Bugfixes
Bugfixes
Improvements:
Bugfixes
Improvements:
Bug fixes:
Improvements:
No changes.
No changes.
Bug fixes:
Improvements:
Bug fixes:
Improvements:
No changes.
No changes.
No changes.
No changes.
Bug fixes:
Bug fixes:
Security:
Security:
Security:
Bug fixes:
Improvements:
Lithium 1 has been released.
Bug fixes:
Improvements:
No changes.
No changes.
No changes.
No changes.
Security:
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
Improvements:
Krypton 1 has been released based on Frequent Release 22.6.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
No changes.
Notice:
Iodine 1 has been released based on Frequent Release 21.15.
No changes.
No changes.
Improvements:
No changes.
Bug fixes:
Bug fixes:
Bug fixes:
Improvements:
Bug fixes:
No changes.
Bug fixes:
No changes.
No changes.
Improvements:
Improvements:
Bug fixes:
Bug fixes:
Bug fixes:
Improvements:
Helium 1 has been released based on Frequent Release 21.4.0.
Bug fixes:
Bug fixes:
Bug fixes:
Bug fixes:
Improvements:
Bug fixes:
No changes.
Improvements:
Bug fixes:
Gallium 1 has been released based on Frequent Release 20.19
No changes.
Bug fixes:
No changes.
Improvements:
Unordered reactions in mdl rxn and extended mdl rxn formats are now arranged when the string is directly pasted into the canvas.
The following abbreviated groups have been added to the default list of abbreviations:
New features:
No changes.
New features:
Improvements:
Bug fixes:
No changes.
Improvements:
Bug fixes:
Improvements:
Bug fixes:
No changes.
No changes.
Bug fixes:
Bug fixes:
Improvements:
Bug fixes:
Known Issues:
Improvements:
Bug fixes:
No changes.
Fermium 1has been released based on Frequent Release 20.8.
No changes.
No changes.
No changes.
Bug fixes:
Improvements:
Bug fixes:
Bug fixes:
Improvements:
Bug fixes:
Bug fixes:
Improvements:
Bug fixes:
Improvements:
Bug fixes:
No changes.
Improvements:
Bug fixes:
Known issues:
Improvements:
Known issues:
No changes.
Improvements:
Bug fixes:
No changes.
Europium 1has been released based on Frequent Release 19.21.
Bug fixes:
Bug fixes:
Improvements:
No changes.
No changes.
Bug fixes:
I/O
Importing CAS Registry Numbers®
Bug fixes:
I/O
Bug fixes:
Editing
MarvinView
Importing CAS Registry Numbers®
Improvements:
Search
No changes.
Bug fixes:
Editing
No changes.
Known issues:
Bugfix
I/O
No changes.
No changes.
Bug fixes:
Editing
I\O
OSX
Improvements:
Stereocalculation
No changes.
Bug fixes:
Editing
GUI
I\O
Improvements:
GUI
Stereocalculation
No changes.
No changes.
Deuterium 1has been released based on Frequent Release 19.7.
Improvements:
Analysis Box
GUI
Bug fixes:
Editing
Bug fixes:
Editing
Molprinter
No changes.
Bug fixes:
Editing
No changes.
Bug fixes:
Editing
Installer
OpenJDK11bundled installer for Windows, OSX, and Redhat platform has been released.
Bug fixes:
I/O
There was a significant slowdown in the import of SMILES of some molecules with a huge ring system.
Improvements:
I/O
Bug fixes:
Editing
API
I/O
No changes.
Improvements:
GUI
No changes.
Bugfix
Molprinter
Improvements:
GUI
Improvements:
Editing
Improvements:
I\O
GUI
MolPrinter
Bug fixes:
Editing
Bug fixes:
Editing
Improvements:
Editing
Bug fixes:
Editing
Carbon 1has been released based on Frequent Release 18.22.
Bug fixes:
Editing
Analysis box
Clipboard
Improvements:
Editing
Help
Bug fixes:
Editing
No changes.
No changes.
No changes.
Bug fixes:
Editing
Analysis box
Clipboard
Image generation
No changes.
No changes.
Improvements:
Naming
Mac OS
Bug fixes:
Printing
MarvinView
Improvements:
Editing
Bug fixes:
Editing
No changes.
Bug fixes:
Editing
MarvinView
Image generation
Improvements:
Editing
Bug fixes:
Editing
Molconvert
No changes.
Barium 1has been released based on Frequent Release 18.8.
Improvements:
MarvinSketch
{warning} From this version on OLE format can be copied using the Copy as...(Ctrl+K) option.
API
Improvements:
I/O
Editing
Bug fixes:
MarvinView
Printing
Bug fixes:
Editing
I/O
Bug fixes:
Editing
I/O
Bug fixes:
I/O
OLE
Improvements:
Editing
Bug fixes:
Stereocalculation
I/O
Installer
No changes.
Bug fixes:
MarvinView
I/O
Improvements:
Editing
Bug fixes:
Editing
I\O
No changes.
No changes.
Bug fixes:
No changes.
Bug fixes:
Editing
Improvements:
Editing
Stereo calculations
OLE
Bug fixes:
Editing
Image IO
IO
Bug fixes:
Editing
Improvements:
Bug fixes:
Editing
Send to back context menu of graphical objects did not work.Text box
Image IO
Bug fixes:
I\O
Bug fixes:
Editing
I\O
No changes.
No changes.
Bug fixes:
Editing
OS
2D clean
I/O
MarvinView
Bug fixes:
GUI
Bug fixes:
Editing
I\O
2D clean
No changes.
2D clean
No changes.
Improvements:
Editing
I\O
Bug fixes:
Editing
Improvements:
Editing
I\O
Bug fixes:
Editing
No changes.
Bug fixes:
Editing
No changes.
Bug fixes:
Improvements:
Editing
I\O
Bug fixes:
Editing
Improvements:
Editing
Bug fixes:
Editing
Improvements:
Editing
Bug fixes:
Editing
Display
I/O
Image generation
No changes.
No changes.
Improvements:
Editing
Bug fixes:
Editing
Molconvert
Image generation
Improvements:
Editing
I/O
Bug fixes:
Editing
Display
I/O
Improvements:
Editing
Bug fixes:
Editing
Naming - Name to Structure
No changes.
No changes.
Bug fixes:
Editing
Bug fixes:
Editing
Some Linux environment the last file open location was not remembered.
No changes.
Bug fixes:
Editing
Improvements:
Editing
Bug fixes:
Editing
Bug fixes:
Editing
Bug fixes:
Editing
Copy/Paste
OLE
I/O
No changes.
Improvements:
MarvinSketch
MarvinSpace
MarvinSpace development is discontinued.MarvinSpace is not part of the Marvin suite and MarvinSketch installer anymore. A separate installer can be downloaded from here.
Bug fixes:
Core
Improvements:
Editing
Bug fixes:
Editing
I/O
No changes.
Improvements:
Editing
Bug fixes:
Editing
No changes.
No changes.
Improvements:
Bug fixes:
Editing
Bug fixes:
Editing
Services
Bug fixes:
Editing
I/O
Bug fixes:
Editing
Improvements:
I/O
No changes.
Improvements:
Editing
Bug fixes:
Editing
Improvements:
Marvin GUI
Bug fixes:
Editing
OSRA
Import/export
Improvements:
2D clean
Bug fixes:
Editing
Display
Import/export
Improvements:
Editing
Bug fixes:
Editing
No changes.
No changes.
No changes.
Bug fixes:
Editing:
No changes.
Improvements:
GUI
Bug fixes:
Editing
IO
Improvements:
Editing
GUI
Bug fixes:
Editing
Improvements:
Editing
Improvements:
Editing
Bug fixes:
Editig:
No changes.
No changes.
Improvements:
Editing
Bug fixes:
Editig:
Bug fixes:
Editing
Rendering
GUI
Bug fixes:
Editing
No changes.
Bug fixes:
I/O
Improvements:
Editing
I\O
Marvin GUI
Bug fixes:
Editing:
Improvements:
I/O
Bug fixes:
Editing
Improvements:
Editing
I\O
Bug fixes:
Editing
I/O
Improvements:
I/O
Known issues:
Improvements:
Editing
Bug fixes:
Editing
Improvements:
Editing
Bug fixes:
I/O
Improvements:
Marvin GUI
Bug fixes:
Editing
Known issues:
I/O
Improvements:
Editing
Bug fixes:
Clipboard
Editing
Image export
Applet
2D Cleaning
No changes.
Improvements:
Editing
Improvements:
OLE
Bug fixes:
I/O
Editing
Image export
Bug fixes:
Installation
Improvements:
No structure
Bug fixes:
Editing
Improvements:
Editing
Bug fixes:
Textbox
Bug fixes:
.NET
Bug fixes:
2DClean
Improvements:
Templates
Improvements:
Abbreviated groups
Improvements:
Customization
Editing
Bug fixes:
2D Cleaning
Customization
MarvinGUI
Pop -up dialogues did not work on Mac.
Typing in the Insert Abbreviated Group window's textbox froze the application.
Bug fixes:
Editing
Improvements:
Journal styles
Bug fixes:
2D Cleaning
Improvements:
I/O
Charge painting
Customization
Bug fixes:
Painting
Saving
2D Cleaning
Bug fixes:
Import
Bug fixes:
Editing
Import
Improvements:
Document
Charge
Bug fixes:
I/O
Improvements:
Journal
Bug fixes:
Editing
No changes.
Improvements:
Editing
Improvements:
No changes.
Improvements:
MarvinSketch
Bug fixes:
MarvinSketch
Editing
API
Bug fixes:
Editing
MarvinSketch
On Turkish locale since 15.2.9MarvinSketch 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 v3000molfile failed in some cases.
Improvements:
Marvin GUI
Improvements:
Editing
Naming
Marvin GUI
Bug fixes:
Editing
Improvements:
Editing
I\O
Marvin GUI
Naming
Bug fixes:
Editing
Applet
Applet settings were overwritten by the user settings.
Improvements:
Editing
I\O
Marvin GUI
Bug fixes:
Editing
I/O
Improvements:
Editing
Marvin GUI
Bug fixes:
Editing
I/O
OLE
Improvements:
Editing
Marvin GUI
I/O
Bug fixes:
Editing
I/O
Improvements:
MarvinGUI
Bug fixes:
MarvinGUI
Editing
I/O
Bug fixes:
Stereo calculation
Editing
Image export
Improvements:
MarvinSketch GUI
Editing
Bug fixes:
Editing
Improvements:
MarvinSketch GUI
Bug fixes:
Naming
Bug fixes
Molecule representation
Painting
Improvements:
MarvinSketch GUI
MarvinBeans
Applet
Bug fixes:
Painting
Editing
Improvements:
Export/Import
Improvements:
MarvinSketch GUI
bondLength and image export parameter bondl are also introduced.
Valence Check has been improved for negatively charged polyhalogen ions.Bug fixes:
Editing
Improvements:
MarvinSketch GUI
Bug fixes:
Editing
Export
Improvements:
MarvinSketch GUI
Import/Export
Bug fixes:
Editing
Improvements:
Bug fixes:
Stereo search was wrongly positioned in case of double bonds.Improvements:
Improvements:
Bug fixes:
Bug fixes:
New features:
Bug fixes:
Bug fixes:
New features and Improvements:
Bug fixes:
New features and Improvements:
Bug fixes:
New features and Improvements:
Bug fixes:
Bug fixes:
New features:
Bug fixes:
Bug fixes:
Import/Export
Structure Representation
No changes.
New Features and Improvements:
API
Bug fixes:
Applet
New features and Improvements:
Structure Representation
Bug fixes:
Structure Representation
Image I/O
MarvinSketch GUI
New features and Improvements:
Bug fixes:
Structure Representation
Image I/O
Editor
MarvinView
Improvements:
Structure Representation
Image I/O
Bug fixes:
Import/Export
Improvements:
Editing
Bug fixes:
Editing
Import/Export
Image I/O
Position of subscript numbers in labels changed when zooming in.
There were patches around atom labels when EMF image was exported with transparent background. Stereochemistry
Retrieving parity information could change the result of the CIP stereo recognition.
Bug fixes:
Editing
Image I/O
New features and Improvements:
Molecule representation
Editing
Clean 2D
Import/Export
Calculator Plugins
Applet
MolConverter
Bug fixes:
Editing
Import/Export
Elemental Analyzer
OLE
Applet
Deprecated and removed methods:
Deprecated or Removed Methods in version 14.7.7.0
No changes.
Bug fixes:
Import/Export
Bug fixes:
Applet
New features and Improvements:
Image I/O
Import/Export
Bug fixes:
Editing
Image I/O
Molecule representation
New features and Improvements:
CHEMAXON_LICENSE_URL environment variable or the chemaxon.license.url java system property is set.Import/Export
d2s:osra will request OSRA to be used.Molecule representation
chemaxon.struc.MolBond.equals()compares the bonds by reference and not by the end points.Clean 2D
Applet
Bug fixes:
Editing
NullPointerException.NullPointerException.MarvinView
Import/Export
java.lang.ArrayIndexOutOfBoundsException when reading parallel bonds atoms.Now chemaxon.formats.MolFormatExceptionis thrown instead.d2s:-ole formatoption, the optical structure recognition of images was disabled as well.Molecule representation
Clean 2D
Image I/O
Structure Checker
Calculations
Conformers
Deprecated and removed methods:
Known issues:
Structure Checker
Bug fixes:
Import/Export
No changes.
Bug fixes:
Clipboard handling
Import/Export
StackOverflowError wrapped in an IOException.New features and Improvements:
Clipboard handling
MarvinView GUI
Import/Export
Applet
Bug fixes:
Editing
Molecule Representation
Valence Check
Clean 2D
Import/Export
Calculations
Known issues:
New features and Improvements:
MarvinSketch GUI
Editing
MarvinView
MarvinSpace
Import/Export
SMILES import handles CACTVS-type representation of coordinate bonds ('|' character).Please note that the export does not handle it.
Terminal H and OH are added to nucleic acids by nucleic acid import.
Name to Structure (n2s)
CAS Registry Numbers® can be converted to structures even when they contain coordinate bonds¹.
Conversion of nitrogen-substituted acetohydrazides is now supported.
Elements with isotopes, such as (14)C, are converted in name to structure by default, and, optionally, they can be converted with document to structure using the "d2s:elements" format option.
Some OCR errors have been fixed in carbon ranges for homology groups, for example, "Ci_10alkyl".
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.
Molecule representation
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
New stereo analysis API.
3D alignment
Hydrogens are taken into consideration during alignment process.
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
The Java COM Bridge (Jacob) version was updated from v1.15-M3to v1-17.
Bug fixes:
MarvinSketch GUI
MSketchPane setPiece(Molecule) method did not work; it set the molecule on the canvas instead of putting it on the cursor.
Starting points of electron flow arrows drawn from radicals and/or lone pairs were changed when lone pair visibility was switched off and then on again.
R-logic label was not taken into account by zoom action even if visibility option "R-logic" was switched on.
Painting
Electron flow arrows starting from an atom, a negative charge, or an automatically calculated lone pair disappeared when lone pair visibility was turned off and then turned on again.
Editing
Menu option "Link Node" was not disabled when an atom had less than two bonds.
A contracted tripeptide disappeared from view when it was expanded, but 2D Clean brought it back.
It was not possible to draw an electron flow arrow from an atom to an incipient bond between this atom and an abbreviated group.
Erasing a structure without an R-group attachment left "1" on the canvas, which behaved as an atom.
When an atom was selected and the "R-group attachment" button of the Markush toolbar was used, the selected atom was changed to an R-group attachment point; however, a new R-group attachment should have been added to the selected atom in this case.
Dragging with the R-group attachment tool, a bond was created connecting two R-group attachments.
Using the R-group attachment tool, R-group attachments could be added to an existing R-group attachment.
Load/Save handling in UI
Lone pairs were lost at "Copy As...> PDF" at Mac OS X.
PDF export did not use the color scheme setting.
Clipboard handling
During PDF export, atom labels were turned upside down with some font types.
MarvinViewGUI
Import/Export
MRV/CML
After MRV export and reimport of a structure, its text box font color turned into the frame color of the text box and the font color turned to a not defined color (black).
Format recognition
'(S)-(-) Propanolol' was recognized as SMILES.
Chemical Registry Numbers® were recognized as MDL MOL format.
Name to Structure (n2s)
Automatic format recognition failed for names using unicode hyphens.
Names of some spiro compounds containing aromatic components were not converted.See, for instance, 6-(2, 5-dimethylphenyl)-5'-methylspiro[chroman-4,2'-imidazol]-4'-amine.
Document to Structure (d2s)
Some names containing a space character (for instance, "malonic acid") were not detected.
When using document to structure using the MRecordReader API, the MRecord.getMolString() method returned null.
The character position property of recognized names was sometimes wrong.
Spiro and fused ring system names were not recognized in HTML documents when the brackets were represented by HTML entities.
Processing an HTML document failed when the document was declared to be in XHTML format, but was not actually a valid XML (for instance, contained unclosed tags).
Processing a USPTO XML patent file in the current directory failed when it referred to CDX structures files.
Some structures embedded in Office documents were not extracted.
Structure to Name (s2n)
Names could not be generated for structures with lone pairs (MolAtom.LP).
The name generated for OH- was "oxidanide" instead of the preferred form "hydroxide".
An extra locant was included in the name of cyclic structures with multiple hetero atoms with one of them having non-standard valence, for instance, 1λ6,4-thiomorpholine-1,1-dione instead of 1λ6-thiomorpholine-1,1-dione.
In cases where a cyclic substituent was connected indirectly to the parent through an ether, sometimes wrong names were generated.
Name generation failed for structures with a methanethione parent.
Molecule representation
java.lang.ArrayIndexOutOfBoundsException was thrown when a multicenter atom being the only member of an S-group was removed.Valence Check Valence Check did not accept chlorine and heavier halogens with 1negative charge and with 2, 4or 6pieces of fluoride ligands.
Stereochemistry
Incorrect stereogenic center was found in some spiro compound.
Aromatization
General aromatization handled selenium differently than sulfur.
Clean 2D
Cleaning of position variation bonds could make bonds overlap.
Datatransfer
OLE
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
Bug fixes
Import/Export
OLE objects from Accelrys Draw 4.1and further versions could not be redirected by MarvinOLE server.
OLE opened in 3D rotation mode (F7) mode.
Bug fixes:
Applet
Bug fixes:
Bug fixes:
Applet
Bug fixes:
MarvinSketch GUI
setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor.Import/Export
CXSMILES/CXSMARTS
CXSMARTS containing valence property information was recognized and read as SMARTS.
SKC
New features and Improvements:
MarvinSketch Dialog
'Zoom to scaffold' checkbox option has been added to the "Preferences > Save/Load" tab.
Structure Checker
Bug fixes:
Editing
Import/Export
Clean 2D
Cleaning of position variation bonds could create overlapping bonds.
Cleaning of bridged systems could result in overlapping atoms.
Calculations
Topology Analysis
Missing method has been added: TopologyAnalyserPlugin.getFsp3().
logD
New logD training documentation has been added.
Structure Checker
Fixer options in MarvinSketch are updated with newly defined settings.
External checkers can be loaded from JAR file in case the JAR file contains a space.
No changes.
New features and Improvements:
MarvinSketch GUI
Peptide cycles and bridges can be drawn according to IUPAC recommendations.
IUPAC numbering can be displayed on the atoms of each molecule using the "View > Advanced > Atom Numbering > IUPAC Numbering" menu item.
Lone Pair (LP button) was removed from the "Special nodes" group of the "Periodic Table > Advanced" tab, so it cannot be reached from the GUI anymore.
MarvinSketch Menu
The "Calculations > Predictor" menu option has been removed from the default Marvin menu.
Painting
Drawing of electron flow arrows has been changed.Single electron flow arrows can now start either from a radical or from an electron of a lone pair.Electron pair flow arrows can only start from lone pairs.
Atom property values belonging to the same atom are now separated with semicolons instead of commas.
When lone pairs were displayed on a structure, the charge symbol was nearly invisible.
Load/Save handling in UI
The same last-used folder is saved for the "File > Open" and the "File > Insert file" functions.
Graphical object handling
Electron flow arrows can be started from or targeted to multicenter atoms.
MarvinViewGUI
Import/Export
MRV/CML
Namespace has been introduced to mrv format.
MOL, SDF, RXN, RDF
New export option, cc, is introduced to V2000 export in order to write absolute chiral flag if there are only ABS enhanced stereo labels in the molecule.
New import option, z, is introduced to MDL import that converts carbon atoms with "Z" label to R-group attachment points.
SMILES/SMARTS
[Z] is imported as R-group attachment point from SMILES.
CXSMILES/CXSMARTS
New export option, b, has been introduced to CXSMILES/CXSMARTS in order to turn off the export of bicyclostereo-information.
Name to Structure (n2s)
Name and corporate ID resolution webservice now supports NTLM authentication.
Names with a missing dash before the suffix locants are now recognized.
Non-standard IUPAC specification of stereochemistry inside suffix locants is supported.
Names with superscript locants of a bridged ring system numbering are denoted by spaces are now supported.
As a result of numerous Improvements: to the systematic name conversion algorithm, more names are converted by n2s and detected by d2s.The accuracy of structure generation has also increased.(For instance, 5% more names were detected and converted in a large, diverse set of patents.)
An example custom dictionary has been added to the documentation.
Document to Structure (d2s)
Chinese names are now detected in text documents using an approach which recognizes names in Chinese sentences without the spaces that separate words in English.
In addition to OSRA, the CLiDE and Imago Optical Structure Recognition tools (Chemical OCR) can be used to convert images to structures.These tools need to be installed separately from Marvin.
When processing USPTO patents in XML format, the section in which a name is found is recorded as metadata (title, abstract, citation, description, or claim number).Additionally, document metadata is extracted (patent title and ID, inventors and assignees, IPCR categories).
When processing a USPTO patent XML document, referenced CDX files are imported automatically if they are in the same directory as the XML file.
Processing of USPTO XML patents has become faster: an average 20% speed-up, more than ten times faster process for some patents.
PDF document pages with images in the JBIG2format are now supported.
PDF documents generated by Adobe Acrobat Paper Capture Plug-In and ExperVision are now handled specially, since they contain both an original scanned image of text and the text resulting from OCR of the image.This allows much faster processing of such documents, and avoids double hits for the same text.
PDF documents with many small high-resolution images are now processed much faster, even when Optical Structure Recognition is used.
The document creation date property is stored as a java.util.Date object instead of string.
Structures returned by image recognition tools (OSRA, CLiDE, Imago) are better filtered to avoid false positives.
OCR processing for scanned texts can be disabled using the -ocr format option.
Processing of PDF documents with scanned black and white images ( e.g. , most non-searchable patent documents) has become approximately two times faster.
Structure to Name (s2n)
When retrieving a Chemical Registry Number® from , the InChiKey of the structure is used to search for the structure.This allows more structures to get a number in such cases where several different SMILES with chemically irrelevant differences are associated with the structure.
Molecule representation
New method, SelectionMolecule.addAtom(MolAtom, boolean), is introduced.
New methods, MolAtom.getBondArray() and Sgroup.getBondArray() are introduced.
Calculations
NMR (CNMR, HNMR Prediction...)
Various phosphorus-proton spin-spin coupling parameters have been added to the predictor database.
Geometry (Topology Analysis, Geometrical Descriptors, PSA, MSA)
"Fsp3" option has been introduced in the Topology Analysis plugin for calculation of sp3 carbon atom fraction.
Elemental Analyzer
Charge is taken into account in atomic mass calculation.
Chemical Terms
Chemical Terms's (CT) Structure Checker functions accept XML configuration as string parameter, thus Structure Checker XML configurations can be used in JChem Cartridge via CT.
New checkErrorCount Chemical Terms function returns the number of errors/issues found by the checker(s) in the configuration.
Structure Checker
Checker "substructure checker" has become available in Marvin Beans, so installing Marvin Beans will install the fully functional Structure Checker application.
Set Structure Checker configuration can be copied to the clipboard as action string from Structure Checker GUI and Structure Checker Editor.
The "excluded" list of Structure Checker's Abbreviated Group Checker accepts quotation marks in command-line.Possible definitions can be the following: "abbrevgroup:excluded=Ph,Ala,Gly", "abbrevgroup:excluded='Ph,Ala,Gly'" or "abbrevgroup:excluded="Ph,Ala,Gly"".
The checkers and fixers can be localized or customized according to individual requirements.
Build/Installation
Mac OS X installer images were not digitally signed, and GateKeeper in newer OS X versions (10.7.5+) reported our installers as damaged and refused to install them.
Bug fixes:
MarvinSketch GUI
Aliphatic/Aromatic atom query property had three options ("a", "A", and "A,a") instead of the necessary two ("a" and "A").
MarvinSketch Dialog
In case of long names, only a part of the whole name appeared on the naming panel.
Editing
Deleting an atom having an R-group attachment did not delete the attachment.
The end of an arrow did not stick to the midpoint of an existing arrow.
Load/Save handling in UI
In MarvinView, "File > Save All...> Advanced > Into SEPARATE FILES" did not save the last structure.
History functions
When the "Stereo" atom property had been changed, Undo/Redo did not work properly and the IUPAC name was not updated.
Graphical object handling
Labels written in text box were shifted when they were pasted either as an OLE object or as a PNG image.
MarvinViewGUI
When a structure which contained an R-group definition was opened from MarvinView for editing in MarvinSketch, the structure appeared with 0% zoom factor.
Text elements (atom labels, atom indices, text box contents, IUPAC name) were not resized in MarvinView while zooming the structure using the "View > Transform > Zoom" function.
Printing in MarvinView
When choosing "Print > All Visible", the structures overlapped in the preview, and "Print > All Visible > Print to PDF" resulted in an empty file.
MarvinSpace
A bug occuring at PDB import has been fixed.
The "Edit > Cut" menu option has been fixed in the MarvinSpace menubar.
Import/Export
Aliphatic and aromatic query property, when they are used together, is not imported and exported any more.The "no property", no aromatic or aliphatic query property, has the same meaning.
Only lower case file extensions were recognized.
MRV/CML
MRV files that contained circular R-group references without attachment point information could not be imported.
MOL, SDF, RXN, RDF
Export of structures containing multicenter S-groups to format MOL V2000 resulted in a non-standard file.
Newline characters in molecule name were not escaped.
MDL MOL import did not use MDL valence model for non-charged metals.
Atom list embedded to atom list in MDL file formats resulted in invalid atom list elements after import.
CDX/CDXML
Reactions containing anonymous alternative groups were not imported from CDX format.
XML files with complex header could have been recognized as CDXML.
SMILES/SMARTS
Query Hydrogen atom with parity definition confused SMARTS import.
SMILES export did not throw exception when the molecule contained not supported reaction stereo information.
Newline characters in molecule name were not escaped.
SMILES import read Meitnerium atom (Mt) as any atom (*).
Strings containing valence property were recognized and imported as SMILES instead of SMARTS.
CXSMILES/CXSMARTS
Import of CXSMILES/CXSMARTS strings that describes the coordinates of atoms with option c added 'CIS OR TRANS' stereo information to double bonds in small rings.
Single or aromatic bonds could be lost during CXSMARTS export and import.
InChi/InChiKey
InChI was not recognized in MolConverter as one line molecular format that can be given as the argument of -s option without specifying the format.
Reactions could not be exported to PDF.
Name to structure (n2s)
Names with a cis- or trans- imine bond were failing to be converted to structures
Ions, such as "bismuth(3+)", were imported with valence property set to 0.
Ortho substitution on acetophenone generated wrong structures.
Some E/Z and R/S stereochemistry was missing in structures imported from names when the locant of the atom or bond with stereochemistry was not specified explicitly.
The "H-" ion was missing from names containing "hydride", e.g. , sodium hydride, they only had e.g. , "Na+ instead of the correct NaH.
Names containing atoms with both a non-standard valence (λ) and a positive charge were converted to structures with an extra implicit hydrogen on that atom.
Primary and secondary amine oxides were represented as N-OH instead of [N+]-[O-].
The "Name" format was not automatically recognized for names with XML/HTML character references, such as "&##946;" or "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
ElementalAnalyser.setMolecule(String) threw exception if the formula contained () brackets (e.g.C6H11N3.2(HCl)).
Protonation (pKa, Major Microspecies, Isoelectric Point)
Minor bug has been fixed on the distribution chart.
Isomers (Tautomers, Stereoisomers)
Stereoisomers plugin failed to generate all stereoisomers for tricyclic compounds.
Generic tautomer generation threw exception on some molecules.
Some invalid 3D structures were not filtered out during stereoisomer generation although 3D-filter option was turned on.
Some cycloolefine stereoisomers were mistakenly filtered out as duplicates, so they were missing from the generated list of stereoisomers.
Structure Checker
In Structure Checker GUI, the scroll bar was missing in the report tab if the report contained four to six structures.
When the Structure Checker configuration contained multiple substructure checkers, their order would change during structure checking process.
Deprecated and removed methods:
Bug fixes:
Applet
Bug fixes:
MarvinViewGUI
MarvinSpace
No changes.
No changes.
New features and Improvements:
Image I/O
Calculations
Bug fixes:
Painting
R/S stereo labels were not displayed when there was an R-group on the canvas.
S-groups, created from structures containing a position variation bond, retained the grey patch of the position variation bond when the group was contracted.
Editing
An atom of an expanded S-group could not be replaced with an S-group correctly
Clipboard handling
On Mac OS X, copy-paste (from MarvinSketch to, e.g. , TextEdit) did not transfer the atom colors.
Graphical object handling
Formatting the head of a graphical arrow to a half-left arrow using the Document Style dialog crashed the display of the arrow.
Import/Export
MRV/CML
MRV and CML export failed with the woodstock xml processor.
InChi/InChiKey
InChi export did not return standard InChi when the absolute stereo was not set in a non-chiral molecule.
Document to Structure
Documents with many consecutive names would lead to extremely long processing time (appeared as hanging, unless reaching the timeout).
Molecule representation
Clean 2D
Stereo clean created non-IUPAC standard depiction of certain tetrahedral configurations.
Data Transfer
OLE
Applet
Applet parameter extraBonds did not work therefore the bond type menu appearance could not be changed.
Image I/O
Calculations
Protonation (pKa, Major Microspecies, Isoelectric Point)
"Keep explicit hydrogen" option caused exception during pKa calculation.
NMR (HNMR, CNMR Prediction, ...)
When the mouse cursor was moved over an NMR peak on the chart, the relevant atom was not highlighted on NMR predictor molecule preview panel.
Services
SOAP webservices:
Parameters did not load from WSDL properly in SOAP version 1.1webservices.
New features and Improvements:
MarvinSketch GUI
MarvinSketch GUI has been refreshed: Icon set has been changed in MarvinSketch.Menu items have been rearranged.Several dialogs, tooltips, menus has been renamed.
A new Marvin configuration has been added to MarvinSketch.Already existing Marvin configurations have been renamed.
MarvinSketch now starts with the native "Look & Feel" on Windows and on Mac OS X.
MarvinSketch Dialog
At the first launch of MarvinSketch after installation, a dialog asks the user to select the desired skin for the GUI configuration.
The Open dialog has been modified.Selecting molecules to load from a multistructure file happens now directly on the Open dialog.
New dialog, called "Insert file", has been introduced into MarvinSketch for adding structures from new files to the canvas contents.
The Save dialog has been extended with an Advanced panel to set saving options.
Painting
Drawing quality has been improved: join of single bonds has been refined.
Superatom S-group attachment points are denoted by numbers instead of asterisks.
Editing
MarvinSketch GUI can handle unlimited number of attachment points on Superatom S-groups.There are new menu options for adding and removing attachment points in the Atom menu and in the contextual menu.
Bond length can be scaled.Bond length and size of other objects can be set by dragging the displayed corners of the bounding rectangle.Scaling is also available on the Document Style dialog.Scaling does not work when the structure has been rotated in 3D mode (with F7).
Load/Save handling in UI
New loading mechanism has been introduced in MarvinSketch.New menu option, Insert file, has been added to the File menu; it appends the contents of the chosen file to the structure on the canvas.
New saving mechanism has been introduced in MarvinSketch.
New save mechanism has been introduced for MarvinView.
Reactions and structures containing R-group definitions cannot be saved either in separate files or separately in the same file.
Clipboard handling
Images of chemical structures can be imported from the clipboard via the configured image import service or locally installed OSRA.
Template Library
New template set, Organometallics, has been added to the Template Library.
New amino acid templates have been added (e.g., pyrrolysine, selenocysteine, "any/unknown/undetermined aminoacid").
The following amino acid templates have three attachment points: arginine, cysteine, histidine, lysine, selenocysteine, serine, threonine, tryptophan, tyrosine.
Integration
The new Automapper has been introduced in MarvinSketch.
MarvinSpace
Copy and Paste functions have been added to MarvinSpace.
3D editor: Molecules can be edited in 2D in MarvinSketch, and aligned to the original 3D molecule.
Import/Export
MRV/CML
Import and export of more than two Superatom S-group attachment points are supported.
MRV schema
New element, AttachmentPointArray, is introduced in format MRV to describe the new Superatom S-group attachment point representation.
MOL, SDF, RXN, RDF
The import of template based MDL MOL files is introduced.
Import and export of more than two Superatom S-group attachment points are supported from MDL MOL based formats.
SKC
Import and export of more than two Superatom S-group attachment points are supported.Superatom S-groups having at least one crossing bond are exported in their expanded form.
CDX/CDXML
Import and export of more than two Superatom S-group attachments point are supported.
Curved lines can be imported from CDX files.
CXSMILES/CXSMARTS
Generic, Polymer, and Mixture type S-groups are stored in CXSMILES/CXSMARTS format.
SMILES/SMARTS
In SMILES import, radicals are not added anymore to atoms with atomic number above chlorine, except for bromine and iodine.If implicit hydrogen can not be added to or removed from the atom (as it is in brackets in the SMILES definition), then a valence property is set to correct its valence if necessary.
Peptide
Amino acids: Cysteine, Aspartic acid, Glutamic acid, Histidine, Lysine, Asparagine, Glutamine, Arginine, Serine, Threonine, Selenocysteine, Tryptophane, and Tyrosine are imported with three attachment points from peptide format.
New 1-Letter and 3-letter amino acid codes were added: U and Sec for selenocysteine; O and Pyl for pyrrolysine; X and Xaa for "any/unknown/undetermined amino acid"; B and Asx for "Aspartic acid or Asparagine"; Z and Glx for "Glutamic acid or Glutamine"; J and Xle for "Leucine or Isoleucine".
FASTA
Peptide, DNA, and RNA import from FASTA format has been introduced.
Name to Structure (n2s)
Custom name-to-structure webservices can now be configured to receive the name in the middle of the URL, not just at the end, by using the [NAME] marker in the configuration URL.
More forms of ranged generic names are supported, such as "-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 20seconds).
Structure to Name(s2n)
The new format option "cas##" allows the retrieval of Chemical Registry Numbers® from publicly available sources hosted by the U.S.National Institutes of Health (“NIH”) and the Wikimedia Foundation..
Molecule representation
Valence Check Valence Check does not deal with free attachment points.
Calculations
Protonation (pKa, Major Microspecies, Isoelectric Point)
log[%] vs.pH distribution chart is introduced in case of pKa calculation.
Major miscrospecies calculation is supported for molecules with coordinate bonds.
NMR (HNMR, CNMR Prediction, ...)
NMR predictor considers novel coupling types.
Updated trainingset has improved the NMR shift prediction accuracy in both 1H and 13C NMR predictors.
1H NMR calculation has become faster as no 3D conformer generation is applied.
Geometry (Topology Analysis, Geometry, PSA, MSA)
Setting any Chemaxon supported aromatization method (general, basic, loose) is available in TopologyAnalyserPlugin which affects the result of many topology analyser calculations (e.g., aromatic atom/bond/ring count).
Chemical Terms
New sortableFormula() function is introduced.The generated sortable formula can be used to sort formulas in alphabetical order.
cxcalc
pKa training library can be used without relying on user home.Use option --correctionlibrarypath to read custom training file.
New sortableFormula option is introduced.The generated sortable formula can be used to sort formulas in alphabetical order.
cxtrain
New option, -p, has been introduced to save the training result to custom path.
Automapper
New Automapper tool is introduced.It maps reactions more accurately.
Automapper tool requires Standardizer license.
Structure Checker
"Traditional nitrogen representation allowed" option is available in Valence Error Checker.
External structure checker and fixer manager is integrated into Structure Checker GUI application.It is accessible from the preferences menu as "Checker/Fixer Manager".
Known issues:
MarvinSketch Applet
External checker classes do not load if browser uses Java SE 6.Please, use Java SE 7for successful checker class loading.
Bug fixes:
MarvinSketch Menu
The "Recent Files" list was not updated with the new file name when the file contained multiple structures and more records were selected.
Painting
There was a gap between the lines of the double bond and the single bonds when two single bonds connected to the same (non-visible) carbon atom on one end of a double bond.
Electron flow arrows partially hid lone pairs in some cases.
Clipboard handling
When copying and pasting between Marvin applications in Linux, an exception was thrown which froze the application where the copy operation had been performed.The exception originated from the applied freehep library, which has been updated.
MarvinSpace
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 9.0.1containing 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 5.0and containing contracted Superatom S-group was not imported.
CDX import read half headed arrows as full headed.
CXSMILES/CXSMARTS
CXSMARTS export did not keep CIS/TRANS information for symmetrical structures.
Extended part of CXSMARTS was not written correctly for any halogen query atoms.
SMILES/SMARTS
Unique SMILES string generation for a fragment could have differed depending on the fragment count of the molecule
Peptide
User defined custom amino acid dictionary caused wrong custom amino acid structure or java.lang.ArrayIndexOutOfBoundsException during peptide import.
Name to Structure (n2s)
When calling a custom name-to-structure webservice, names with special characters (including space) were not URL encoded, possibly resulting in failed conversions for such names.
Name containing fused rings and converted to all uppercase letters were not recognized.
Name to Structure could get stuck in a deadlock during the first usage when that occurred concurrently in several threads.
When using the "name converters" API, converters were not properly removed after using thread-local converters.
Document to Structure (d2s)
When interrupted while doing OCR or OSR, document to structure logged an exception about the interrupt.This caused in particular a warning dialog to appear in Instant JChem during a document import.
Names were not recognized when they contained a complex bracketed bond locant followed by a comma, such as "2(7)" in tricyclo[6.3.1.02,7]dodeca-2(7),3,5-triene.
Scrolling back in MarvinView could have caused failures for very large documents (more than 1000structures) 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
Clean 2D
Clean 2D failed to preserve cis/trans stereo information in some cases.
Calculations
Deprecation:
Molecule representation
Valence Check: MoleculeGraph.VALENCE_CHECK_AMBIGUOUS, MoleculeGraph.ValenceCheckState, MoleculeGraph.setValenceCheckState(ValenceCheckState), MoleculeGraph.getValenceCheckState() MoleculeGraph.getPossibleAttachmentPoints(MolAtom)
S-groups: SuperatomSgroup.getAttachAtoms(), SuperatomSgroup.getLegalAttachAtoms(), SuperatomSgroup.getFreeLegalAttachAtoms(), SuperatomSgroup.isFreeLegalAttachAtom(MolAtom), SuperatomSgroup.isLegalAttachment(MolAtom), SuperatomSgroup.sortXBonds(), MolAtom.getAttach(), MolAtom.setAttach(int), MolAtom.setAttach(int, Sgroup)
Elemental Analysis: ElementalAnalyser.setMolecule(SMolecule)
Other deprecated methods Molecule.exportToFormat(String), Molecule.exportToBinFormat(String), Molecule exportToObject(String)throws java.lang.IOException.
Structure to Name (s2n)
The method chemaxon.marvin.io.formats.name.nameexport.IUPACNamer.generateName(Molecule) , though not documented, was public for internal reasons, and used a non-thread-safe way to receive options.It is now deprecated in favor of chemaxon.formats.MolExporter(Molecule, String format) , where format can be for instance "name" for IUPAC name, "name:t" for traditional name.
Automapper
chemaxon.marvin.modules.AutoMapper
Removed methods
Molecule representation
MolAtom.setMassnoIfKnown(String), MolAtom.isNobleGas(), MolAtom.isArrowEnd(), MolAtom.valenceCheck(), MolAtom.getEdgeCount(), MolAtom.getEdge(int), MolAtom.getEdgeTo(MolAtom), MolAtom.haveSimilarEdges(MolAtom),MolBond.ARROW(), MolBond.isCoordinative(), MolBond.isArrow(), MolBond.getNode1(), MolBond.getNode2(), MolBond.getOtherNode(MolAtom), MolBond.cloneEdge(MolAtom a1, MolAtom a2)MoleculeGraph.AROM_CHEMAXON, MoleculeGraph.AROM_DAYLIGHT(), MoleculeGraph.setSetSeqs(int id), MoleculeGraph.getAromrings(), MoleculeGraph.getNonAromrings(), MoleculeGraph.getAromrings(int), MoleculeGraph.getNonAromrings(int), MoleculeGraph.mergeFrags(), MoleculeGraph.getFragIds(), MoleculeGraph.getfindFragById(int fragId, MoleculeGraph frag), MoleculeGraph.getNode(int), MoleculeGraph.setNode(int, MolAtom), MoleculeGraph.insertNode(int, MolAtom), MoleculeGraph.removeNode(MolAtom), MoleculeGraph.removeNode(MolAtom, int), MoleculeGraph.removeNodeVector(), MoleculeGraph.getEdgeCount(), MoleculeGraph.getEdge(int), MoleculeGraph.setEdge(int, MolBond), MoleculeGraph.insertEdge(int, MolBond), MoleculeGraph.insertEdgeInOrder(MolBond, MolBond[]), MoleculeGraph.replaceEdge(MolBond, MolBond), MoleculeGraph.removeEdge(MolBond), MoleculeGraph.getEdgeArray(), MoleculeGraph.getEdgeVector(), MoleculeGraph.getAllEdges(), MoleculeGraph.regenEdges(), MoleculeGraph.sortEdgesAccordingTo(MolBond[]), MoleculeGraph.mergeNodes(MolAtom that, MolAtom), MoleculeGraph.mergeFrags(int, int)Molecule.mergeFrags()RgMolecule.setAbsStereo(boolean, int, int), RgMolecule.createMol(String), RgMolecule.getBtab()RxnMolecule.getBtab(), RxnMolecule.getStructureCount(int), RxnMolecule.getStructure(int, int), RxnMolecule.addStructure(Molecule, int), RxnMolecule.removeStructure(int, int)CEdge, CNode, CGraphMDocument.setGUIProperyContainer(MPropertyContainer)
Bug fixes:
Import/Export
Bug fixes:
Import/Export
Calculations
Bug fixes:
Molecule representation
Import/Export
New features and Improvements:
Import/Export
Bug fixes:
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
MRV and CML export wrote out characters incorrectly which are not supported by the character set.
MOL, SDF, RXN, RDF
SDF files having invalid header could not been imported.
Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to Chemaxon compressed MOL format (CSMOL).
SMILES/SMARTS
MolExporter.exportToObject() added an extra newline to SMILES.
Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation.
InChi/InChiKey
Absolute stereo flag was missing during InChi export/import and InChiKey export.
Molecule representation
Valence Check
Calculations
New features and Improvements:
MarvinSketch GUI
Typing abbreviated group names is now case sensitive.
MarvinSketch Dialog
"Cancel" button has been added to the "Customize" dialog.
Painting
The font size and type of circled charge symbols can be modified on the "Display" tab of the "Preferences" dialog.
Position variation bond has been recolored for better visibility in a projected presentation.
Clipboard handling
When pasting unrecognized format onto the canvas, "Import as" dialog appears, and the user can choose the correct format.
Structures can be copied as "Daylight SMARTS" and "Chemaxon SMARTS (CXSMARTS)" formats.
MarvinViewGUI
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
SKC import has been improved.
CDX/CDXML
Mapping of reaction agents can be imported.
Name to Structure (n2s)
Initial support for Chinese IUPAC and common names has been added, e.g., 2-??-4-????.
Names with extra closing brackets can be converted when OCR error correction mode is enabled.
Name to structure now also works when bridge and spiro numberings are represented by using unicode superscript numbers, such as: tetracyclo[12.4.0.02,6.07,12]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., "&##xblah") are now ignored instead of making the document processing fail.
Image to structure conversion using OSRA is working on Mac OS X.
Text OCR for scanned documents is now supported on Mac OS X.
Documents compressed in xml.bz2and xml.xz formats can be processed directly.
The memory usage has been reduced when processing documents with several thousand hits.This improvement is in addition to the memory Improvements: already present in version 5.11.
Option "+/-groups" has been added to enable (+) or disable (-) the conversion of groups and fragments, such as "ethyl", "nitro", "phenoxy", etc.
OCR of scanned PDF documents has been improved on Windows OS thus reaching the same performance level as that of OCR on Mac OS X and Linux OSs.
Structure to Name(s2n)
The speed of batch conversion using a timeout (which is enabled by default) has been increased by about 15%; the earlier instability in case of timeout relying on the deprecated Thread.stop method has been avoided.
Molecule representation
The size of the Molecule object has been decreased.
Data Transfer
OLE
New settings are available for both administrators and end-users (from the "Edit > Preferences > MarvinOLE" menu) to preset the displayed OLE document in a maximized child window.
MRV files are read and validated by DOM (document object model) in Marvin OLE.
Clean 3D
MMFF94forcefield has been added to Generate3D.Use option "[mmff94]" to switch it on; use "molconvert -H3D" for detailed help.
Calculations
Isomers (Tautomers, Stereoisomers)
Performance improvement: Tautomerization will not apply "Clean2D" if the output result has no 2D coordinates.
Resonance structure is taken into account in dominant tautomer generation.
Conformation (Conformers, Molecular Dynamics, ...)
New MMFF94forcefield implementation has been introduced in Conformer Plugin and Molecular Dynamics Plugin.
Services
Result structure of Marvin Services result panel can be copied to clipboard.
Structure Checker
New checkers have been introduced:
Absolute Stereo Configuration
Chiral Flag
E/Z Double Bond
Multiple Stereocenter
Relative Stereo
Wiggly Bond
Fixer of checker "Query Atom": "Convert to Carbon" has been added.
Fixer of checker "Query Bond": "Convert to Single Bond" has been added.
Excluded list of abbreviated groups can be specified in "Abbreviated group" checker, i.e., checker will not find (and fix) abbreviated groups that are indicated in this list.
Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call.
Integration of external structure checkers and fixers into Chemaxon products has become easier via MarvinSketch GUI.
In case of more than one fixer, a logical order of priority has been preset.
New property change event to indicate when an editable MarvinView component is opened in MarvinSketch: sketchInView.
New property change event to indicate when a new MarvinSketch or MarvinView window is opened from the viewer: windowOpened.
New property change event to indicate when a MarvinSketch or MarvinView window, opened from the viewer, is being closed: windowClosed.
Java Web Start
Name to Structure and Document to Structure are now available in the Java WebStart distribution of Marvin.
Bug fixes:
MarvinSketch GUI
When a group abbreviation differed from an atomic symbol only in upper and lower case letters (e.g., NO and No), the abbreviated group could not be reached by typing.
MarvinSketch Dialog
Focus did not appear on the "Source" and "Import Name" dialogs with Java 7.
Painting
The charge was not displayed in circle on the bracket of an S-group when the "Show charge in circle" was set on the "Preferences" panel.
Charge label masked the adjacent bond in several cases.
Editing
Deleting "extra" explicit hydrogens from an atom with valence error resulted in the appearance of erroneous implicit hydrogens on this atom.
When there were several disconnected structures on the canvas, partial clean was very slow.
It was possible to create a molecule with R-group definition containing a single attachment point (and no other atoms or bonds).
Sprouting did not work for Alias atoms.
The two ways of deleting implicit hydrogens (with eraser directly or selecting them first then deleting) behaved differently.
Load/Save handling in UI
"File > Open" dialog froze when an mrv file contained a dashed arrow and the preview pane was checked.
When opening a multi molecule file and selecting a range that is open ended, a false error message appeared, which stated that there were too many molecules selected to open.
IUPAC name with alpha or beta signs could not be imported.
MarvinViewdid not open when importing a file from command line failed.
It was not possible to append a name to an existing .name file in MarvinSketch.
Clipboard handling
It was not possible to drag a structure from MarvinView in "Translate or Drag" mode.
Ctrl + V shortcut for pasting structures did not work in MarvinView in case of "Spreadsheet" view.
Graphical object handling
MBracket object "BRACES" did not render correctly when the orientation was set as "SINGLE".
Applet
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
Superatom S-group brackets were imported from MDL files.
CXSMILES/CXSMARTS
CXSMARTS I/O lost the charge from generic metal atom.
CDX/CDXML
Reaction agent not having reactant and product (e.g., >CC1=CC=CC=C1>) was read as reactant from CDXML files.
Name to Structure (n2s)
RS - as the marker of racemates - was not converted properly, for instance in (2RS)-1-(Adamantan-1-ylamino)-3-phenoxypropan-2-ol.
Lower CamelCase chemical names (such as 2-cyclopropylPiperazine) were not converted to chemical structures.
Common names, which are also non-chemical names, were recognized as chemical names during automatic format recognition, e.g., "Royal Blue".
E/Z bonds were sometimes set to the opposite value (in cases of non-trivial CIP rules).
For some rare inputs, which are not valid names, n2s created invalid structures that could be exported to mol format but could not be opened.
Both "phenylene" and "phen-1,3-ylene" were wrongly converted to benzene.Now all forms convert to the correct structure with two attachment points, including "m-phenylene", "1,3-phenylene", and "phen-1,3-ylene" (similarly for the o-, p-, 1,2-, and 1,4- forms).
Document to Structure (d2s)
Processing of multiple XML documents in concurrent threads was slow and sometimes skipped some hits.
Names separated by the "non-breaking space" character were not recognized.
Some names split by extra spaces were not found.
English names were not recognized in Japanese documents when the ideographic comma character followed them.
SMILES with aromatic atom after non-aromatic ones ("Cc1...") and with triple(##) or explicit single(-) bonds were not recognized.
Text OCR failed when the images in PDF were encoded in a certain variant of the CMYK color space.
Structure to Name(s2n)
Some characteristic group names were missing when expressed as a prefix of a sulfonyl group, for instance, in "propanamidosulfonyl".
Names could not be generated for structures containing "-[N+]≡" substituent.They are now named using the "azaniumylidyne" IUPAC name component.
Peptide
During automatic format recognition, non-latin characters were recognized as peptide sequences.
Molecule representation
S-groups
Multiple S-group expanded incorrectly when it had an embedded S-group.
S-groups/R-groups
S-group creation was not possible for a structure within an R-group definition of a reaction; a warning message was given.
Clean 2D
Calculations
Protonation (pKa, Major Microspecies, Isoelectric Point)
Microspecies calculation of furan returned incorrect molecular formula at low pH.
Charge (Charge, Polarizability, ...)
Resonant charge calculation generated exception when the major form of the molecule is invoked with explicit hydrogen atoms.
NMR (HNMR, CNMR Prediction, ...)
Outdated HOSE database caused NullPointerException when predicting 1H NMR spectrum for some rare diastereotpic molecules.
Isomers (Tautomers, Stereoisomers)
D, T count in region labels of multifragment generic tautomers was computed incorrectly.
TautomerizationPlugin API did not clean the explicit hydrogens in the result molecule after tautomer generation which might have resulted in wrong stereo (R,S) specifiaction on chiral centers.
Geometry (Topology Analysis, Geometry, ...)
The result of topological polar surface area (TPSA) plugin depended on the call order of setMolecule() and setpH() methods.
cxcalc
Calculation "ringcountofatom" returned only the ring count of atom number zero.
cxcalc returned irrelevant error message for calculations containing "ANY" bonds.
Thole polarizablility (tpol) calculation didn't interrupt when clean3D failed.
Backend / Core
Removing explicit hydrogens on some large PubChem compounds caused infinite loop.
Structure Checker
"Remove Stereo Care Box" was offered as fixer for results returned by "Query Bond Checker".
Fixer "Expand group" not only expanded but also ungrouped the abbreviated groups when using it via structurechecker command-line.
API
Deprecation:
Structure Checker
Deprecated checker action strings: aromaticity, chiralflag, circularrgroup, missingrgroup, rare, reactionmap, unusedrgroup, valence, wedge.
Deprecated fixer action strings: clearabsstereo, aliastocarbon, crossedtowiggly, converttosingle.
Deprecated fixer class names: AbsentChiralFlagFixer, AbsoluteStereoFixer, CrossedDoubleBondFixer, CovalentCounterionFixer, ExplicitHydrogenFixer, IsotopeFixer, RgroupReferenceFixer, WigglyDoubleBondFixer.
Bug fixes:
Datatransfer
Structures copied from ChemDraw, Accelrys Draw, or Symyx Draw could not be pasted onto MarvinSketch.
New features and Improvements:
Datatransfer
The imageImportServiceURL setting also affects the behavior of clipboard operations (drag and drop, paste).
Bug fixes:
Painting
Rounding error occurred in case of nearly 180degree bond angle and it caused overflow error when resizing the structure.
Import/Export
New export option, BOM, is introduced for non-binary chemical file formats in order to write out Byte Order Mark (BOM) if UTF-8encoding is used.
Structure to Name (s2n)
Since 5.11.0, names generated for bridged cyclic structures with explicit bridge head hydrogen contained a spurious "hydrogenio" prefix.
Clean 2D
Clean 2D got stuck in an infinite loop when fullerene-like molecules were cleaned.
Calculations
Atom index issue might have occurred when molecule contained explicit hydrogen.
Protonation (pKa, Major Microspecies, Isoelectric Point)
"averagemicrospeciescharge" calculation in cxcalc and "Isoelectric Point" calculation in MarvinSketch threw "ArrayIndexOutOfBoundsException" in the reported cases.
NMR (HNMR, CNMR Prediction, ...)
The calculated chemical shifts of equivalent atoms were not consistent in case of compounds with symmetric ring systems.
Bug fixes:
MView applet
Atom and Bond set coloring was not working properly when Marvin View Applet was called from JavaScript.
Image I/O
When imageImportServiceURL startup option was not set for MarvinSketch, the same setting on the Preferences panel was lost.By default shortcuts and startup scripts do not specify this command line startup option.
Java WebStart
chemaxon-core.jar, fontbox-1.7.1.jar and pdfbox1.7.1.jar were missing.
Calculator Plugins
New features and Improvements:
Image I/O
MarvinSketch GUI
A new "imageImportServiceURL=[URL]" program argument was added to the MarvinSketch application.
MarvinSketch applet
A new "imageImportServiceURL" was added as an applet parameter.
Graphical object handling
When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.
Import/Export
Document to Structure (d2s)
Names broken over two lines with a hyphen (-) are now recognized.
Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin11") are now recognized.
Name to Structure (n2s)
In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol.Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.
Bug fixes:
Painting
If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.
Image I/O
Import/Export
MOL, SDF, RXN, RDF
Aliphatic query properties of atoms with query string were not read from MDL formats.
After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.
Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.
SDF import returned structure with incorrect S-group embedding.
SMILES/SMARTS
SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.
Molecule representation
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
--pH command line option did not work in hydrogen bond acceptor-donor calculation.Structure Checker
structurechecker command line tool.
New features and Improvements:
Import/Export
Bug fixes:
Calculations
NMR (HNMR, CNMR Prediction, ...)
NMR Prediction did not use the mixed prediction algorithm, so NMR shift predictions were less accurate.
Chemical Terms
The -g (ignore error) option of evaluate did not work when -x (extract) option was used.
Structure Checker
New features and Improvements:
MarvinSketch GUI
Molecule properties like SDF fields can be added/edited/deleted in MarvinSketch GUI.
Bond properties can be added/edited/deleted in MarvinSketch GUI.
Lone pair can be displayed as a line.The option can be set from the "Preferences" panel.
Charge can be displayed in a circle.The option can be set from the "Preferences" panel.
An aromatic benzene template has been added to the Generic templates.
Data transfer
Clipboard handling
Java wrapper for CXNSharedAddin library has been introduced to handle tabular data transfer from/to Microsoft Office applications.
Import/Export
CDX/CDXML
Graphical arrows "retrosynthetic" and "equilibrium" are imported from CDX and CDXML files.
Name to Structure (n2s)
Names, such as "methyl ether", are used either to denote a group (CH3-O-*) or the dimethyl ether compound (CH3-O-CH3), as well.The default behavior still is to generate the complete compound, but a new name option "expectGroup" has been added to get the group instead.
A name converter can now prevent a name from being converted (even by other lower-priority converters).See the API of the chemaxon.naming.NameConverter class.
Document to Structure (d2s)
Peptide 3letter 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 60seconds.Default is 0meaning infinite timeout.
A new option has been added to disable the extraction of OLE embedded structures from Office documents (option name: "d2s:-ole").
Structures imported from the custom name dictionary now have the "Type" property set to "custom" instead of "common".
Memory usage has been significantly reduced when processing large PDF documents (for instance hundreds of scanned pages).
Structure image conversion by OSRA has become faster, resulting in more structures converted when previously a timeout was reached.
CAS Registry Numbers® (which typically include commas) are not converted by default by d2s anymore (they are still converted by n2s).The old behavior can be activated by using the "d2s:CASnames" format option.
The unwanted interpretation of some common words as chemical names, that are frequent especially in patents, has been avoided.For example, the 'amino' group when used in the phrase 'amino acid', or 'Ser' when it is not the abbreviation of Serine but 'Ser.No.' for 'serial number'.
Structure to Name(s2n)
Multiple name generation tasks can now be run in parallel at full speed to make use of multiple CPUs and cores.
Multiple name import tasks now run faster, as partial locking is no longer required and has been removed.
Generated names now use unicode characters when needed, for instance, 6λ4-thiadispiro[5.2.59.26]hexadecane instead of 6$l^{4}-thiadispiro[5.2.5^{9}.2^{6}]hexadecane.The pure ASCII output can be generated using the "name:ascii" format option.
Image I/O
New parameter imageImportServiceURL has been added to the image importer module.The URL can be set on the "Preferences" dialog or as an import option.
VMN import
VMNs of type "display" are now read.
VMN abbreviated group list has been extended: carbon chains up to 50members 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: C0is transformed to CHK; C1is 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
MolAtom.BRIDGEATOM_H, is added to Hydrogenize.removeHAtoms(MoleculeGraph, int) method to remove hydrogens connected to bridgehead atoms.Valence Check
Local valence check has been introduced, which calculates the valence by considering only the neighboring atoms.Although the new valence check is the default, the old one is also available.
S-groups
ElementalAnalizerPlugin calculates Polymer Formula for molecules containing SRU or RepeatingUnit S-groups.
Calculations
Charge (Charge, Polarizability, ...)
Dipole Moment Calculation plugin: calculates the net molecular polarity.
NMR (CNMR Prediction, HNMR Prediction)
New, mixed HOSE code/CXN model has been introduced, which results in more accurate NMR shift prediction.
C-F and H-F couplings are considered during NMR shift calculation.
Diastereotopic protons are supported in HNMR Prediction.
The tautomers of the predicted molecule are accessible via the Options > Select Tautomers...option of the NMR GUI.The spectra of the selected tautomers with defined percent composition are added to the predicted spectrum.
Chemical Terms
"molString" and "molFormat" Chemical Terms functions are accessible under the name "molConvert" as well.
Structure Checker
Structure Checker is going to be moved to the MarvinBeans package.Until it is done, the new Structure Checker GUI is available in both JChem and MarvinBeans packages as Structure Checker JChem and Structure Checker , respectively.
Substructure Checker feature is accessible only in Structure Checker JChem until the complete relocation of Structure Checker.
Improved R-group Attachment Error Checker detects R-group definitions having incorrect R-group attachment orders.Fixer is not available for this feature yet.
New Explicit Hydrogen Checker options are ready for use.
Checkers that are not recognized as internal or external checker are called: "Invalid Checkers".Invalid Checkers cannot be used in valid Structure Checker configurations; they need to be removed to perform proper working behavior.
Build/Installation
Marvin Beans and JChem installers - for Linux - bundled with Java 1.6.0_33have been introduced.
Bug fixes:
MarvinSketch GUI
The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.
Several mnemonics were duplicated or missing in the menu of MarvinSketch.
Painting
Bond topology representation was not visible in R-groups.
Dialogs
Periodic table view 'Blocks' showed Helium color coded as a part of 'p block' instead of the correct 's block'.
Import/Export
Load/Save handling in UI
MarvinSketch did not overwrite the former PDF file when changes were made and it was saved as a PDF again with the same file name.
MRV, CML
The string value of a query property was imported as element.
MOL, SDF, RXN, RDF
Registry number of a molecule that is a property of an other molecule was not imported from RD file.
SMILES/SMARTS
Cis/Trans information was not exported for bonds being in two rings.
CXSMILES/CXSMARTS
Query pseudo atoms represented by CXSMARTS lost their valence property during import.
R-group definition of an Rg-molecule described in CXSMARTS was imported as CXSMILES.
CDX/CDXML
Reaction agent was not possible to read from CDXML file.
From CDXML file containing only a product of a reaction, the product was imported as reactant.
Name to Structure (n2s)
Names ending with "group", such as: "cyclohexyl group" were not imported.
Chirality specified without locant was sometimes not included in the generated structure, for instance in (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate.
Document to Structure (d2s)
Several names separated by a comma were sometimes wrongly recognized as a single name.
Document to structure was leaking some memory in a way that was problematic for extremely large documents (tens of thousands of structures in a single document).
When using the d2s API, waiting threads could be left behind when large documents were converted but the structures were not read until the end.This is now fixed, provided the client calls MolImporter.close().
Document to structure was not processing text from PDFs with non-standard fonts, for instance English text encoded in Japanese fonts.
Certain images in PDFs were not processed correctly by OSRA during optional image-to-structure conversion.
Names found in documents may have included unwanted trailing characters when the next word started with an open bracket, for instance, "cholesterol [28]" instead of "cholesterol".
Structure to Name(s2n)
The group "[NH3+]-" was given traditional name "aminio", instead of the correct "ammonio".
Names were generated for structures with link nodes, as if the link nodes had been absent.
Incorrect names were generated for structures with one attachment point.
Molecule representation
Meitnerium appeared at a wrong position in the periodic table of MarvinSketch.
Explicit hydrogen that connects to an atom having more than one wedge bond was not converted to implicit one.
S-groups
When an expanded SuperAtom-Sgroup was inside an other S-group, its attachment points had invalid implicit hydrogen count.
Stereochemistry
Clean 2D
Clean 2D inserted wiggly bond into a Kekule form of a 0dimensional 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
Structure Checker
Abbreviated Group checker options did not work as expected: checker recognized both expanded and contracted groups regardless of the selected option.
Build/Installation
Desktop icons were missing from the Marvin Beans for Linux installer.
New features and Improvements:
Applet
Class reorganization for more efficient applet loading.
New features and Improvements:
Import/Export
MDocSource implements Iterable<Molecule>.
MOL, SDF, RXN, RDF
New option for MDL MOL format import, Fsg, has been introduced to ungroup superatom s-groups with more than two attachment points.
Bug fixes:
Import/Export
New features and Improvements:
MarvinViewPrinting
Resolution of PDF printing has been increased.
Datatransfer
Legacy MRV '\n\ header (5.7) format is supported in Marvin OLE.
New features and Improvements:
Import/Export
MOL, SDF, RXN, RDF
Coordination bond is written and read from extended MOL file.
Name to Structure (n2S)
More extensive support for the retrieval of CAS Registry Numbers® from publicly available sources hosted by the U.S.National Institutes of Health (“NIH”) and the Wikimedia Foundation.
Clean 2D
New clean option, Toff, is introduced to ignore template based cleaning.
Coordinate bond length has been increased for a better view of its arrow representation between atom labels.
Bug fixes:
MarvinView
MarvinViewdid not display the SD file property if no property values were attributed to the first entries.
Painting
The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.
Editing
Import/Export
Byte Order Mark (BOM) was not written out during the export.
Default line separator was not unique in MolExporter.
CDX/CDXML
Empty CDX and CDXML files could not been imported.
Molecule representation
Stereochemistry
Calculations
New features and Improvements:
Import/Export
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)
The speed of major microspecies calculation has been improved when "Take major tautomeric form" option is used.
NMR
Bug fixes:
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
CDX files containing labels without chemical structures were not read.Now, these labels are read in text boxes.
SKC
SKC import put an R-group attachment point to Superatom S-groups.
Stereo information was lost at importing a peptide from an SKC file.
Wedge bond information of a contracted S-group was lost during the SKC import.
Molecule representation
Valence Check Valence Check allowed any number of bonds on carbon atoms having implicit hydrogens.
RgMolecule.fuse() resulted inconsistent molecule when it was invoked on RgMolecules having SuperAtom S-group in its definition.Stereochemistry
Nitrogen being one of the fusion points of ring systems was detected as chiral when the carbon atom at the other fusion point had four explicit ligands.
Aromatization/dearomatization
Dearomatization failed for porphyrin-like ring systems.
Calculations
Charge (Charge, Polarizability, Orbital Electronegativity)
Charge calculation was not consistent on fragmented molecules.
Isomers (Tautomers, Stereoisomers)
Different rational canonical tautomers were generated for some molecules when they came from different sources (e.g., InChi and SMILES).
Tautomer distribution was not calculated for various porphyrin-like structures.
Geometry (Topology Analysis, Geometry, PSA, MSA)
Negative or zero Van der Waals and Solvent Accessible molecular surface area values were generated for molecules with inconsistent chemical structures.
Structure Checker
Abbreviated group checker did not identify expanded and contracted groups correctly.
New features and Improvements:
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
The page format settings on the print dialog is now stored and do not need to be reset when starting a printing job from MarvinSketch or MarvinView.
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
DNA nucleic acid sequence can be imported in four ways: ACGT, A-C-G-T, dAdCdGdT or dA-dC-dG-dT.RNA nucleic acid import accepts sequences like both ACGU and A-C-G-U.
Molecule representation
Molecule/atom/bond properties
Similarly to MolAtom, general properties are possible to be added to MolBond.
New, simple way is provided to replace isotopes.data and elements.zip used in PeriodicSystem.java.
S-groups
New method is introduced to set a data S-group to behave as relative after specifying its absolute position
R-groups
A new, fast method is available to delete one or more molecules from an R-group definition.
Calculations
Isomers (tautomer., reson.)
Rational tautomer generation option has been introduced.Generation of All tautomers and Canonical tautomer can take this new option into consideration.
Improved generic tautomer generation in case of aromatic molecules.
NMR Predictor
NMR Predictor is available in MarvinSketch.It accurately predicts 13C and 1H NMR spectra of standard organic molecules.
Services
LocalService allows to set URL based JAR path.
Structure Checker
New checker: Absent Chiral Flag checker; when the molecule is chiral and all stereo centers are precisely marked, absolute chiral flag can be applied to the molecule.
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
Bug fixes:
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.
MarvinViewGUI
MarvinSpace
MarvinSpace: JOGL 1.1was replaced by the most recent version 2.0.This resolves various MSpace launch and initialization issues (in particular Applet problems on MacOSX).
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
The rb atomic query property was not displayed at the mouse tooltip when it was set through its keyboard shortcut: ".rb".
Chemical Structure Painting
Positioning of R-group labels was incorrect.
Datatransfer
Clipboard handling
Copy as PDF used 100x100px as image metrics and not the appropriate size for the current scale in Mac OSX.
Import/Export
MOL, SDF, RXN, RDF
The subscript information of the S-group generic bracket was not exported to MOL V3000 and V2000 formats.
Export of compressed MOL files allowed too large coordinate values, which caused distortion in the molecule after importing it.
After importing an RDfile that contains an empty S-group, its brackets didn't appear.
SDF
Data S-groups were lost after exporting it to SDF format.
SMILES, SMARTS
Export to abbreviated group format did not work since 5.8.
CXSMILES, CXSMARTS
CXSMILES import added radicals to atoms that have coordinate bond to a central, metal atom.
I/O of atom alias "," was not working in CXSMILES format.
CML, MRV
Format mrv had missing closing tags at the end of the generic S-group lines.
MolExporter exported to MRV format using operating system specific line ending, '\n'.
CDX
Standalone list atoms and labels were read as text boxes from CDX files.
Component grouping was not recognized during CDX import.
SKC
During the export to SKC format, chiral flags were lost and "AND enantiomer" flags were displayed.
CDX/SKC
When opening a ChemDraw CDX file or an ISIS/Draw .skc file containing structures with abbreviated groups, the attachment point of these groups was rendered incorrectly.
Structure to Name (s2n)
There were extraneous numbers in generated names for structures containing atom values.
Generation of IUPAC names for large structures might have stopped before the timeout.
Name to Structure (n2s)
The n2s import option to specify the location of the custom dictionary was not thread-safe, and was not accessible in d2s.
Name to structure failed to return a result on some very long names (several hundreds of characters).
Document to Structure (d2s)
Non-chemical data in embedded structures, for instance text labels, were not extracted from embedded documents.
Some embedded structures were not extracted from office documents.
Reactions embedded in documents were not extracted.
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
A NullPointerException appeared in the console instead of an error message when using molconvert to convert an image with skiperror parameter set without OSRA installed.
Molecule representation
Valence Check
Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
False positive valence error was on aromatic rings which have sulfur ligand that is part of a ring.
Removing explicit hydrogen atoms from LiH, CaH2, SH4, PH5, PbH2, PbH4 did not keep the original hydrogen count.
Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.
S-groups
Bracket positioning did not take the implicit hydrogen atoms into account.
If data were added as "relative", the cleaning or arrange methods did not take them along with the fragment/component/molecule.
The chirality of expanded S-group's atom changed, when there wasn't enough space in the canvas for the expanded S-group.
After expanding S-groups, atoms of the molecule could overlap.
Removal of explicit hydrogen being the only atom of an S-group was unsuccessful.New flag, SGROUP_H, has been introduced, 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
Fragmantation of an Rg-molecule resulted inconsistent molecules.
Clean 2D
In case of selection, stereoinformation of the molecule during two dimensional cleaning was lost.
Aromatization/dearomatization
General aromatization worked incorrectly in case of molecules with a bond connecting 2rings but not being part of any ring.Solving this problem, deprecated method int[] getSSSRBondSet(), was removed and, instead, BitSet getSSSRBondSet() was introduced.
Calculations
Protonation (pKa, reson.)
The predicted pKa of certain CH acids were extremly low.
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
Exception was thrown during conformer generation if Visualize H bonds option was selected.
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
Elemental Analyzer calculated wrong molecular formula for molecules, that contains bond to a centroid.
Bug fixes:
Calculations
Marvin Services did not return string result in some cases.
Backend / Core
Import/Export
Structure Checker
Bug fixes:
Molecule representations
Import/Export
MOL, SDF, RXN, RDF
File format "molV3000" was recognized only when it was imported from a file having "mol" extension.
Load/Save handling in UI
Bug fixes:
Aromatization/dearomatization
Aromatic ring count returned zero in those cases, where the aromatic ring contained charged carbon with two aromatic and one single bond.
New features and Improvements:
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
Accuracy of pKa calculation for amides has been improved.
Tautomerization of molecules containing nitroso group results in chemically more feasible isomers.
Speed of standard tautomer generation has been improved significantly.(On average about one hundred times faster.)
Bug fixes:
MarvinSketch GUI
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
Element type in some non-standard PDB file was not recognized properly.
VMN
Charge and implicit hydrogen information was not read from VMN files.
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
Aromatic ring count returned zero in cases where the aromatic ring contained negatively charged carbon with two aromatic and one single bond.
Calculations
Protonation (pKa, etc.)
CH acid type structures might have caused errors during pKa calculation.
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: 10valence electrons around a nitrogen are only allowed for nitro groups.
Backend / Core
Import/Export
NullPointerException was thrown by MoleculeImporter if "d2s:+cas" or "d2s:-cas" format string was specified.
Character encoding
Some special characters were converted incorrectly from UTF.
New features and Improvements:
MarvinSketch GUI
MarvinViewGUI
Import/Export
CML, MRV
New option to MRV and CML export, :C N , is introduced, where 0< N ≤ 9and N is the length of the decimals of the exported coordinates.For example, mrv:C5
Name to Structure (n2s)
Conversion of systematic names has been increased by about 5%, and increased accuracy of the generated structures.
Prefix "nor" has been implemented (e.g., 17-Hydroxy-19-norpregn-4-ene).
Name with stereo-markers "r" or "s" where such stereoconfiguration cannot be present are now interpreted as "R" or "S".This allows names that have been completely lowercased to be converted correctly.
Document to Structure (d2s)
Document to Structure supports the following common office document formats: doc, docx, ppt, pptx, xls, xls, odt in addition to pdf, xml, html and txt.
Format options have been added to d2s, to specify what input formats should be converted (for CAS 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
Valence Check
Calculations
Isomers (tautomer., reson.)
Tautomerization can take into account the possibility of ring closure when "All tautomers" function is selected.
NMR Predictor Beta
"Copy to Clipboard" and "Export Prediction to PDF" actions have been implemented.
cxcalc
Advanced logging in cxcalc: logging errors and execution times is available.
Structure Checker
Chiral flag error checker options have been improved.
Custom fixers use annotations replacing property files.Backward compatibility is ensured for both custom checkers and fixers.
Pattern based report file generation is available as a new option in structurecheck commandline.
MarvinSpace
Bug fixes:
MarvinSketch GUI
MarvinView3D window could not be opened from the sketcher if MarvinView 2D window had been opened before.
Applet
Applet settings could influence the client side desktop application settings.
Painting
The query properties were wrongly painted in some cases and covered the atom labels.
3D rotate action activated automatically when joining a structure in hand to a bond of a 2D structure on the canvas.
Double bond was not painted in centered position in case of terminal bonds when the label of the connected atom was displayed or both of the atom labels were displayed.
Single arrow type brackets were not painted.
The orientation of explicit hydrogens was incorrect when explicit hydrogens were added to the (selected) upper methylene C atom of a cyclohexane.
Import/Export
MOL, SDF, RXN, RDF
Handling of special characters (-, ", space) in extended MDL MOL format IO was wrong.
RDF file exported by Instant JChem was not imported correctly to ISIS/Base.
SMILES, SMARTS
In some rare cases, the unique SMILES of a molecule depended on the numbering of the atoms.
CML, MRV
Parity value in CML format was stored the opposite way as the CML standard defines it.Now the correct value is stored which leads to backward inconsistency with CML files generated by Chemaxon applications in previous versions, but correct values are read from standard CML files.To avoid running into similar problems in the future, now a version information is stored both in CML and MRV formats.This information contains a version number of the file format and the application version by which the file was generated.The parity value is changed to opposite in MRV format as well to be consistent with the CML format but it does not lead to backward inconsistency in this case: parity values stored in not versioned MRV files are converted to their opposite while parity values from versioned MRV files are not.
View settings were not applied in exported pdf file.
VMN
VNM format sometimes was recognized wrongly as mol2.
Image I/O
The molecule source was generated in unnecessary cases.
javax.imageio left temp files open if the ImageOutputStream was not closed properly.
Structure to Name (s2n)
The generated names for bridged and spiro ring systems were missing E/Z stereodescriptors for double bonds in large rings.
Some unconventional names were generated with suffixes such as amido, sulfonyl, carbonyl, ...mentioned as prefixes.For instance 2-[(2-chlorophenyl)amido]benzoate for [O-]C(=O)C1=C(NC(=O)C2=C(Cl)C=CC=C2)C=CC=C1.The generated names is now 2-(2-chlorobenzamido)benzoate.
Name to Structure (n2s) Stereochemistry was not indicated in the displayed structure when cis or trans is used to specify the configuration of the two substituents of a ring system.
Cycloalkane substituents of fused ring systems were aromatized.
The stereochemistry of chiral atoms in subsitutents was sometimes inverted.
Name to Structure was blocked on some very long names with unbalanced parentheses.
Document to Structure (d2s)
Some types of smiles strings were not recognized by Document to Structure, in particular those with stereochemistry or acyclic structures with two-letter heteroatoms.
Peptide
Numbers or sign "-" in the name of custom aminoacids were not accepted during the import of peptides (exception was thrown).
Molecule representation
Valence Check Valence Check gave false valence error for aromatic oxygen having +1charge.
Structure Checker
Known issues:
Structure Checker
Bug fixes:
Stereochemistry
Structure Checker
New features and Improvements:
MarvinSketch GUI
Import/Export
Molconvert has a new option, :D, which is important if the molecule has parity information and has 0dimension.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.
Bug fixes:
MarvinSketch GUI
Import/Export
Bug fixes:
MarvinSketch GUI
Import/Export
MOL, SDF, RXN, RDF
The line break in the Sgroup Attachment Point information section of the Extended MOLFile (MOL V3000) format was wrongly inserted in case of longer peptide sequences containing Cysteine.
CML, MRV
From version 5.8.1, molecules having parity information are exported in 2D form instead of 0D form in order to avoid incorrect parity representation.
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
Hydrogens attaching to sgroups were not treated as special ones and from version 5.8.1, their removal is optional.
Data Transfer
OLE
Calculations
Structure Checker
New features and Improvements:
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.)
MarvinViewGUI
Import/Export
Structure to Name (s2n)
New name format option: "source" has been introduced to print the names present in the source molecule data.For instance, molconvert name:source input.sdf.
Name to Structure (n2s)
n2s handles stereochemistry of cyclic monosaccharides.
Extended support for common names: n2s can convert 123thousand common names – including synonyms – corresponding to 34thousand structures instead of the previous 63and 28thousand, respectively.
Document to Structure (d2s)
Automatic text OCR (optical character recognition) has been added to support document to structure conversion of scanned (non searchable) PDF documents.
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
Chemaxon Extended SMARTS represents R-group (Markush) structures.
CML
CML bondStereo implementation has been completed with atom references.
CML format has been changed: there is no indentation, there are line-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 2011document and to paste it to Marvin.
More verbose logging from OLE .NET panel (catching managed bridge exceptions via COM) has been introduced.
Bug fixes:
MarvinView
Sometimes molecules were lost when switching from "Spreadsheet mode" (Table>Options>Table Type) to "Molecule matrix" mode.
When a zero length structure file was opened, the content of the previous file remained in the viewer until the first repainting.
Scrolling up and down increased the number of molecules and changed their orders.
Painting
Until the first repaint, textbox was smaller than required, and the content was cropped to its size.
Import/Export
Structure to Name (s2n)
Incorrect name was generated for chiral allenes, for instance: (2M)-1,3-dichloropropa-1,2-diene, the correct is 1M.(The locant was previously in the middle of the cumulated double bond system, but is now at the beginning of it, as prescribed by IUPAC.)
Fixed generation of names in the case where a radical marker "yl" was missing, for instance "...(4-methylbenzene)sulfonyl..." instead of the correct form "...(4-methylphenyl)sulfonyl..."
Name 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)
The total length (getEstimatedTotalCharacters) was not available to progress listeners during Document to Structure conversion of PDFs using the API.
SMILES
CXSMILES IO error due to non-escaped characters appeared.
The name imported from SMILES format was wrong in rare cases, when special characters (e.g., |) were in the fields part of the extended SMILES.
Calculator Plugins
logP and pKa calculations threw error at heavy atom count 300.
Generic tautomer generation might have threw an error if the molecule contained Hydrogen isotopes.
Bug fixes:
Molecule Painting
Valences higher than nine were wrongly displayed if the valence property visibility was turned off.
Calculator Plugins
Some property calculations threw ArrayIndexOutOfBoundsException when the input molecule contained multiple fragments.
Build/Installation
OLE defect occurred during side-by-side installations.
New features and Improvements:
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
Traditional name for known class names (e.g., acylcholine) is generated.
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
Hashed bond type has been implemented in Marvin."Hashed to Down Wedge" conversion has been changed to "Hashed to Hashed" conversion.
Clean 3D/optimization
Verbose mode has been added to Generate3D.Use option "[verbose]" to switch on; use "molconvert -H3D" for detailed help.
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
chemaxon.marvin.util.ColorGenerator class provides an easy way to generate the required number of different colors.
Several core functions are deprecated.
APIsupport for running checkers and fixers multiple times automatically.
Bug fixes:
MarvinSketch
The Java beans and applet parameter for switching the valence property visibility OFF was missing.
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
MarvinViewprinting
Several MarvinView display property was missing in MolPrinter
Painting
Error highlight was partially visible and often disappeared on mouse move.
Molecule Painting
Positive charge of hydrogen was not scaled properly in case of small magnification.
Import/Export
Structure to Name
Incorrect names where generated when the parent structure has identical substituents orientated differently, for instance: 4-formamido-1H-pyrazole-3-carboxamide
Inchi Key
Inchi slowdown with inchikey call for 10000s of structures.
OSRA did not work in Marvin unless its library was set in the PATH.
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
Allene parity lost by removing explicit hydrogens.
Aromatization/dearomatization
Aromatization of an aromatized structure created new aromatic ring
Elemental analysis
The Elemental Analyzer did not support Position-Variation bonds in formula calculation.Known issue: Dot-disconnected formula calculation is not working correctly in case of Position-Variation bonds.
Bug fixes:
Import/Export
Importing Molfile which starts with "BM" failed with OSRA related error message.
SD files started with "P3" was recognized as PPM file instead of SDF.This bug was a result of changes in Marvin version 5.5.
Bug fixes:
Import/Export
Bug fixes:
Import/Export
Data Sgroup was converted incorrectly to cxmiles.
Opening PDF files, NullPointerException occured in some cases.
New features and Improvements:
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).
MarvinViewGUI
Applet
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
There is a significant speedup of sequential and random Markush enumerations.(Hundreds of times speedup for average patent Markush structures.Speedup depends on the complexity of Markush structures.)
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.
API
Applet API has been improved with validateMoleculeStr(String str) and validateMoleculeStr(String str, String format) methods.
Bug fixes:
MarvinSketch GUI
MarvinViewGUI
MarvinViewprinting
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
ArrayIndexOutOfBoundsException did not work in case of SmilesImport and Chirality calculation.
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 64bit environment.
2D clean
Bad 2D cleaning in case of fused ring system.
Aromatization/dearomatization
Aromata.isDaylightAromatic considered (O=[N+]1C=CC=C1) incorrectly.
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").
Marvin Beans installer could not start with 64bit Java 1.6under OS X 10.5.
New features and Improvements:
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.
Bug fixes:
MarvinSketch
Pressing the Shift key when the mouse cursor was on an atom threw an ArrayIndexOutOfBoundsException.
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
pKa prediction threw ArrayIndexOutOfBoundsException in case of oximes.
Tautomerization threw ArrayIndexOutOfBoundsException in case of a few complex aromatic systems.
Bug fixes:
Calculator Plugins
Structure Checker
New features and Improvements:
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
Visualization of aromatic rings and triple bonds have been improved.
Compatibility
Minimum Java requirement of Marvin is 1.6.
Data Transfer
If a selection is made on the structure in the MarvinSketch window that has been opened from the MView pane, the closing of the MarvinSketch window (or clicking on the transfer button) transfers the selection back to the MView pane.
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
Electron flow arrows are redesigned.It is now separated to logic and display part.
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 Chemaxon Extended 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::
AromaticityErrorChecker searches for aromatic systems that can't be dearomatized or rearomatizing with the given method does not reproduce the initial molecule.
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
Integrate new MCES algorithm into AutoMapper.
API
Implementation of MoleculeGraph.getAtomCount(int atomicNumber).It returns number of atoms in the molecule with the given atomic number.
Bug fixes:
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 1to 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
MCS based alignment bug: bad similarity score was returned for CCC1CCCCC1.CCCCCCC1CCCCC1 .
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
When a chem terms column was added in IJC that generated InChI, it occurred a lots of errors and JVM could crash.
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
In the Save As Image dialog, there was a typo in the file type filter list.
ArrayIndexOutOfBoundException in template parameter handling.
Bug fixes:
MarvinSketch
Fix generic template toolbar removal ability throught ttmpls parameter.Avoid warnings in template related code.
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
JChem and Marvin Beans installers for Windows also extract shell script for cygwin.
Calculator Plugins
Preserve exocycyclic groups in Bemis-Murcko frameworks.
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
Lasso selection mode can be set to be the default in MSketchPane.
A new function, isChiral has been added to TopologyAnalyzer.
Bug fixes:
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
The loading of the isotopes.data file from the java cache failed if its uncompressed version was stored in the cache (i.e.if the uncompression was done automatically by the webserver, and not by Marvin).
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
Tautomer generator threw ArrayIndexOutOfBoundsException in some cases.
Markush Enumeration
Homology enumeration produced inconsistent molecules for some VMN input.
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.
Bug fixes:
MarvinSketch
Highlighting of electron flow arrows was wrong when the base or end point was a bond.
Applet
Import/Export
MDL MOL and SDF
The index of the multicenter atom was incorrectly created during MDL MOLFile export in case of structures where the R-group was connected to the multicenter atom (position variation bonds).
SKC
Implicit hydrogens were missing from the atoms after the import or paste of structures in ISIS/Symyx Sketch file format (SKC file format).
CDX
CDX files including rotated graphical objects exported from old versions of ChemDraw could not be imported.
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
Structure Checker threw NullPointerException instead of ignoring incorrect configuration file.
API
New features and Improvements:
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
The S-group and the R-group storage has been changed.
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
SMARTS representation of X.
CDX/CDXML
CDX/CDXML import has been improved: TLC plates, table objects and r-logic are imported now.
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 MMFF94forcefield 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
All Topology Analysis functions require a valid license.
Installer
Full 64bit support: 64-bit installers are available for all platforms.
Registration of file associations can be turned-off with one checkox.
Bug fixes:
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
On Mac OS X, in Safari, the opening of the Periodic Table (or other modal) dialog caused freezing the MarvinSketch 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-1occurrences 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
InChi with AuxInfo failed to paste in into Marvin.
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
Moieties (Repeating Units without crossing bonds) were ignored in Markush enumeration.
HBDAPlugin threw ClassCastException in some cases.
Bug fixes:
MarvinSketch
Lone pair placement wrong in some case.
Simple arrows could not be deleted at enpoints.
Import/Export
molconvert.bat cxsmarts:qh failed with explicit H.
Bug fixes:
Applet
Molecule representation
Small brackets were displayed looking like a box when reading polymer Sgroups from MOL V2000format.
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
New features and Improvements:
Molecule representation
Calculator Plugins
Import/Export
Bug fixes:
MarvinSketch
Scaffold zoom was not working.
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
R group sign was misplaced when inserting a graphical object into the sketch.
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.
Bug fixes:
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
New features and Improvements:
IUPAC Name2Structure
Non standard capitalization of names in the custom dictionary are also accepted.
Marvin OLE support
It is possible to change the default editing mode of Marvin objects in MS Office applications to Stand Alone mode (i.e.upon double click the object is opened in a separate office document) by excecuting the corresponding registry setting (.reg) files.
Bug fixes:
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_19or 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_19or 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.
New features and Improvements:
MarvinSketch
A new option for direct structure search in a public database has been introduced: Find Structure in PubChem.
Applet
A message dialog containing a progress bar is displayed if the loading of a module takes more than 100milliseconds, 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.
Bug fixes:
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
Certain resources (like template files) could not be loaded-in with Java 1.6.0_19and above versions.Since Java blocked loading resources from untrusted content.
Painting
The lone-pair placement was incorrect in some cases.
Import/Export
Mrv: Reaction arrow parameters exported into Mrv files with Marvin 4.1.13or 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
"evaluate --list-functions" threw NullPointerException if the user's Evaluator configuration file was missing.
New features and Improvements:
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 64bit.
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
Bug fixes:
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.
MarvinViewdid not display associtated file in OS X.Dragging molecule file into MarvinView did not work either.
MarvinSpace
Import/Export
Mol2export 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.
Bug fixes:
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
Applet could not be reffered from JavaScript in Chrome.
Calculator Plugins
Avoid NullPointerException in logPFragmentCreator.
logP calculation in cxcalc did not produce output under Linux.
Bug fixes:
MarvinSpace
MarvinSpace could not be launched without a valid conformer license.
Applet
API
chemaxon.struc.StaticMolecule.getExplicitHcount() returned with null value instead of zero when no explicit hcount was defined for any atoms.
Marvin OLE
An empty molecule was returned by the first invocation of the getMol method of Marvin OLE server after setMol.
Documentation
Complete apidoc for Structure Checker API
Installer
The Marvin installer did nothing in silent mode ( -q command line parameter) if an earlier version of Marvin was already installed previously.
Bug fixes:
Structure Checker Progress bar remained on the screen during structure fixing.
Applets
New features and Improvements:
MarvinSketch GUI
Structure Checker add-on, a tool for detecting molecule features or drawing errors is integrated.
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 15degrees 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 100molecules 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.
MarvinViewGUI
Text search in molecule tables.
Marvin View can now open name files even when not all names are supported.
Save layout in MarvinView.
MolConverter
New parameters: -U for union output (fuse) and -I for processing input molecules in index range.
Marvin Space
3D molecular alignment is integrated into Marvin Space.
Save structure in Marvin Space.
Applets
Move Marvin applets (JMSketch, JMView) into the chemaxon.marvin.applets package.
Chemical Structure Painting
Electron flow arrows start at closest lone pair electron.
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
MarvinSketch and MarvinView documentation (JavaHelp) supports Favorites, which allows help topics to be saved and reused.
Licenses
License files can be merged with the command line tool.
API
MarvinBeans.jar has been devided into several small jars.
New methods in Marvin Applets API: JMSketch.clean2D(), JMSketch.clean3D().
APIto add custom file formats to clipboard functionalities in Marvin.
Bug fixes:
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
Add missing chiral modifiers in the name of pure hydrocarbons.
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
New features and Improvements:
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
New public example demonstrating the usage of text boxes with formatted text.
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
Bug fixes:
MarvinView
Import/Export
MarvinViewand MarvinSketch sometimes crashed when bad InChI was imported.
Chemical Structure Painting
The Wireframe with Knobs display option did not work.
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
Resonance plugin displayed a warning without a license (although it is a free plugin).
New features and Improvements:
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
Bug fixes:
MarvinSketch
Custom menus were not loaded after restarting MarvinSketch.
MarvinView
Print All did nothing if multiple pages were sent to the printer from MarvinView.
Licenses
Fixed the displayed state of licenses to be installed.(Replaced "Invalid" with "To be installed".)
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
Bracket overwrote lone pairs, image generation clipped off lone pairs/charge symbol.
Calculator Plugins
New features and Improvements:
API
Bug fixes:
MarvinSketch
Initialization problem in MarvinSketch if it was initialized through MarvinOLEServer.
Calculator Plugins
New features and Improvements:
MarvinSketch
A splash screen image is shown during the initialization of the MarvinSketch standalone version.
Import/Export
Partial charges are saved in mol2file format based on the calculation result of the charge plugin (charge license required; if it is not found then the mol2file 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
A new method has been implemented in the Structural Frameworks plugin of the Geometry plugin: checkMolecule().
The major tautomer generation has been sped up.
Stereoisomer plugin can generate stereoisomers with given chirality as constraint.
Bug fixes:
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
Homology templates were missing in applets.
Installation
Marvin/JChem batch files could not handle quotes in the parameter list.
Licenses
The use of the setLicense or setLicenseFile API resulted in unusable client licenses unless they had the "Server Mode Allowed" field.
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 1.02version has been integrated.
InChiKey can be exported.New export option: inchi:key
Calculator Plugins:
Added average microspecies charge calculations to cxcalc ( averagemicrospeciescharge ) and Chemical Terms ( averageMicrospeciesCharge() ).
Documentation:
chemaxon.marvin.MolPrinter and chemaxon.formats.MolConverter API are improved.
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) .
Bug fixes:
MarvinSketch:
Undo sets viewport to lower-right corner/Undo-Redo scaling.
Number of missing from menu label AND1and AND2in 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:
The chemaxon.marvin.MolPrinter.setMol method ignored atom sets.
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:
Name to Structure was not running freely from Marvin.
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
The Alignment plugin can be used with Conformation Plugin license.
API
Bug fixes:
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
MarvinViewhid the right side of text boxes.
MarvinViewdid not display SD file property when first entries are missing the value.
MarvinViewfreezing 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
MarkushEnumerationPlugin.getRandomStructure() did not return random structures, always the first enumerated was returned.
Licenses
Markush license exception was incorrectly thrown by JChemSearch.
API
MolImporter.getRecordCount returned 2* the expected number.
First (record number) column displays the value returned by MDocSource.getDocLabel.
New features and Improvements:
Compatibility
Minimum Java requirement of Marvin is 1.5.
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.
23new 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:value1name2: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
Bug fixes:
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
Clean 2D improvement.
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
Bug fixes:
Import/Export
New features and Improvements:
MarvinSketch
New template group: the generic groups that are used in searches in Beilstein.
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
Explicit valence setting of atoms is available from menu .
MarvinView
Applet
celli_jand the possibility to escape characters.Import/Export
Text format import from cdx.
Installer
Marvin Beans installer for Linux with Java.
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.
Bug fixes:
MarvinSketch
Keyboard shortcuts did not work properly.
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 .
Bug fixes:
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
The command license -l produced bad output, not listing properly installed 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.
Bug fixes:
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
Slight improvement in multimolecule file opening, the index of the stucture in the preview is automatically offered.
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
Important change in the licensing of calculator plugins: all plugins work in evaluation mode without a license.
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-8859-1and 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 12lines match at least one MDL format.
API
Clean 2D
Clean 2D considers electron flow arrows.
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).
Bug fixes:
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-16encoding 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
New option/parameter to display the label of carbon atoms in structures.
Moleculear representation
Get smallest set of smallest ring bond indexes.
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.
Bug fixes:
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
Bug caused parity error for certain strained structures fixed.
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
Evaluator config files defined by the user are read from .chemaxon/MARVIN_MAJOR_VERSION (UNIX / Linux) or chemaxon/MARVIN_MAJOR_VERSION (Windows) directory.
API:
Bug fixes:
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
Some certain structures cleaned ugly.
Template Handling
The nitro abbreviation template has been changed from neutral to the ionic form.
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).
F6and F7did 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 2support: 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:
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 base64encoded (cx)SMILES/(cx)SMARTS output.
UTF-8character encoding support for applet parameters.
Unique SMILES export has been changed because of the modification in aromatization.
Molecule representation:
Allow N with valence 5in 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
New calculations: fragment count, ring system count, largest ring system size, smallest ring system size, aromatic ring count, aliphatic ring count, size dependent ring counting functions (ring count of given size, aromatic ring count of given size, aliphatic ringcount of given size, ring system count of given size).
Geometry Plugin
Molecule projection calculations in GeometryPlugin: minimal projection area, maximal projection area, minimal projection radius, maximal projection radius.
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
The calculation algorithm has been improved using approximately 13,000experimental logP values collected from the PhysProp database.Nevertheless, the original unique algorithm that makes possible to accurately predict novel compounds still provides the basis of the calculation.
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:
Updated developer's guide and examples.
Bug fixes:
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 0instead 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:
Double bond stereo information was sometimes lost during SMILES import (if a double bond was between two stereo double bonds).
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:
Calculator Plugins: New methods in pKaPlugin: getMacropKaValues(int, double[], int[]) and getMacropKaValues(int).
Bug fixes:
Molecule representation:
Bug fixes:
MarvinSketch GUI:
Customization dialog was not displayed.
Complete missing configuration names.
Licenses:
License management did not work via JavaScript calls (e.g.get molecule in "name" format) due to Sun's security restriction.
New features and Improvements:
MarvinSketch GUI:
Default file location can be set in the Save/Load tab of Edit > Preferences.
Licenses:
Environment variables and Java system property is introduced for license install.
Bug fixes:
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:
MarvinSpace could not load String representation of molecules given by applet parameter.
Licenses:
Exception was thrown from license manager.
Molecule representation:
Replacing atom in Sgroup with Asp caused ArrayIndexOutOfBoundsException.
Atom coloring did not work after subsequent molecule loading.
Calculator Plugins:
Exception in enumeration of structures with multicenter S-group.
Tautomer generation failed if certain features were present in the structure (e.g.enhanced stereo).
New features and Improvements:
MarvinSketch GUI:
API:
Bug fixes:
Molecule representation:
Import/Export:
There was a slowdown in MView when loading molecules during scrolling.
CalculatorPlugin:
Calculator Plugins threw exception for molecules with pseudo atoms.
New features and Improvements:
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:
D/T symbols are used by default for Deuterium/Tritium in the following cxcalc/Chemical Terms calculations: isotopeformula , dotdisconnectedisotopeformula , isotopecomposition.
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).
Bug fixes:
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:
A number of atoms disappeared from the product by 3D clean of a reaction, and the same number of explicit hydrogens appeared in the starting material.
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
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.
Bug fixes:
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-16character 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
Bug fixes:
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-16encoding support for MolInputStream
APIchanges:
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 0second 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:
MDocument.simplifyMolecule()
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:
API:
Background color settings for MolPrinter: MolPrinter.setBackgroundColor(java.awt.Color).
Bug fixes:
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 40parameters.
MarvinSpace: lone pair visibility correction.
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.
Bug fixes:
Redo bug fixed.
Bugfix in Clean 2D
Fix bug by flipping.
MolAtoms were not selected when selectionChanged property change event invoked.
GUI:
Text box improvement: its highlighting color is lighter than other highlighting colors because dark colors obscured the text for short strings.
API:
Clear undo queue: MSketchPane.clearHistory().
New property to set default save format: defaultSaveFormat
Bug fixes:
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
See options of the tautomers calculation in cxcalc
New method in TautomerizationPlugin API: setMaximumTautomerizationPathLength(int)
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.
Bug fixes:
Fixing arrow initialization problem in RxnMolecule clean.
In PDB export, the -c option did not work properly.
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
Bug fixes:
In Graph invariant.
Arrow mirroring Bug fixes.
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.
Bug fixes in MolImporter.
Bug fixes 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:
Bug fixes:
Bug fixes in Clean 2D.
Bug fixes in aromatization.
Fix parity error during H removal.
Potential deadlocks are fixed in MarvinSketch initalization.
Bugfix in Parity.
Bug fixes in calculator plugins (Tautomerization,pKa,Ionizer).
Bug fixes:
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:
MarvinViewdrops 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 Bug fixes in pKa calculation.
Improved canonical tautomer generation.
Fixing broken peptide snake.
Bugfix in peptide import/export
Fixing minor bugs in clean 3D
API:
implicitizeHydrogens(int) is final.Subclasses should implement implicitizeHydrogens(int, MolAtom[]) instead.
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
Available in MarvinView as an optional 3D structure viewer.
Enhanced secondary structure visualization
Charmm pdb file support for both structures and crystals
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 TIP3water
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:
New S-group types: MIX (mixtures) and COM (components).
Daylight style mapping, mapping style guessing
Changes in MarvinSpace 1.3.1
Bug fixes:
Import/Export:
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 Mol2import/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-R32767are saved in MRV and V3Molfiles .In V2Molfiles , only R1-R999are 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:
3Dimensional 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
APIchanges:
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.
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:
Toolbar templates are not handled together with the other templates appearing in their own window.Toolbar template sets can be specified using the new ttmpls parameter, the old tmpls parameter is used only for other template sets.
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.
Bug fixes:
Molecule.calcHybridization() assigns HS_S to hydrogen atoms.
Bug fixes:
In aromatization.
In ionizer.
In Marvin Beans installer.
NullPointerException at refreshing empty cells in view table
Import/Export:
Minor Bug fixes 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:
Adding the dot-disconnected molecule formula calculation to Elemental Analysis.
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.
Bug fixes 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 Bug fixes:
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 Bug fixes:
Minor bugs in Calculator Plugins.
Clean 2D produced zero coordinates.
Edit source bullet import bug.
Potential deadlock at the closing of a MarvinSketch applet.
H removal throws exception on Markush structures.
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.
Bug fixes.
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.
Bug fixes:
Hydrogenize bug fixed: tetrahedral geometry of alcohol O is now maintained.
Minor Bug fixes in aromatization, in 2D cleaning and in molconverter.
Trivalent radicals are displayed and their MRV import is fixed.
Bug fixes 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:
MarvinPane.setAtomSymbolsVisible(boolean) applies to 3D molecules only; atom symbols are always visible in 2D.
Improved aromatization
Svg export gives UTF-8encoded output.
Bug fixes:
In CmlImport
In 3D cleaning
R/S and canonical smiles calculation speedup.
3D:
Improved 3D cleaning efficiency.
New Clean3D options.Time limit in the 3D cleaning process.
Bug fixes:
The R/S label is not displayed on the first atom of the structure.
Fonts are not scaled on the printed page.
Bug fixes in R/S calculation.
Implicit hydrogen hides upper bond.
Plugins: logP calculation is supplemented with metal fragments.
Bug fixes:
RGfile import with nonstandard header.
Fixing bugs according to the user's response and improvement of pKa calculation quality.
Smarts import: atom expressions of type [C,c] are imported as [##6].
Colored MarvinView labels at celular level
Bug fixes:
Error in extended SMILES export
NullPointerException at adding new structure to My Templates
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 V2molfiles if the b import/export option is used with 0argument.
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 = 2setting is removed.Use bondDraggedAlong and MSketchPane.setBondDraggedAlong(boolean) instead.
Serialization: DPoint3and CTransform3D became Externalizable.
New applet parameter: molChanged0to evaluate a JavaScript code when the molecule is loaded.
Bug fixes: 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).
APIchanges in Sgroup, SuperatomSgroup, and MultipleSgroup: the copy and the newInstance methods are replaced by copy constructors and cloneSgroup.
Other
Line thickness can be set for wireframe mode using the wireThickness applet parameter and the MarvinPane.setWireThickness bean method.
Line thickness for graphics line, polyline, rectangle and text box objects can be set using MPolyline.setThickness.
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.
Bug fixes:
In MolConverter
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 0are 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 CML2atom/bond attributes (instead of the deprecated builtins), reactions, stereochemistry, residues.Because of efficiency reasons, deprecated CML-1data types are not supported any more.
Base64encoding/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:
Analitic gradients implemented in Dreiding forcefield for optimization and Clean 3D
Document editing with graphics objects in sketcher
The MDocument class stores the molecule and other graphics objects like polylines and rectangles.The document can be saved in Marvin Document format.
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- 0.25mol/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.
Bug fixes: in MViewPanel.setParams, in Dreiding forcefield, PDB import, atom lists in V3molfiles, resize of MViewPanel and MSketchPanel, R-logic, etc.
Enhanced stereochemical representation support in extended molfiles.
Improved Charge and pKa calculation.
Bug fixes:
In SMILES q option.
APIchanges
Calculator Plugins:
logP: New atom types.
pKa:
Hydrogen bound defined between aromatic carboxyl and phenolic hidroxyl groups in pKa plugin.
Calculation of the sulphonamid acid molecules were improved.
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:
Background color, rendering style and navigation mode are stored separately for 2D and 3D.Cleaning a molecule in 3D also switches automatically to the 3D parameter set in that cell.Cleaning in 2D switches back to the 2D parameters.
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.
APIchanges:
MoleculeGraph.calcCenter returns the geometrical center instead of the center of mass.
Applets
Java 1.0compatibility is no longer maintained.The minimum Java VM version required to run the applets is 1.1 (Netscape 4.06, MSIE 4or 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 V2format:
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.
APIchanges
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.
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.
Bug fixes: 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.
APIImprovements: 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.
Bug fixes: 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).
Bug fixes:
Improved printing layout of MView tables.
Improvements: in Copy / Paste of reactions.
Molweight calculation.
Handling agents of reactions.
Signed Marvin applets
Open, save, cut and paste can be used with signed applets.Examples can be launched by selecting " Signed applets ".
Marvin applications with Java Web Start
Examples for using the MarvinSketch and the MarvinView applications via Internet.
New applet/bean parameters
valenceErrorVisible applet/bean parameter and property in MarvinSketch.Its value can be also modified from menu: View/Misc/Valence Errors.
reactionErrorVisible applet/bean parameter and propert in MarvinSketch.It can also be set from menu: View/Misc/Reaction Errors.
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.
APIchanges
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:
In PdbExport, Hydrogens are added with the common "H" option instead of "h".
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:
autoScale property was added, it can be accessed via setAutoScale() and getAutoScale() methods.
SketchPanel Improvements::
Autoscale is avaible both in AWT and Swing versions.
depending on the autoScale property automatic scaling is done when loading molecules
The select all function can be triggered by Ctrl+A.
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:
autoTabScale property enables automatic uniform scaling of cells.
MarvinViewImprovements:
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
Residue symbol is imported for standard residues.
Residue sequence number is imported.
New export and import options.
Export does not hydrogenize the molecule automatically, use the h option for this.
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");
APIfor 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.
APIsimplification: 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.node1and edge.node2unchanged (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.
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.
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.
1. New query bond types: "single or double", "single or aromatic", "double or aromatic", "chain" and "ring".
1. SMARTS export handles the heteroatom (Q in molfile) type intelligently.
1.
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.
1. Cell selection in MarvinView can be controlled using the selectable parameter.
1.
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.
1.
In Marvin 2.2and 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 2and MS Explorer 3).Reasons:
1.
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.
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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.
1. Marvin is rarely tested in the oldest (and buggiest) browsers.
If you are absolutely sure that you want your Marvin page work with Netscape 2and MS Explorer 3too, 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.
1. CML (XML) export.
1. The getSelectedIndex() method in MarvinView.
1.
Default value of the rescaling parameter in MarvinSketch is changed to "mag" because generally this value is the most useful.
1. The MarvinView-only package ceased to exist, the new Edit/Structure function made it irrelevant.
1.
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 1.1compatible 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).
1. 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.
1. New in MarvinSketch: The menubar parameter enables or disables the menu bar in the Swing sketcher.
1. New in MarvinView: Molecules start rotating in 3D automatically if you set the animate parameter in MarvinView.
1. New in MarvinView:Border between cells in molecule tables.
1. 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.)
1. 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 4and later, there is no such problem.On the other hand, a bug (or feature?) in Netscape 4.6makes the use of JavaScripter impossible as a separate applet.That's why we merged the two applets now.
1. New: Three new molecule file formats: "sybyl" (the SybylImport and SybylExport modules), "xyz" ( XyzExport ), and "pov" ( PovExport ).
1.
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.
1. New: The atomStrings parameter enables the usage of atom aliases and SMARTS strings in the sketcher.
1.
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 .
1. New: The new detach parameter makes it possible to detach the sketcher from the web page immediately when the applet is loaded.
1. 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 1.0b3has problems if you write more than one molfile lines in one HTML line.
1.
Removed: Backward compatibility with the old style (1.0-1.1) usage of getMol() and getM() removed.It didn't work with MSIE anyway.
1. Incompatible change: MSketch.getMol(x) and MView.getM(n,x).
In Marvin 1.1.4and 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".
1. 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">.