fails, then it also tries ISO-8859-1 and windows-1252. The guessed encoding can be printed using molconvert query-encoding.
Energy is stored in the second line of XYZ files.
MDL formats
Import of SDfiles without structure fields.
Energy is imported from the header line, the "Energy" SDF property is removed.
Format recognition optimized: other recognizers are not called any more if the first 12 lines match at least one MDL format.
API
Clean 2D
Calculator Plugins
Huckel orbital coefficient calculation in HuckelAnalysisPlugin.
Markush enumeration ID can be generated for enumerated molecules.
logP calculation methods were introduced; available methods: "VG", "KLOP", "PHYS", "user defined", "weighted".
logP calculation is trainable, the "user defined" logP calculation method can be trained with experimental logP values provided by the user.
cxcalc can be used for training the plugin calculations (currently only logP is trainable).
MarvinSketch GUI
Correction in geometric transformation when placing SMARTS with the help of the Periodic System dialog window.
Help menu opened very slow on Mac.
MarvinSketch web start application did not launch with Java 1.5.0_16.
Import/Export
UTF-16 encoding is recognized and imported correctly if the file starts with a byte order mark (BOM).
Reaction arrow did not display (from rxn file) with exporting to image.
Clean 2D
Calculator Plugins
New Features and Improvements
MarvinSketch/View
Moleculear representation
API
chemaxon.marvin.io.MDocSource and chemaxon.marvin.io.MFieldAccessor are added to public API.
New abstract method in chemaxon.marvin.io.MDocStorage.Listener : storageSizeFinalized(MDocStorage) .
Documentation
chemaxon.util.iterator.IteratorFactory is added to apidoc and to the documentation.
Improved MarvinSketch applet examples for molecular property calculations.
Bugfixes
Import/Export
SMILES import removed parity from rigi N stereo.
Cxsmiles export generated unimportable output.
Molecule Representations
Adding a bond to terciary N did not add + charge automatically and displayed valence error.
Reaction arrow head missed after import steps in mview and molconvert.
Adding and then removing explicit hydrogens created stereo bonds.
Clean 3D
Calculator Plugins
New Features and Improvements
MarvinSketch
New, explicit way of defining lone pair and radical electrons on atoms.
The following menus were (temporarily) removed from the Template Library: File > Close, Options menu (the functions are out of order).
The Structure > Clean 3D > Select Conformer menu option is renamed to Display Stored Conformers.
Applet
Import/Export
The lone pair and radical electrons can be exported to cxsmiles format.
Also recognize names that are part of the traditional dictionary (now that name recognition should only be tried when most others have failed, it is not as problematic to load the dictionary during recognition).
Chemical Terms
API:
MarvinSketch
Explicit hydrogen was added automatically to newly placed atom after adding explicit hydrogen from the Structure menu.
Explicit lone pairs disappeared when editing the molecule with the sprout function (mouse drag).
Source window sometimes failed to open from plugin result dialog.
Extra selection of the radical atom was invoked.
Import/Export
Add missing structures to nameimport dictionary, fix suffix and stereo handling on esters.
Molfile recognition failed if first line includes only spaces.
Clean 2D
Template Handling
Calculator Plugins
Changed default SDF tag names of cxcalc calulations acceptorsitecount (ACCEPTOR_SITE_COUNT), acceptorcount (ACCEPTOR_COUNT), donorsitecount (DONOR_SITE_COUNT) and donorcount (DONOR_COUNT).
Calculation result list often disappeared when the result display window was resized.
Parameter files of several plugins included invalid xml syntax.
API
New methods to close streams in MolExporter: flush(), close(int).
F6 and F7 did not work if MViewPane was a JTable cell.
New features and Improvements
MarvinSketch:
Converting IUPAC Names to structure:
from .name files
through the Edit > Enter IUPAC Name option
when pasting IUPAC names to the canvas of MarvinSketch
OLE 2 support: improved support of pasting MarvinSketch objects into MS office documents, and ability to edit the inserted object inside the Office document. More memory efficient, stable on Vista. JNI-based communication, multi-document server.
Accelerated initialization of MarvinSketch and MarvinView at startup, both as standalone version, and as implemented component in other applications.
Flip Group option: Flip a selected group in the molecule around the bond connecting this group to the rest of the structure.
Recent file list length is configurable in the Save/Load tab of Edit > Preferences
The save and load of GUI properties can be set only with one checkbox at the preferences Save/Load tab in the future.
The magnification (zoom factor) of a molecule is now saved in MRV format if it is enabled on the Save/Load tab of Edit > Preferences.
MarvinView:
(Batch) conversion of IUPAC Names to structure when opening .name files.
Printing is redesigned. New options: Print to PDF and Print Preview.
Applet:
New applet parameter to listen for mouse events.
Calculator Plugins are accessible from JavaScript via Chemical Terms.
Import/Export:
IUPAC name import (converting IUPAC names to structures):
opening .name files
batch conversion of names (in .name files) by molconvert
direct conversion of names to structures through the Edit > Enter IUPAC Name option
on-the-fly conversion of IUPAC Names to structure when pasting IUPAC Names to the canvas of MarvinSketch
IUPAC name export: improved support for amino-acids and peptides.
Compressed base64 encoded (cx)SMILES/(cx)SMARTS output.
UTF-8 character encoding support for applet parameters.
Unique SMILES export has been changed because of the modification in aromatization.
Molecule Representation:
Allow N with valence 5 in aromatic rings .
Aromatization to accept all atom types in aromatic rings.
Clean 3D:
Major Clean 3D core modifications: the fragment-fragment fuse code is rewritten. The new version places greater effort to avoid situations where excessive coordinate generation time is elapsed. The performance of multiple conformer generation is also improved.
New Dreiding force field implementation introduced.
Hyperfine parameters tuned: excessive runtime when invoked with looser optimization limit fixed.
Calculator Plugins:
Tautomerization Plugin
Generic tautomer generation.
New tautomerization options: protect double bond stereo, protect all tetrahedral stereo centers, protect labeled tetrahedral stereo centers only.
Topology Analyser Plugin
Geometry Plugin
Markush Enumeration Plugin
Structure coloring and scaffold aligning options in Markush enumeration.
Position variation bonds in Markush enumeration.
New Markush enumeration options: orienting scaffold uniformly and coloring enumerated structures.
Speeding up random enumeration.
Huckel Analysis Plugin
Eigenvalue and eigenvector calculations (cxcalc: "huckeleigenvalue" and "huckeleigenvector").
Some cxcalc calculations have been renamed: "energy" to "localizationenergy", "pichargedensity" to "electrondensity", "totalchargedensity" to "chargedensity".
Removed aromatic restriction from Huckel E/Nu order calculations.
logP plugin
Chemical Terms:
Chemical Terms is available from Marvin in command line and API (until now it was available only in JChem).
It can also be used in JavaScripts (in applets).
New functions: abs(), fragmentCount(), ringSystemCount(), smallestRingSystemSize(), largestRingSystemSize(), ringCountOfSize(), ringSystemCountOfSize(), aliphaticRingCountOfSize(), aromaticRingCountOfSize(), minimalProjectionArea(), maximalProjectionArea(), minimalProjectionRadius(), maximalProjectionRadius(), genericTautomer(), mostStableTautomer(), markushEnumerationsDisplay(), randomMarkushEnumerationsDisplay().
New (optional) parameters are available for enumerations() and randomEnumerations() functions.
Functions available only in JChem: match(), matchCount(), disjointMatchCount(), dissimilarity().
AND, OR, NOT boolean operators in Chemical Terms (alternatives for &&, ||, ! operators).
Option to set output format in Evaluator command line application if result is molecule.
Evaluator command line application can list available Chemical Terms functions.
API:
Both aromatization methods aromatize query atoms if they have double and single bonds in the ring.
Atoms belonging to the following atom groups can be recognized by the name of the group: alkali, alkaline earth, other metal, transition metal, lanthanides, actinides, metalloids, halogens.
Calculator Plugins:
New calculations in TopologyAnalyser and TopologyAnalyserPlugin (see the list of calculations above).
New calculations in GeometryPlugin (see the list of calculations above).
New calculations and options in TautomerizationPlugin.
New calculations and options in MarkushEnumerationPlugin.
New and renamed calculations in HuckelAnalysisPlugin.
Molecule file format recognizers are called in the priority order defined by the recogn argument of the MFileFormat constructor. Deprecated Recognizer.getPriority(), use MFileFormat.getPriority(subformat) instead.
MoleculeIteratior interface moved to chemaxon.util.iterator.
Documentation:
Bugfixes
MarvinSketch:
Atom > Stereo > R/S menu was missing.
MarvinSketch always dropped confirmation dialog when exiting in OLE mode.
In MarvinSketch, scale factor was loading in an improper time.
Zooming after atom font changing shouldn't delete the set atom font.
Atom font changes from Format dialog disappeared when scrolling.
Automatic mapping of long chain substituents was incorrect.
MarvinView:
Applet:
Molecule representation:
Wedge bonds were displayed incorrectly after adding explicit H atoms to chiral centers.
Implicitization of explicit hydrogens was sometimes incorrect.
Clean2d placed wedge on symmetric atoms.
Planar ligands in 3D returned 0 instead of EITHER in parity.
There was a minor bug in the valence check algorithm.
MRV export of the molecule in reaction editor threw NullPointerException.
A valence error was given to pyridine oxide drawn with aromatic bonds.
The head of the reaction arrow disappeared after 2D or 3D clean.
The reaction arrow overlapped a reactant upon hit coloring of reactions.
Atom coloring didn't work after subsequent molecule loads.
ArrayIndexOutOfBoundsException was thrown when drag&dropping expanded S-groups from the canvas to MyTemplates.
The reaction arrow was duplicated after 2D clean.
Replacing atom in S-group with Asp caused ArrayIndexOutOfBoundsException.
In SMILES format, double bond lost cis/trans info after aromatization.
M, MH, X, XH are not aromatic query atom.
Import/export:
Clean 3D:
There were errors in gradient calculation. The fix also improves the optimization performance for some deformed initial structures.
Possibly corrupted stereochemical requirements caused a bug when invoked directly from the sketcher.
Using chirality when invoked from the sketcher sometimes failed.
Hyperfine produced unpredictable results. Now MD parameters are modified (lower initial temperature) and very strict optimization limit is used.
Energies calculated by the building process and the dreidingenergy plugin were slightly different.
Optimization limit error message fixed.
Calculator Plugins:
An exception was thrown during enumeration of structures with multicenter S-group.
Random Markush enumeration generated larger link node enumerates than in definition
Random enumeration hasn't thrown exception in case of invalid input structures (R-group in the variable part of multiposition bond).
NullPointerException was thrown in some cases of random enumeration when molecule contained possible valence error. Now a more informative RuntimeException is thrown.
Random Markush enumeration has returned null for non-generic structures instead of the structure itself.
DotForumla functions of Elemental Analyser threw exceptions on empty molecules.
New features and Improvements
Applet:
API:
Molecule representation:
Bugfixes
MarvinSketch GUI:
Customization dialog was not displayed.
Complete missing configuration names.
Licenses:
MarvinSketch GUI:
Licenses:
MarvinSketch GUI:
Zooming after atom font changing deleted the settings of atom font.
SMILES was transferred instead of the molecule source by Plain Text copy.
Atom font changes from Format dialog disappeared by scrolling.
MarvinSpace:
Licenses:
Molecule Representation:
Replacing atom in Sgroup with Asp caused ArrayIndexOutOfBoundsException.
Atom coloring did not work after subsequent molecule loading.
Calculator Plugins:
MarvinSketch GUI:
API:
Molecule representation:
Import/Export:
CalculatorPlugin:
MarvinSketch GUI:
Shift button expands/contracts all "hold-in-hand" S-groups and abbreviation groups (not just standard templates).
New icons has been added to the collection, which are not included in the toolbars by default, but can be added using the View > Customize option. These icons (category > command) are as follows: Reset View (View > Reset View), Aromatize (Structure > Aromatize), Dearomatize (Structure > Aromatize), Add explicit hydrogens (Structure > Add explicit hydrogens), Remove explicit hydrogens (Structure > Remove explicit hydrogens), Add absolute stereo (Structure > Add absolute stereo (CHIRAL)), Remove absolute stereo (Structure > Remove absolute stereo (CHIRAL))
The Erase icon has been changed (from an upside-down pen to a rubber)
CalculatorPlugin:
API:
Added "public String getIsotopeComposition(boolean)" method to chemaxon.marvin.calulations.ElementalAnalyserPlugin; D symbol is used for Deuterium and T for Tritium in results returned by "public String getIsotopeComposition()".
Enumeration plugin is renamed to MarkushEnumeration plugin. chemaxon.marvin.calculations.EnumerationPlugin class is deprecated, use chemaxon.marvin.calculations.MarkushEnumerationPlugin instead of that.
Parameters are renamed in cxcalc calculations: from enumerationcount to markushenumerationcount , enumerations to markushenumerations (old names are still available).
Import/Export:
R-group defintions were missing on molecule picture after image export.
Cis/trans stereo info was sometimes wrongly exported into smiles.
CML and MRV import failed when the input file did not contain any molecule
MOL/SDF export caused a null pointer exception when energy field was corrupted (NaN or Infinity)
The chemaxon.struc.MDocument.parseMRV(String) method failed with NullPointerException .
SmilesImport fix: If ringcorrection called set CIS|TRANS flags for bonds located in two small sssr.
CxSmilesImport fix: ringcorrection (CIS flag setting for small rings) moved before setting the extra chemaxon information (in cxsmiles).
Clean 2D:
The 2D cleaning of structures containing double bonds connected to a ring was sometimes wrong.
The arrangment of template based 2D clean was missing.
The 2D cleaning of a selected (sub)structure was sometimes inappropriate.
Clean 3D:
MarvinSketch GUI:
Zoom mode (F6) and zoom tool were unsynchronized.
Drawing a bond to an R-group definition by click-drawing resulted in inconsistent molecule.
Specifying outer bonds by selecting the atom before defining the Link Node did not work.
Drawing link node attachment point by Rgroup definition was not correct.
The location of the filechooser dialog (by Open , Save and Save As ) was wrong in some cases.
MarvinView:
Applet:
MarvinSketch:
Position variation bond. It is available under the Structure > Add menu.
Extended font support: Texts (atom labels and text box content) can be formatted using any font that is available in the operating system.
Global IME support in Textboxes (allows entering East Asian characters).
Recent file list added to file menu.
MarvinView:
Recent file list added to file menu.
"Print All" and "Save As" options are enabled in "File" menu, and they work properly
MarvinSpace:
Displaying coordinate system.
Reading PDB files as simple Strings
Import/Export
Molecule file header and footer can be retreived using MRecordReader.getHeaderAsString() and getFooterAsString().
Related incompatibility: the MRV file header and footer are not part of the record returned by MRecord.getString() any more. Prepend the header and append the footer to get an importable molecule.
Image export option to show E/Z labels.
East Asian character encoding support for applet parameters
The default behavior and some options of PDBImport have been changed. Bonds are recognised in hetero groups by default, bond order is assigned. Optional hydrogen assignment/removal and the possibility to omit CONECT records has been implemented. PDB import does better recognize connectivity and bond order of hetero components.
Bugfixes:
Atom > Stereo > R/S menu was missing in MarvinSketch GUI
Marvin applets did nothing by OLE copy
MarvinSketch always dropped confirmation dialog when exiting in OLE mode.
UTF-16 character encoding fix in cell headers of MarvinView
Fix on adding explicit H atoms to chiral centers.
Implicitize hydrogens bugfix.
Fixed IUPAC name export failure involving spiro compounds.
Superfluous hydrogen atoms were assigned during PDB import
LonePairCounter.getLonePairCount() failed for structures containing list and not-list atoms. This also affected AutoMapper
AutoMapper bug (wrong mapping of long chain substituent) has been fixed.
Import/Export:
Image export options are added for displaying lone pairs
MRV import accepts comments in old MRV files
EMF and PDF exports uses the new version of Freehep API (2.1.1)
Bugfix: Saving EMF and PDF in Marvin applets often gave emtpy or corrupt file.
MarvinSketch:
Toolbar drop-down list box is added
Drag&Drop of templates works beside the template toolbar
Bugfixes:
tmpls, ttmpls, xtmpls parameters did not work
setEnabled(false) function did not disable toolbars
Help button did not work in the desktop application
Insert > IUPAC Name required license and kept complaining about the missing license
Abbreviation groups assigned to My Templates worked only after restarting MarvinSketch
Desktop icons are optionally created under Linux by the Marvin Beans installer
Wedge arrangement around stereocenter having four ligands was improved
MarvinView: "Print All" and "Save As" option is temporary unavailable in grid view until its reimplementation
MarvinSpace:
Animation can be stopped from menu
Electrostatic potential uses the same coloring method as Charge Plugin in MarvinSketch
Calculator Plugins:
TautomeriztionPlugin: "Protect aromacity", "Protect charge" and "Exclude antiaromatic compounds" options were added
EnumerationPlugin: the visualization of the result of Markush library size calculation was improved
Dreiding energy can also be displayed in kJ/mol unit in GeometryPlugin and in ConformerPlugin
MarvinSketch:
Customizable GUI with a brand new design
Configuration choices (including ISIS Draw and ChemDraw like menu and icon arrangements)
Chain drawing, displaying the last carbon number
Enhanced Query, S-group and R-group drawing features
When MarvinSketch canvas is empty, the scrollbars are disabled
MarvinView:
Spreadsheet-like view for displaying fields in SD and RDfiles
Bugfix in OS X: the scrolling down button was covered by the resize button of the window
Import/export:
Insertable Marvin OLE component into Office documents
IUPAC name generator, with real-time name display in MarvinSketch, support for peptides and amino-acids, and numerous name improvements
Gaussian Input/Output
Cube import: changed default behavior - reads in volumetric data by default (former import option 'V'), skips it if import option 'M' is specified
UTF-16 encoding support for MolInputStream
API changes:
Metadata for file formats handled by Marvin is represented by class MFileFormat. File formats can be found using MFileFormatUtil.findFormats. User defined formats can be registered with registerFormat.
Metadata for import or export options is represented by class OptionDescriptor. Export options for a given format can be retrieved using MolExportModule.getOptionDescriptors.
Record reading. MRecordReader implementations can be used to parse records without creating Molecule objects. An MRecordReader can be created using MFileFormat.createRecordReader or MFileFormatUtil.createRecordReader.
Only narrow ends of wedge bonds are considered in 2D representation of the molecules, following IUPAC recommendations. To convert your existing 2D molecules created with the both-end interpretation to the new convention, use the ConvertWedgeInterpretation Standardizer action.
Related incompatibilities: *
MolImportIface and MDocumentImportIface interfaces are replaced by the abstract class MolImportModule. Record skipping related methods removed (isSkippingSupported, skipMol and skipToNext), use MRecordReader.skipRecord or MRecordImporter.skipRecord instead.
MolExportModule: the open method throws MolExportException, loadMarvinModule removed and replaced by MFileFormatUtil.createExportModule, getOptionSign removed. Both MolExportModule and MolExportException moved to chemaxon.marvin.io, the old versions in chemaxon.marvin.util are deprecated.
The canonical encoding name is returned by MFileFormatUtil.getEncodingFromOptions and stored by MolExportModule.setEncoding, MolConverter.createMolConverter and the constructors of MolImporter, MolExporter and MolConverter. These methods and constructors may throw IllegalCharsetNameException or UnsupportedCharsetException.
Import/export modules (not recommended to use directly!) moved from chemaxon.marvin.modules to chemaxon.marvin.io.formats and its subpackages.
Calculator Plugins:
Multiprocessor support in cxcalc
Tautomerization:
New tautomer generation rules were implemented
Estimation of the tautomer distribution as function of pH was improved
pKa, logP: Accuracy of the predictions were improved.
Added EnumerationPlugin: enumerates Markush structures
ElementalAnalyserPlugin:
"Dot-disconnected isotope formula" calculation added
"D" and "T" symbols can be used for "Deuterium" and "Tritium" in isotope formulas
pKaPlugin: "Take major tautomeric form" option added
logPPlugin: "Take major tautomeric form" option added
logDPlugin: "Consider tautomerization" option added
New surface area calculations in MSAPlugin:
Water accessible surface area (ASA)
Water accessible surface area of all atoms with positive partial charge (ASA+)
Water accessible surface area of all atoms with negative partial charge (ASA-)
Water accessible surface area of all hydrophobic atoms (ASA_H)
Water accessible surface area of all polar atoms (ASA_P)
GUI: "Restore defaults" button added to options panel
Integration of user-developed calculations made easier
Reaction auto-mapping:
New mapping style was introduced, CHANGING, this is the default ChemAxon-style mapping from now on (see also the Reactor documentation).
Three kind of mapping strategies have been introduced: BEST which is the slowest but exhaustive search, STANDARD, the default, fairly reliable automapping strategy, and FAST which is a crude mapping strategy.
Numerous bug fixes, eg. symmetrical ring maps are shifted.
Queries, Groups and Markush structures:
Coordination compounds: drawing, MRV, MDL Mol, Extended SMILES IO
Markush structures: position variation (Markush bond) and frequency variation drawing; MRV, MDL Mol, Extended SMILES IO; Enumerating Markush structures (sequentially/randomly)
Components, Unordered Mixtures and Ordered Mixtures: drawing, MRV, MDL Mol IO
Polymers: drawing, MRV, MDL Mol IO
Repeating units with repetition ranges: drawing, MRV, MDL Mol IO
Improved editing of hydrogenized structures
Improved branching in 3D
API:
Graphics:
MBracket class, supports parentheses, square brackets and chevrons.
New MTextBox attributes "halign" and "valign" for aligning the text, see setHorizontalAlignment and setVerticalAlignment.
Incompatible change: java.awt.Graphics2D is used as the first argument of MObject.paint() and its implementations.
GUI:
Invoking Paste action from API: MarvinPane.doPaste()
Removed MarvinPane.addSaveImageMenu and MViewPane.makeSaveImageMenu because the menu of multiple image formats is replaced by only one "Save Image(s)" menu item. It can be added to a custom "File" menu using MarvinPane.getCommonActions().getSaveImageAction().addTo(menu).
Applet Parameters:
New: listenpropertychange.
Deprecated: preload, background.
Incompatibilities:
MProp. convertToString(String) became a final method calling the abstract convertToString(String, int) with 0 second argument.
fuse(CGraph graph) and fuse0(CGraph graph) have been made final. Subclasses should implement fuse(CGraph graph, boolean check) and fuse0(CGraph graph, boolean check) instead.
API:
Fixed bugs:
Import/export:
There was a critical property based smiles export bug
There was a NullPointerException in Parity
GUI:
Plugin options panel could not be closed using only the keyboard after running the calculation
Edited molecule was not updated in viewer by closing the sketcher.
Rotating a group in expanded form removed the group definition.
Update isotope number in selection by D and T shortcuts.
Type-over atom D did not work.
In OS X, the scroll down button of sketcher scrollbar was covered by window resize button.
Fix a small refreshing problem in MarvinSpace.
Quick setting of component visibility on mouse drag in MarvinSpace.
Calculator Plugins:
Misc:
API:
Bugfixes:
Change frames to dialogs to avoid focus problem of model dialogs.
"Any" bond was invisible in OS X.
ElementalAnalyser and ElementalAnalyserPlugin: scientifically correct rounding of molecular weight (mass)
CleanUtil.arrangeComponents() bug for reactions containing Sgroups.
Bug in abbreviated group visibility.
Correcting a bug of getting the most frequent natural isotope of Hydrogen. It returned 0, though the correct result is 1.
Marvin Beans batch files accept 40 parameters.
Improvement in IUPAC name export. Very significant performance increase for large molecules, fixing about half the previously existing naming failures (due to timeouts) for typical datasets. New export option to setup naming timeout.
Bugfixes:
GUI:
API:
Clear undo queue: MSketchPane.clearHistory().
New property to set default save format: defaultSaveFormat
Bugfixes:
IUPAC Naming: fixed timeout errors.
Fixing bug "Phosphorus loses chirality after explicit-H-removal"
Calculator plugins:
Added dominant tautomer distribution calculation to Tautomeriztion plugin
cxcalc: dominanttautomerdistribution calculation
Related changes in TautomerizationPlugin API
Maximum allowed lenght of the tautomerization path can be set in Tautomeriztion plugin
GUI:
Remove small blue corners in MarvinView (except in tables).
Hide dashed line in bond forming electron flow arrows.
Fixing undo and copying error in reactions.
API:
New image export option to display atom numbers.
New PropertyChangeEvent to indicate when selection changes.
New method in the MolPrinter class to set display options.
In the chemaxon.marvin.util.MolExportModule class, the optionSign2 field is replaced by getOptionSign() method.
IUPAC name generation improvements, in particular for ions.
Bugfixes:
Import/export:
Image export option ("noatsym") to hide atom symbols in 3D mode.
SUBSTRUCTURE section is also generated in mol2
Bugfix in MRV import: absolute stereo flag could not be set.
Fix superatom S-group export bug in MRV export.
GUI:
Fix NullPointerException by displaying MViewPane with menubar.
Graphical reaction arrows.
Bugfix in arrow drawing.
API:chemaxon.marvin.util.MPainterUtil
is deprecated, use
chemaxon.marvin.MolPrinter
IUPAC name generator, for interactive and batch naming
Bugfixes:
In Graph invariant.
Arrow mirroring bugfixes.
Infinite loop fix in Parity.
Converting to "base64:gzip:mrv" did not work.
Exception by missing atom list definition fixed.
ArrayIndexOutOfBoundsException in RxnMolecule.removeNode()
Non-transformable polyline point highlighting fix
Import/Export:
RDfile properties can be hierarchized or flattened.
Data sgroup improvements in MRV import/export.
Bugfix in MRV export.
Bugfixes in MolImporter.
Bugfixes in Peptide import.
Bad EOL (End Of Line) characters in the output of the InChi export was fixed.
GUI:
Double-clicking at selection unselects selected atoms.
Bugfix in printing: Texts components covered each others on the printed view table.
Removed unnecessary confirmation dialog by closing viewer detached sketch frame.
Deleting problem of multiple is solved.
Corrected the wrong location of plus sign in reactions.
API:
MarvinPane.setEnabled(boolean) is implemented.
MViewPane.setDraggable(boolean) allows or denies drag operation in cells.
New property change event in MarvinView: selectedIndex
Molecule.draw is deprecated, use chemaxon.marvin.util.MPainterUtil instead of that.
New MarvinSketch applet parameter: buttonmenubar
Text Box improvements
Bugfixes:
Bugfixes:
Import/Export:
EMF/PDF creating does not drop HeadlessException in headless mode.
Fix EMF export bug (structure was invisible if canvas contained any text box).
Problem with both super atom and data sgroups in mol import.
ArrayIndexOutOfBoundsException in unique SMILES export.
Plugins:
In Tautomerization.
In Charge.
In pKa.
In PolarGroups.
Parity error during H removal.
GUI:
Fix endless loop by rings join.
Exception in custom amino acid loading is fixed.
API:
MarvinView drops events by opening/closing detached sketcher/viewer.
New methods: ConformerPlugin.getEnergy(), ConformerPlugin.getEnergy(int).
Plugins:
Bugfix in MSA calculation.
Acceptor count and donor count is displayed on the plugin result window.
Bugfix in Major Microspecies calculation.
Minor bugfixes in pKa calculation.
Improved canonical tautomer generation.
Fixing broken peptide snake.
Bugfix in peptide import/export
Fixing minor bugs in clean 3D
API:
Plugins:
New option added to conformer plugin to set the conformer diversity limit. API: setDiversity(double)
New option added to pKa plugin to handle the acid/base state depending on the submitted micro state. API: setpKaPrefix(int), getpKaValues(int, int)
MarvinSpace
Import/Export:
InChi import can load structures without AuxInfo.
PDB import:
multi model proteins
nucleic acid backbone
non-standard pdb file related changes (missing mandatory blocks etc.)
charmm pdb ATOm record support
new class for Water molecules
support for DOD and TIP3 water
recognition of water H (even when it's denoted by O)
H-O-H bonds
GUI:
Improved display performance for large structures.
Bugfix in 3D rotation: Front atoms did not follow mouse movement.
Atom/bond coloring bug for abbreviated groups is fixed.
CxSmiles conversion in Edit Source window is fixed.
Marvin applications uses user's home as default directory in the File Open dialog.
New methods in API: JMSketch.undo(), JMSketch.redo(), MSketchPane.undo() and MSketchPane.redo()
MarvinSpace 1.3.2:
Charmm grid support
Displaying bonds in water molecules
Secondary structure visualization of nucleic acids
Others:
Changes in MarvinSpace 1.3.1
Bugfixes:
Import/export:
In SMARTS import
In CxSmiles import/export
In 3D cleaning
Calculator plugins:
In pKa calculation
In logP calculation
in logD calculation
GUI:
Bugfix in pseudo atom display
Out of memory error by dearomatizing huge view tables
Minor bugs in loading/saving journal styles settings
Import/Export:
EMF export
Preliminary Mol2 import/export
Image export: atom and bond set colors, wire thickness, stick thickness ball radius, daylight down wedge, anybond style and atom mapping visibility can be specified.
Molecule and document properties with special data types (not only strings) are exported and imported in MRV, SDfiles and RDfiles . Supported data types: boolean, int, double, int[], Molecule, MDocument.
molconvert: optionally skips molecule on error and continues with the next molecule (option -g) (default: as before, exits on error).
R-groups:
the maximum R-group number is increased to 32767 (from 32), the minimum is decreased to 0 (from 1). R0-R32767 are saved in MRV and V3 Molfiles . In V2 Molfiles , only R1-R999 are saved. The values of following constants are changed: MolAtom.RGROUP_MAX =32767, RgMolecule.RG_ID_MASK, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH.
RgMolecule.indexOf(CNode), indexOf(CEdge), getNode(int) and getEdge(int) are applied to the graph union instead of the root structure.
GUI:
Integration of MarvinSketch and MarvinSpace:
3 Dimensional structure building: allows to modify ligand in the binding pocket.
Visualization of plugin results: 3D structure display, colored molecular surfaces.
Save options in viewer.
Viewer handles huge SD files.
Journal based drawing style templates
Multipage molecular documents
Plugins:
Plugins are grouped
Added OrbitalElectronegativityPlugin to Charge group
Added StereoisomerPlugin to Isomers group
Added ConformerPlugin and MolecularDynamicsPlugin to Conformation group
Added GeometryPlugin and MSAPlugin (3D molecular surface area calculation - methods: van der Waals, solvent accessible) to Geometry group
Improved calculation methods in several plugins (pKa, logP, logD, etc.)
Possibility to save multimolecular plugin results from GUI (e.g. conformers)
License handling: added graphical license handler interface
press the 'Manage license keys' button on the Edit / Preferences / Licenses tab, in MarvinSketch or MarvinView, or else
use the license command line script
MarvinSpace 1.3
Ribbon representation of protein secondary structure
Interactive editing of molecules/ligands in MarvinSketch
Copy/Cut/Paste, Drag&Drop functions
High resolution image export in various formats (PNG, BMP, Targa, JPG), arbitrary size
New coloring types: secondary structure, rainbow, b-factor (temperature factor), SETOR residue colors, color palettes
Interactive change of the isovalue of Gaussian Cube surfaces
Enhanced selection tools: binding pocket, residues etc.
Enhanced labels (colors, size, placement), more built in types (e.g. residue labels, secondary structure label)
Improved error handling, out of memory does not terminate
Progress bar, better feedback about processes
API changes:
Added Molecule.cloneMoleculeWithDocument(): clones the molecule with its non-molecular data (graphics objects: polylines, arrows; electron flows; text boxes).
Added Molecule.arrangeComponents(): avoids overlapping components (reaction components, R-group definitions) by translations.
Added MolImporter.skipRecord(), nextDoc(), getRecordCount(), getRecordCountMax(), estimateNumRecords(), seekRecord(int), isRewindable().
Sgroup.setGUIStateRecursively returns true if the state was changed.
CGraph became abstract, MoleculeGraph(parent) and Molecule(parent) constructors removed to avoid confusion with copy constructors.
The implementation of seeking in MolImporter required the extension of the molecule/document import interfaces:
MolImportIface.isSkippingSupported(), skipMol() and MDocumentImportIface.getGlobalProperties() must be implemented.
The implementation of the sticky midpoints of MPolylines required incompatible changes in the graphics classes:
MPoint.getX(), getY(), getZ(), setLocation(DPoint3) and setXYZ(double, double, double) are replaced by getLocation(CTransform3D) and setLocation(DPoint3, CTransform3D), MObject.calcCenter(DPoint3), transform(CTransform3D, int) and getPointRef(int) are replaced by by calcCenter(DPoint3, CTransform3D), transform(CTransform3D, int, CTransform3D) and getPointRef(int, CTransform3D).
Applet/bean parameter changes:
Deprecation:
bondWidth property/applet parameter is replaced by bondSpacing
RxnMolecule.getStructureCount, getStructure, addStructure, removeStructure methods are replaced by getComponentCount, getComponent, addComponent and removeComponent.
AWT applets have been removed from Marvin Applets package.
.NET support in Marvin Beans.
Bugfixes:
Bugfixes:
Import/Export:
Minor bugfixes in SMILES and in SMARTS import.
Atom value in molfile.
Bugfix in PDB import.
Fix RXN incompatibility in MDLCompressor and in MolImporter.
GUI:
Speed-up slow viewer/sketcher performance on very large structures.
Shortcut for clear screen.
Plugins:
MarvinSpace:
Import/Export:
Non-ASCII characters are escaped in MRV import/export.
SMILES fields can be separated with TAB separators.
Slow image export bug fixed.
Minor bugs fixed in CML import.
Bugfixes in PDB import. Note, that PDB import is no longer compatible with the original implementation which is still applied for XYZ files.
Bugfix in the SMILES import of aromatic bonds.
Minor CxSmiles import/export bug.
API:
Skin parameter/menu is denied in MViewPane and in MSketchPane. It is available ony in Marvin applets/applications.
Giving of the encoding in MolConverter was changed. Both input and output encoding can be specified.
GUI Bugfixes:
Link node drawing problem.
Copy from R-group definition did not work.
Last page of the view table was not printed if there were empty cells.
PropertyChangeEvent was not invoked when molecule was changed.
Down wedge looked like Up wedge on the toolbar.
Pseudo atom exception in sketcher.
Missing attachment point option in popup menu.
Right click raises exception for reactions with abbrev. groups.
Opening molfile with embedded groups caused exception.
Other Bugfixes:
Import/Export:
IUPAC InChi
MDL Molfiles, RGfiles etc.: Implicit H is stored as attached data when needed.
Improved PDB import.
Hydrogenize bug fixed: tetrahedral geometry of alcohol Oxygen atom is now maintained.
Volumetric data import/export for CUBE files (not processed by Marvin)
Implemented trivalent doublet and quartet. (RAD3_DOUBLET, RAD3_QUARTET)
Applets:
New methods: MSketch.getSelectedMol, MSketch.getMolMass, MSketch.getMolExactMass, MSketch.getMolFormula, MView.getMolMass, MView.getMolExactMass, MView.getMolFormula, JMSketch.getMolMass, JMSketch.getMolExactMass, JMSketch.getMolFormula, JMView.getMolMass, JMView.getMolExactMass, JMView.getMolFormula
New sketcher parameter: undetachByX.
MarvinSpace beta, includes public API:
Dynamic loading of JOGL libraries.
Better handling of PDB files including not standard complient variants.
Save graphic scene as PNG image file.
Basic Gaussian Cube file support.
Improved User Interface.
Bugfixes.
Plugin:
New parameter in ResonancePlugin: take major contributors (-m, --mcontrib).
New parameter in TautomerizationPlugin: take dominant tautomers (--d, --dominants).
Bugfix in TautomerizationPlugin.
Sgroup names can contain almost any ascii character.
Bugfixes:
Trivalent radicals are displayed and their MRV import is fixed.
Bugfixes in cxsmiles, in 2D cleaning and in parity calculation.
MarvinSpace 1.0-alpha is released as part of Marvin 4.0.
MarvinSpace is a 3D molecular structure visualization tool for displaying macromolecules, protein-ligand complexes as well as small molecules.
Release notes: At present MarvinSpace is available as standalone desktop application and as Java Applet. Java Beans and the public API will be released later.
Import/export
Link node outer bonds imported and exported in CML, MRV and MDL.
MRV: atom and bond set colors are stored, animation of a chemical process can be stored. Parity is stored in 0D.
CML: MRV tags and attributes are no longer supported but they can be imported. If you have a CML document that is created by an older Marvin, it is recommended to save that in MRV format!
RDfiles with missing "M END"s are also imported.
MS BMP image format (only export).
SDF import: reading sdf-s containing empty structures
Atom types are read in case insensitive manner in mol/sdf import.
cxsmiles import/export: Pseudo atom types
SMILES import/export: Handling of radicals and unusual valences
Support for localized encoding of structure files.
Double bond with a wiggly bond neighbour are treated as unspecified E/Z configuration.
Improved unique smiles canonicalization
Improvements in chirality calculation
Clean wedges function
GUI:
New templates in MarvinSketch: Aromatics, Bridged Polycycles, Bicycles, Crown Ethers, Cycloalkanes, Fullerenes
My Templates are available in the MarvinSketch applet (only in Swing).
Wrap long data fields in MarvinView
Shortcut + SHIFT click: automatically ungroup abbreviated groups
View implied lone pairs
Improved rendering quality
Attach data to atoms (Data S-groups)
Drawing of h<n>, D<n>, s<n>, s, rb<n>, rb, u query properties
Plugins
Calculator plugin handling is completely rewritten:
Dynamical loading of plugins and parameter panels based on configuration by PluginFactory
Separated graphical plugin result display: CalculatorPluginDisplay
Graphical parameter panels are generated from XML: <plugin class name>Parameters.xml if exists, otherwise asked from the display class: CalculatorPluginDisplay.getParameterPanel()
Configuration files calc.properties (Calculator) and plugins.properties (MarvinSketch, MarvinView) together with the parameter panel configuration XMLs and custom plugin JARs are placed in the xjars directory under Marvin root.
CalculatorOutput used by Calculator is renamed: CalculatorPluginOutput (and subclasses are found automatically by the following naming convention: output class name = <plugin class name>Output)
CalculatorPlugin API is slightly changed.
A custom plugin example with test application is added.
Added MRV result molecule output to cxcalc.
Added options JPEG / PNG image save and copy & paste image to chart result display in MarvinSketch / MarvinView.
Changes in specific plugin calculations:
Added IsoelectricPointPlugin.
Added TautomerizationPlugin and ResonancePlugin.
Added microspecies distribution calculation (msdistr) to cxcalc.
New topological properties in TopologyAnalyser and TopologyAnalyserPlugin:
asymmetricAtomCount(), balabanIndex(), carboRingCount(), carboaromaticRingCount(), cyclomaticNumber(), distanceCount(int atom, int distance), distanceDegree(int atom), eccentricity(int atom), hararyIndex(), hyperWienerIndex(), isAsymmetricAtom(), isConnected(), isConnected(int atom1, int atom2), plattIndex(), randicIndex(), shortestPath(int atom1, int atom2), stericEffectIndex(), szegedIndex(), wienerIndex(), wienerPolarity().
API
PeriodicSystem: new radius functions getAtomicRadius(int z), getCovalentRadius(int z), getVanDerWaalsRadius(int z).
MSketchPane: new methods isCloseEnabled(), setCloseEnabled(boolean), getMrvWithSettings(), setMrvWithSettings(String), getImage(scale), getImage(size), getBoundRectSize().
MoleculeGraph.getLocalParity(int) to calculate local parity of an atom
Incompatible API changes:
Improved aromatization
Svg export gives UTF-8 encoded output.
Bugfixes:
R/S and canonical smiles calculation speedup.
3D:
Improved 3D cleaning efficiency.
New Clean3D options. Time limit in the 3D cleaning process.
Bugfixes:
Plugins: logP calculation is supplemented with metal fragments.
Bugfixes:
Smarts import: atom expressions of type [C,c] are imported as [#6].
Colored MarvinView labels at celular level
Bugfixes:
Extended SMILES export: d option to write C/T info for ring double bonds.
API:
Plugins:
TopologyAnalyserPlugin is available: calculates molecule properties from topology like number of various ring types, rotatable bonds.
Calculation of molecular polarizability is available in PolarizabilityPlugin.
Improved pKa and logP predictions.Test Results
Added calculation of aromatic system and aromatic ring total charges in ChargePlugin.
Import/export:
Link nodes are imported and exported in MDL molfiles and MRV/CML. See also the related API changes.
MDL Molfiles:
Usg import option to ungroup all S-groups.
Atom coordinates are not rescaled in 2D V2 molfiles if the b import/export option is used with 0 argument.
MdlCompressor can compress Rxnfiles.
SMARTS import: d option for Daylight-conform meaning of "H". Importing ambiguous SMARTS gets a warning message when not using this option.
MRV (Marvin Document) and CML:
reaction arrow type is stored (default, resonance, retrosynthetic or equilibrium), see also the API changes.
valence is imported and exported
Image export:
Options for displaying chiral structures.
Automatic generation of atom coordinates for 0D molecules.
API:
New methods and functions:
MolAtom methods related to link nodes: getMaxRepetitions(), setMaxRepetitions(int), getMinRepetitions(), setMinRepetitions(int), isLinkNode().
RxnMolecule methods for accessing reaction arrow type: getReactionArrowType(), getReactionArrowTypeName(), setReactionArrowType(int), setReactionArrowType(String).
MSketch, JMSketch, MView and JMView applet methods
for accessing molecule properties: getMolProperty(String), setMolProperty(String, String), getMolPropertyCount(), getMolPropertyKey(int), getMProperty(int, String), setMProperty(int, String, String), getMPropertyCount(int), getMPropertyKey(int, int),
for accessing extra atom label and alias strings: setAtomAlias(int, String), getAtomAlias(int), setAtomExtraLabel(), getAtomExtraLabel(int), setAtomAlias(int, int, String), getAtomAlias(int, int), setAtomExtraLabel(int, int, String), getAtomExtraLabel(int, int).
Added JavaScript functions in marvin.js to get JVM and GUI ("awt" or "swing"): marvin_get_jvm() and marvin_get_gui().
Changes:
Valence is not a query property any more, use MolAtom.setValenceProp(v) and getValenceProp() instead of setQProp("v", v) and getQPropAsInt("v").
The simpView applet parameter and MSketchPane.setSimpView(int) are deprecated, the simpView = 2 setting is removed. Use bondDraggedAlong and MSketchPane.setBondDraggedAlong(boolean) instead.
Serialization: DPoint3 and CTransform3D became Externalizable.
New applet parameter: molChanged0 to evaluate a JavaScript code when the molecule is loaded.
Bugfixes: NullPointerException in shapely color mode, deadlock in MarvinSketch applet.
Reaction AutoMapper class API is available.
Calculator Plugin API usage examples in class headers.
Atom symbol/label font can be changed using the atomFont applet parameter.
Import/Export
New formats: ChemAxon Extended SMILES and SMARTS, Gaussian Cube.
Full support of SMARTS. Added features:
Recursive SMARTS $()
Logical expressions in atom and bond: high and low priority "and"(& and ;), "or" (,) and "not" (!).
Degree atom query property (D)
Implicit hydrogens atom query property (h)
Chiral or unspecified atoms @?, @@?
Ring bond query property (@)
Conditional directional bonds: /?,\?
CML and Marvin Document Format fix: atom aliases and query strings are imported and exported.
MDL Molfiles: S-group parent list (M SPL in V2, PARENT in V3) and expansion information (M SDS EXP in V2, ESTATE in V3) are stored.
Incompatible API change in the MolImportIface interface: molecule import modules must implement the createMol() method.
MolConverter and MolExporter fix: created text files are in the local text format (instead of unix) if the useSysEOL boolean argument is true. The molconvert program writes OS dependent end of lines always.
S-groups
Embedded S-group support (in MDL Molfiles and Marvin Document Format).
API changes in Sgroup, SuperatomSgroup, and MultipleSgroup: the copy and the newInstance methods are replaced by copy constructors and cloneSgroup.
Other
MDL Molfile import: S-groups are contracted by default. Importing in expanded form; use the Xsg option.
Abbreviated groups: Abbreviations are given a priority over the element symbols. New abbreviations in the default abbeviated group list.
Improved p K a, log P , log D calculation.
New methods in MolPrinter: getChiralitySupport(), getExplicitH(), isAtomSymbolsVisible(), isEzVisible(), setAtomSymbolsVisible(), setChiralitySupport(), setExplicitH(), setEzVisible().
Marvin Applets: Workaround for browsers without Java - JavaScript communication.
Mac friendly shortcuts for Cut, Copy and Paste.
Bugfixes:
Mac OS X: MarvinSketch and MarvinView applications use the screen menu bar.
Atom and bond sets
Colorable bond sets are introduced, see the bondSet and bondSetColor applet parameters, the MView.setBondSetColor() applet method and the MarvinPane.setBondSetColor() bean method.
Atom and bond set coloring can be used together with other color schemes. Atoms and bonds in set 0 are displayed in Monochrome, CPK, Shapely or Group color scheme, but other sets are displayed with atom/bond set colors if the value of the setColoringEnabled applet parameter is true (default).
Deprecation:
Use the atomSet applet parameter instead of set, atomSetColor instead of setColor and the MView.setAtomSetColor() and MarvinPane.setBondSetColor() methods instead of setSetColor.
Use colorScheme="mono" and setColoringEnabled=true settings instead of the deprecated "atomset" color scheme.
Import/export:
Marvin Document file format
Multiple Sgroup support for MDL molfiles
New image export option to switch off antialiasing: noantialias.
CML improvements: support of CML2 atom/bond attributes (instead of the deprecated builtins), reactions, stereochemistry, residues. Because of efficiency reasons, deprecated CML-1 data types are not supported any more.
Base64 encoding/decoding.
Import options for input files are specified in braces instead of parentheses ("file{options}") to avoid conflicts with ugly SMILES strings ending with a branch specification. For backward compatibility, parentheses still work after filenames (but not after SMILES strings).
3D:
Document editing with graphics objects in sketcher
Calculator plugins
Support electrolite concentration is taken into account in log P and log D calculations.
Concentration of K, Na and Cl ions can be adjusted in the range of 0 - 0.25 mol/l.
log P calculation of zwitterionic compounds also have been improved with considering distance correction factors.
p K a calculation have been extended to carbon-bases. Now basic p K a estimation of Indole derivatives available. Both acidic and basic p K a values are displayed. Microspecies distribution is shown on chart.
Accuracy of p K a calculations is improved for heterocyclic compounds.
Calculation of polar surface area (PSA) based on 2D topological (TPSA) information of molecules are available.
Others:
Recognition of more than four hundred chemical abbreviations.
Help documents can be specified by applet parameters: sketchHelp, sketchQuickHelp, viewHelp, viewQuickHelp.
Molecule.draw paints the molecule to a graphics context.
Standard residue names returned by MolAtom.residueSymbolOf(int) are not all upper case, only the first letter ("Ala" instead of "ALA").
Marvin GUI: Set the visibility of the atom chirality ( R / S ) labels from View/Misc menu.
Double click in Windows operating systems opens chemical files with the MarvinView application.
Deprecation: SketchMolecule (replaced by MDocument), SuperAtom.updateSgroupCrossings() (replaced by Sgroup.findCrossingBonds())
Incompatible change: chemaxon.struc.sgroup.Contractable interface removed, Expandable changed. This change was required because MDL's incomplete multiple group expansion had to be simulated for proper molfile export.
Bugfixes: in MViewPanel.setParams, in Dreiding forcefield, PDB import, atom lists in V3 molfiles, resize of MViewPanel and MSketchPanel, R-logic, etc.
Enhanced stereochemical representation support in extended molfiles.
Improved Charge and pKa calculation.
Bugfixes:
RDfiles containing internal and external regnos: the first molecule or reaction type property is supposed to be the main structure.
API changes
Calculator plugins:
Molecule file formats:
Extended reaction files: AGENTS are imported and exported (in a non-standard way, because MDL's standard format does not support them).
SMILES import: error checking improved.
PDB import/export: bonds of standard residues are not exported and not guessed from coordinates at import. Full atom names (including remoteness indicator and branch designator) are imported and exported.
2D and 3D:
MDL import/export improvements:
Extended reaction file import/export ("rxn:V3").
Rgroups are supported in extended molfile import/export.
RDfiles: Molecule and reaction type properties ($MFMT and $RFMT) are also imported and exported. Use the Molecule.getPropertyObject function to get such properties.
S-groups: automatic contraction after import in sketcher and viewer.
API changes:
Applets
Java 1.0 compatibility is no longer maintained. The minimum Java VM version required to run the applets is 1.1 (Netscape 4.06, MSIE 4 or later version) .
The Swing version of the unsigned applets are no longer available. Use the signed applets instead. To unsign signed jar files, see the FAQ.
The deprecated installer for Marvin Applets is no longer maintained. The set of downloadable Marvin Applets packages has been reduced.
Plugins:
New plugin: Atom polarizability
Chart display in log D plugin
Molecule import/export improvements:
SMILES:
Data fields can be imported from multi-column files.
Better error checking at import: exception is thrown if a ring is formed from two neighboring atoms.
PDB: residues are imported as Sgroups, Sgroups are exported as residues.
Molfiles:
Sgroups are also imported as (PDB) residues. As a consequence, the PDB-specific coloring styles, "shapely" and "group", are also applicable to molfiles containing Sgroups.
Extended (V3) molfile export.
Changes in V2 format:
3D molecule coordinates are stored in Angstrom units. The unit can be specified as an import option.
Illegal atom map values (from molfiles generated by the IDBS ChemXtra data cartridge) are not considered to be error at import.
API changes
New RgMolecule method: RgMolecule.addRgroupsTo.
New flag RxnMolecule.RGROUPED for the getStructure(flags, f) method.
New methods related to explicit Hydrogen removal: MoleculeGraph.calcDehydrogenizedGrinv, implicitizeHydrogens, MolAtom.isImplicitizableH.
The protected removeNode(..., boolean changeNodes) and removeEdge(..., boolean changeNodes) methods in CGraph, MoleculeGraph, Molecule, etc. are replaced by removeNode(int i, int cleanupFlags), removeNode(CNode node, int cleanupFlags), removeEdge(int i, int cleanupFlags), removeEdge(CEdge edge, int cleanupFlags).
Removed the malfunctioning RxnMolecule(parent) and RgMolecule(parent) constructors.
RGfile import/export: root structure can be a reaction.
Note that mixing RGfiles and Rxnfiles is not possible in a standard way so these files can only be imported by Marvin.
PDB import: HETATM records are recognized.
Bugfixes: Invisible atom symbols at image export in Molecule.toObject(String), Sgroup export in MDL formats, Sgroup-related NullPointerException in viewer.
3D cleaning.
New applet paremeters and bean properties
detachable paremeter in the viewer.
atomSymbolsVisible parameter instead of labels which became deprecated.
API improvements and simplifications:
chemaxon.struc:
CGraph and Molecule are not thread safe any more but their methods became 20-30% faster.
Created the SelectionMolecule class for molecule selections, removed the CGraph.selection field.
Created the MoleculeGraph class as the direct ancestor of SelectionMolecule and Molecule.
RgMolecule and RxnMolecule changes:
Nodes and edges are only stored in subgraphs (root structure, R-groups, product/reactant/agent structures).
The graph union is returned by the MoleculeGraph.getGraphUnion() method.
Methods like getNodeCount(), getEdgeCount(), getNode(i), getEdge(i) call the root structure's corresponding method in RgMolecule or the graph union's method in RxnMolecule.
CGraph.findFrags() and CGraph.findFrags(boolean) are replaced by CGraph.findFrags(Class) and Molecule.findFrags()
CGraph.cloneNodes() and cloneEdges() renamed to getNodeVector, getEdgeVector.
CGraph.reallyContains(CEdge) and countRealEdges() removed.
CGraph.getSSSR() returns an int[][] array instead of CEdge[][]
The MolAtom.flags, MolAtom.countFlags and MolBond.flags fields became private.
Molecule import/export:
MolExportModule.convert(Molecule) and close() throw MolExportException instead of IOException.
MolImporter.read() and importMol(byte[]) returns RgMolecule object only if R-groups are present.
Initialization file saving:
MarvinSketch and MarvinView has a common initialization file in the $HOME/.chemaxon subdirectory.
MarvinPane.saveIni(), loadIni(), getIniFile() and setIniFile() are removed and replaced by UserSettings.save(String), UserSettings.tryToLoad(), and DotfileUtil.setDotDirName(String).
Other bean related changes
Buttons and checkboxes in molecule cells can fire java.awt.event.ActionEvent s and java.awt.event.ItemEvent s as javax.swing.AbstractButton objects.
MViewPane.getCanvasComponent is deprecated. Use MViewPane.getVisibleCellComponent.
Template button title is specified using the abbreviation SDF property instead of title .
atomMappingVisible is a new applet/bean parameter and property.
Bugfixes: Copy and Copy as smiles bugs under Mac. Hotkey bug in swing version of Marvin applets at Java 1.4.
skin applet/bean parameter and new menu option (only in SWING).
Improved SD file import (DTn fields).
Bugfix: NoSuchMethodError at drawing R-group definition in AWT mode (if Java version is earlier than 1.2).
Bugfixes:
Molweight calculation.
Handling agents of reactions.
Signed Marvin applets
Marvin applications with Java Web Start
New applet/bean parameters
Import/Export
CML import and better export.
Atom map support for Rxnfiles and reaction SMILES.
Atom label font size and double bond width can be set for image export using the atsiz and bondw options.
If an error occurs while reading a multi-molecule file (an SDfile for example), the remaining parts of the current molecule can be skipped and the file pointer can be positioned to the next one.
MolImportIface interface changed, the skipToNext() method introduced
MolImporter.skipToNext()
Stereochemistry
chiralitySupport applet/bean parameter
ezVisible applet/bean parameter
Other new applet/bean parameters and properties
popupMenusEnabled bean property
atomNumbersVisible applet/bean parameter
Other API changes
The MolAtom.SELECTED and VALENCE_ERROR constants are not public any more, they are replaced by the isSelected, setSelected, hasValenceError and setValenceError methods.
deprecated methods removed: MolAtom.getAbbrev() and abbrevOf() replaced by getSymbol() and symbolOf()
CNode.copy(CNode), MolAtom.copy(CNode) does not copy the edges, CNode.clone() became abstract, MolAtom.clone() does not clone the edges.
Fixed: memory leak and printing problems with Java Plugin, atom lists in molfile, bugs during reaction drawing, MarvinView stdin reading, etc.
SMARTS improvements: "a" (aromatic) and "A" (aliphatic) atom primitives recognized even outside of brackets, ":" (aromatic bond) symbol recognized at file format recognition.
New importConv option (c) to automatically clean up the molecule.
Image export improvements
scale option
getImageSize method
bondWidth applet parameter and setBondWidth bean method.
API changes
Molecule.toFormat, toBinFormat, toObject, MolExportModule.open and MolExportModule.parseOption throw IllegalArgumentException instead of IOException if bad format string was specified
"mag" property renamed to "scale", setMag, getMag, maxMag methods became deprecated (MSketchPane, MSketch, JMSketch, MolPrinter) and replaced by setScale, getScale, maxScale
Fixed: delayed printing, image export option parsing, cml:A, etc.
Extra templates can be specified using the xtmpls parameter.
New importConv option (H) to add/remove explicit Hydrogen atoms.
Common aromatization and explicit Hydrogen addition/removal options for molecule export modules: a, +a, -a, H, +H, -H
Incompatibilities:
Image export:
Scalable Vector Graphics (svg) format.
Implicit Hydrogen display options can be specified for the MolConverter utility and the toObject and toBinFormat methods.
MViewPane.applyRotationMatrix, applyRotationMatrixes: methods to apply the viewing transformation on the atomic coordinates appearing in the molfile
MView applet: atom sets can be selected for different coloring, using the set N . M parameters.
MolPanel changes:
SketchPanel improvements:
New applet and bean methods:
getTabScale(i) to query the magnification in a cell
getBestTabScale(i) to query the best magnification value for a cell
getBestTabScale() to query the smallest best scale value
MViewPane bean only:
MarvinView improvements
JavaScript code can be called at image click in the applet using the "js: javascript " syntax.
Use tabScale to set the magnification in the molecule cells (instead of automatic scaling), use winScale to set the magnification in the zoom windows (same as the old mag parameter).
Many molecules in one cell. Molecules coming from multi-molecule files are merged into one molecule object containing atom sets if MULTISET is specified as the first import option in the mol parameter. To display only the specified sets, use the showSets applet parameter, the MView.setSetVisible() applet method or the MarvinPane.setInvisibleSets bean method.
Atom set colors can be changed using the setColor applet parameters, the MView.setSetColor() applet method or the MarvinPane.setSetColor() bean method.
"Shapely" and "Group" color schemes (for PDB input).
Class library changes
MULTISET can also be passed to the MolImporter constructor through the option string
The newInstance() method of CGraph, Molecule, etc. became public.
PDB
Rxnfile, RDfile and Reaction SMILES import/export
Molecule.getComment() and setComment() methods
New MarvinSketch applet parameter and bean methods: reactionSupport, getReactionSupport(), setReactionSupport().
MolExportModule API changed: the open method has a return value
Beans:
List of properties to save/load to/from the initialization file (~/.mview, ~/.msketch) can be set using the setIniProps method.
Beans can be used in applets that cannot access to disk files:
Ini file is not loaded automatically, only when sketchPane.loadIni() or viewPane.loadIni() is called.
Ini file is not saved automatically, only if the value of the saveIniEnabled property is true.
The dispopts applet parameter is deprecated, use implicitH, explicitH or navmode instead.
New bean methods and applet parameters for customizing 3D rendering: stickThickness, ballRadius.
java.awt.Image objects can be created from molecules using mol.toObject("image");
API for import module creation (MolImportIface).
Import file format can be specified, by writing "filename(format:)" or "filename(format:options)" in the mol applet parameter, or in the command line of molconvert, msketch or mview.
MSketchPane: setMol(File, String) method added, where string can contain the import options, in one of the following forms: "format:options", "format:", "options". The old setMol(File) method removed. MViewPane: setM(int, File, String) added.
MolExportModule.sbuf field renamed to stringBuffer.
MolAtom.getAbbrev() and abbrevOf are deprecated, use getSymbol() and symbolOf() instead.
New 3D rendering mode: sticks.
Display quality can be controlled with an applet parameter.
Molecule import/export:
New XYZ import options: bond length cut-off (f...) and maximum number of connections (C4,H1,Cl1)
Automatic dearomatization after molecule loading.
All export modules recognize the "a", "+a" (aromatize) and "-a" (dearomatize) options. Example: "smiles:a"
Class library, beans
Molecule.aromatize()
Bugfix: MViewPane.getCellCount() returns the total number of cells, not just the number of visible cells.
PropertyChangeEvents generated when the molecule is changed in the sketcher or viewer component.
Event handling fix: PropertyChangeEvent source is the the bean component, not the internal SketchPanel or ViewPanel.
New rendering style: "ball & stick".
Class library, beans:
New image export options: rendering style and color scheme.
Image export options must be separated by commas in format descriptor strings.
Molecule.toBinFormat method to convert molecules into binary formats such as JPEG/PNG/PPM.
The type of the rendering, colorScheme, implicitH, downWedge, navmode properties in PropertyChange events is String just like the argument type of their set methods. (Previously, the two types did not match.)
Binary export formats: GZIP, JPEG, PNG, PPM
User defined export module creation by overriding chemaxon/marvin/util/MolExportModule.
Text field (T) component for MView tables.
cacheMols applet parameter for caching loaded molecules.
loadMols applet parameter for preloading molecules.
File formats
New: XYZ import
New: Extended Molfile (V3.0) import.
CML export options changed, cml:1 -> cml, cml:0 -> cml:A, cml:A writes three coordinates for each atom even if the molecule is 2D (so Jmol can read the file)
MView applet:
Animated XYZ files can be displayed
New parameters: animFPS, animDelay, animSync.
MarvinSketch Applet/Bean:
New: File/New menu item in the bean. If your application using the bean has a File/New Window menu item, then File/New should be moved to File/New/Clear current, and File/New Window should be moved to File/New/New Window. See the MarvinSketch application source (marvinbeans/examples/sketch/chemaxon/marvin/Sketch.java) for details.
"Visual fragment placement" can be disabled: use the simpView parameter or the View/Misc/Object in Hand option if you do not like to see what you are doing.
Bond length related changes.
Class library:
Changes related to atomic coordinates and transformations
New: CTransform3D class for general 3D transformations (like in Java3D)
Molecule.rot(...), tra(...), magnify(...) removed, use transform(CTransform3D T) instead
Atom coordinates became absolute
Molecule.getO() and setO() replaced by getLocation() and setLocation()
Molecule.getCenter() renamed to calcCenter(), and it calculates center of mass instead of geometrical center
New: Molecule.moveTo(location)
CGraph.indexOf changes
Splitted into two methods, indexOf(CNode atom) and indexOf(CEdge bond)
Speed improvement. CNode and CEdge has an index field that contains the object's index in its parent graph. Calling the parent graph's indexOf method returns the value of this field. The index is only searched (in the old way) when the CGraph is not the direct parent.
Valence rules
New: MolAtom.ionChargeOf(Z)
MolAtom.negoxOf(Z, boolean) removed, negOxOf(Z), posOxOf(Z) created instead
SDF properties
"name" and "informat" are no longer stored in the properties hashtable, they became fields of Molecule
Molecule.getProperties() removed
Molecule.clearForImport() -> clearForImport(name)
New methods in Molecule: getName, setName, getInputFormat, setInputFormat, getPropertyCount(), getPropertyKey(n), getPropertyKeys()
Bond length related changes.
API simplification: internal bond length of Marvin fixed to be MolBond.CCLENGTH
bondlen, rescaling applet/bean parameters, setBondlen, getBondlen, setRescaling, getRescaling methods removed, use MSketch.getMol("mol:b=XXX") instead of
The bondlen argument of Molecule.clean(dim, bondlen, opts) removed, use clean(dim, opts)
MolBond.DEFAULT_LENGTH renamed to MolBond.CCLENGTH
MolBond.getDesiredLengthRatio() removed, use the new dimension dependent Molecule.getDesiredLength(bond) method instead
MolAtom.covalentRadiusOf(Z) -> covalentRadiusOf(Z, bondOrder)
The "style" applet parameter renamed to " rendering because of a conflict with a Netscape keyword. The getStyle, setStyle methods of the beans are also renamed to getRendering, setRendering.
New rendering style: "Wireframe with Knobs".
Atoms can be highlighted in the MView/JMView applets by specifying a selection.
All query atoms and extra bond types can be enabled by omitting the queryAtoms , atomStrings , and extraBonds parameters.
"Cis or Unspecified" and "Trans or Unspecified" bond types; "ctu" in extraBonds .
Cleaning options can be specified using the cleanOpts applet parameter.
Optional down wedge bond orientation (MDL or Daylight) using the downWedge parameter.
New MView/JMView applet methods:
getAtomCount(moleculeIndex) to query the number of atoms in a molecule cell
isSelected(moleculeIndex, atomIndex) to query whether the specified atom is selected or not
selectAtom(moleculeIndex, atomIndex, select) to (un)select an atom
selectAllAtoms(moleculeIndex, select) to (un)select all atoms
Real scrolling in MView!
The applet is scrollable if visibleRows is less than rows or visibleCols is less than cols.
The names of the layout i and param i parameters changed to layout and param for the molecule cells, layoutH and paramH for the optional header.
The scroll parameter ceased to exist.
Class library:
RgMolecule for R-groups
Thread safe API for molecules
New methods in CGraph: getCtab(), getBtab(), fragments(), findFrag(), getFragIds(), getLock(), getParent(), etc.
New methods in CNode: getLigand(i), getEdge(i), getEdgeCount()
CNode.findFrag() and CGraph.fuseFrag() removed
CGraph.getEdge(i), CGraph.getNode(i), Molecule.getAtomArray() created; CGraph.getEdges(), CGraph.getNodes(), Molecule.getAtoms(), Molecule.getBonds() removed
Molecule.reuseAtom(Z, i) and Molecule.endReuse(na) created, MolAtom.reuse(Z, mol, i) removed
The two-argument MolAtom.setCharge method removed. Instead of a.setCharge(charge, false), use a.setCharge(charge); a.setFlags(0, MolAtom.FIX_CHARGE);
SMILES import
Class library:
CGraph.fuseFrag(CNode a) has only one argument.
CGraph.removeNode and removeEdge instead of remove and removeRef; removeEdge leaves edge.node1 and edge.node2 unchanged (they were set to null in removeRef).
MolBond.setFlags(int flags, int mask) method introduced.
Stereochemistry: double bonds can also be UP/DOWN (not just CIS/TRANS); CIS and TRANS information can also be stored (not just EITHER). The MolBond.getStereo and setStereo methods and the UP, DOWN, EITHER constants ceased to exists, the STEREO1_UP, STEREO1_DOWN, STEREO1_EITHER, STEREO2_CIS, STEREO2_TRANS, STEREO2_EITHER, STEREO_CARE flags introduced instead.
MolBond.getTopology/setTopology ceased to exist, the TOPOLOGY_RING, TOPOLOGY_CHAIN flags introduced instead.
Structures are colorful by default. Colorization can be disabled by setting colors=mono, both in the sketcher and the viewer.
Spacefill rendering can be enabled instead of wireframe by using the style parameter.
Atom labels can be hidden with the labels parameter.
Up/down and cis/trans either bonds
Classes in chemaxon/beans moved to chemaxon/marvin/beans. The MarvinSketch bean is chemaxon.marvin.beans.MSketchPane, the MarvinView bean is chemaxon.marvin.beans.MViewPane.
The basic applet tag for MSketch and MView is simplified, and also generalized to work with or without Oracle's Java Plugin.
New file format: PDB (for simple, non-macro molecules)
Changes in template handling
The four template sets that come with Marvin became default. Templates only have to be specified as applet parameter if you need a different template set.
Templates moved to directory chemaxon/marvin/templates/ (from templates/).
File extension changed to .t (from .cssdf).
This change was required because of a Netscape restriction related to the loading of JAR file resources.
The JAR files marvin.jar and jmarvin.jar contain chemaxon/marvin/templates/generic.t, so the firewall problem ceased for the generic template set.
If needed, the additional templates may also be put into the JARs by the user with the JAR utility (part of Oracle's JDK). However, doing this increases the JAR size with a noticable amount.
The MolImport module moved into marvin.jar because of the firewall problem.
New query bond types: "single or double", "single or aromatic", "double or aromatic", "chain" and "ring".
SMARTS export handles the heteroatom (Q in molfile) type intelligently.
The heteroatom and the any atom types are specified in the queryAtoms parameter. The anyatom parameter became deprecated but is still present for backward compatibility, with slightly changed behavior. Specifying anyatom with any value (empty string also) is equivalent to specifying "any,hetero" in queryAtoms.
Cell selection in MarvinView can be controlled using the selectable parameter.
New methods in MarvinSketch: getBondlen. getMag, getPiece, getRescaling. New method in MarvinView: setSelectedIndex, The setDispopts method ceased to exist. Display options can be set using the dispopts applet parameter only.
In Marvin 2.2 and later, the Java classes come only in packaged forms: marvin.jar and marvin.zip. It means that support is ceased for those archaic Java-compatible browsers that cannot handle the ARCHIVE option in the applet tag (Netscape 2 and MS Explorer 3). Reasons:
Under certain circumstances, some Netscape versions try to load the class files one by one instead of using marvin.jar. The simplest way to keep Netscape from doing so is to remove the class files.
Most of our users don't understand what ARCHIVE is, and don't use it properly. The consequence is a significantly increased download time.
From now, a missing ARCHIVE option cannot be left unnoticed, because Marvin will simply not run. Much better than turning your user's hair gray.
Marvin is rarely tested in the oldest (and buggiest) browsers.
If you are absolutely sure that you want your Marvin page work with Netscape 2 and MS Explorer 3 too, you must unpack marvin.zip manually. However, we do not recommend this, because you will probably do something wrong. For example, once you will upgrade Marvin and forget to unpack the new marvin.zip. Mixing two different versions will result in malfunction.
Molecules in MarvinView are only editable if the editable applet parameter is set.
CML (XML) export.
The getSelectedIndex() method in MarvinView.
Default value of the rescaling parameter in MarvinSketch is changed to "mag" because generally this value is the most useful.
The MarvinView-only package ceased to exist, the new Edit/Structure function made it irrelevant.
Templates in MarvinSketch: From now on templates are stored in SDfiles (.sdf) or compressed SDfiles (.cssdf). The template file can be optionally compressed with GZIP, but the applet will only work in Java 1.1 compatible browsers in that case. The tmplmol, tmplpar, and ntmpls parameters no longer exist and are replaced by the much more easy to use tmpls parameters. The unit rotation angle can be specified as a new Marvin-specific property M MRV PHI in the template molecule files (instead of the tmplpar parameters).
Applet tags changed: Rewrite your applet tags according to the last solution in MarvinSketch Example 1 . This applet tag can load the AWT and the Swing applets as well.
Note that the file &{marvinjar}; is not packaged now (its name caused too many problems), so you must rewrite your applet tags, otherwise the download time with MS Explorer will not be optimal.
New in MarvinSketch: The menubar parameter enables or disables the menu bar in the Swing sketcher.
New in MarvinView: Molecules start rotating in 3D automatically if you set the animate parameter in MarvinView.
New in MarvinView:Border between cells in molecule tables.
Change in MarvinView: From now the colors can be specified in the same way as in MarvinSketch. Molecule background is molbg, normal table background is bgcolor. (Previously, bgcolor was also the molecule background.)
JavaScripter applet ceased to exist.
Its functionality is moved into a MarvinView module that is automatically loaded at the first js: action.
In the past, JavaScripter was required because scripting applets are not cached by older browsers (namely Netscape 3). An applet that has the MAYSCRIPT attribute is loaded from the net for each page that contains it. In Netscape 4 and later, there is no such problem. On the other hand, a bug (or feature?) in Netscape 4.6 makes the use of JavaScripter impossible as a separate applet. That's why we merged the two applets now.
New: Three new molecule file formats: "sybyl" (the SybylImport and SybylExport modules), "xyz" ( XyzExport ), and "pov" ( PovExport ).
New and changed: The "implicitH" option in the dispopts applet parameter instead of the showH parameter which ceased to exist.
"off" -> "implicitH=off"
"term" -> "implicitH=heteroterm" (because "term" ceased to exist)
"hetero" -> "implicitH=hetero"
"heteroterm" -> "implicitH=heteroterm" (default)
"all" -> "implicitH=all"
New features: if you want the explicit H atoms to be invisible, use "explicitH=off" (default: "all").
If you have 3D molecules, use "dim=3" for MarvinView, to let him know that you want 3D rotation as the default mouse drag action.
New: The atomStrings parameter enables the usage of atom aliases and SMARTS strings in the sketcher.
Incompatible change: The setAtoms, setNoatoms, setNobonds methods, and the atoms, noatoms, nobonds applet parameters ceased to exist and replaced by elements , anyatom, queryAtoms , and extraBonds .
New: The new detach parameter makes it possible to detach the sketcher from the web page immediately when the applet is loaded.
Recommended: In molfiles and compressed molfiles written directly in HTML, you should end all the molfile lines with backslash and also a real newline character like here:
...
000Wun+V70\
iuzV000W60\
iuzVGS2W60\
K72WGS2W60\
...Omitting the real newlines like in "000Wun+V70\iuzV000W60\iuzVGS2W60\K72WGS2W60\", seemed to be safe so far, while the Marvin applets were tested only in Oracle, Netscape, Symantec, and Microsoft JVM's. The reason for discontinuing this practice is that the AppletViewer in Kaffe 1.0b3 has problems if you write more than one molfile lines in one HTML line.
Removed: Backward compatibility with the old style (1.0-1.1) usage of getMol() and getM() removed. It didn't work with MSIE anyway.
Incompatible change: MSketch.getMol(x) and MView.getM(n,x).
In Marvin 1.1.4 and before, x was a boolean variable specifying the format of the generated molfile: MDL mol (false) or compressed mol (true).
From version 1.2, x is a format descriptor string to ease the introduction of new molecule file formats as Marvin evolves. MDL molfile format is denoted by the string "mol", compressed mol is "csmol", SMILES is "smiles".
New: The preload applet parameter.
"Extra features" are planned to be available as external modules in future releases of Marvin. External modules are downloaded only when needed. In Marvin 1.2.3, MDL mol, compressed mol and SMILES export are external modules.
The problem is that older browsers such as Netscape 3, cannot load the external modules when the module is needed by a public method which is called from JavaScript. So if you want your web page containing Marvin to work perfectly with earlier releases of Netscape than 4, then you should preload all the modules which may be needed by JavaScript calls.
For example, if you are using MSketch.getMol("smiles") on your page, then you should also have the following applet parameter:
<param NAME="preload" VALUE="SmilesExport">.