Release notes for 5.2.x releases
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
Bugfixes
- MarvinView
- MView table cell resizing is not working
(forum topic).
- Import/Export
- Aliphatic property was not added to aliphatic C with doublebond and
any bond during SMARTS
(forum topic).
- MarvinView and 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).
- There was a minor bug in license key verification.
New features and improvements
- MarvinSketch
- New icon is added to the "Add Attachment Point" action
(forum topic).
- New keyboard shortcuts: 5 - Single Up, 6 - Single Down, 7 - Wiggly
bond.
- Molecule representation
- Add function that returns improved information of parity.
Bugfixes
- 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
- Complete the missing isLeopardSafari() method in marvin.js
(marvin/sketch/index.jsp did not load in Mac Safari)
(forum
topic).
- Import/Export
- Partial charges numeric format in mol2 is fixed
(forum
topic).
- Molecule representation
- Nitrogen with double bond and explicit H gets stereo value
(forum topic).
- Bug was in setDim method in RgMolecule.
- Chemical Structure Painting
- Bracket overwrote lone pairs, image generation clipped off lone
pairs/charge symol (
forum topic).
- Calculator Plugins
- Canonical tautomer calculation threw ArrayIndexOutOfBoundsException
in some cases
(forum topic).
New features and improvements
- API
- New functions are added that return improved information of parity:
Parity.asymmetricAtoms(MoleculeGraph),
Parity.chiralAtoms(MoleculeGraph).
Bugfixes
- MarvinSketch
- Initialization problem in MarvinSketch if it was initialized through MarvinOLEServer.
- Calculator Plugins
- The chiralCenterCount function in TopologyAnalyser plugin returned now zero for the number of chiral centers of 1,4-dimethylcyclohexane.
No changes
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 mol2 file format based on the calculation
result of the charge plugin (charge license required; if it is not found then
the mol2 file is created without charges).
(forum topic).
- 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
- The arrangement of wedge bonds using the 'Clean wedge bonds' option has
been improved.
(forum topic).
- 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 (see applet parameters).
- 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()
(forum topic)
- 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
(forum topic).
- Stereoisomer plugin can generate stereoisomers with given chirality as constraint
(forum topic).
Bugfixes
- 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
(forum topic).
- The "viewCarbonVisibility" applet parameter did not work
(forum topic).
- 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
(forum topic).
- 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
(forum topic).
- Copy/paste and import/export of a molecule in mrv format having an S-Group with
only one atom did not work
(forum topic).
- The getAromaticAndAliphaticRings method threw NullPointerException
(forum topic).
- 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
(forum topic).
- Template handling
- Homology templates were missing in applets.
- Installation
- Marvin/JChem batch files could not handle quotes in the parameter list
(forum topic).
- Licenses
- The use of the setLicense or setLicenseFile API resulted in unusable
client licenses unless they had the "Server Mode Allowed" field
(forum topic).
New features and improvements
- MarvinSketch:
- The Clear Atom List button is added to the
Periodic System dialog window
(forum topic).
- Icon for Reaxys Generics is added.
- MolConverter:
- Option -m produces multiple output files from multi-molecule input
(forum topic).
- Applet:
- New applet parameters for setting license files
(forum topics: #3715,
#4796).
- Import/Export:
- InChi 1.02 version 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())
(forum topic).
- Documentation:
- chemaxon.marvin.MolPrinter and
chemaxon.formats.MolConverter API are improved.
- API:
Bugfixes
- MarvinSketch:
- Undo sets viewport to lower-right corner/Undo-Redo scaling.
- Number of missing from menu label AND1 and AND2 in
Atom > Stereo > Enhanced menu.
- MarvinView:
- Selected cell becomes unselected after changing table options.
- Import/Export:
- Pseudoatom export bug in MDL Molfile export.
- Chiral center had wrong connectivity at atom.
(forum topic).
- chemaxon.util.MolHandler threw ClassCastException by SMILES.
- Unique SMILES export bugs.
- ClassCastException threw by endless loop for invalid SMILES import.
(forum topic)
- 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
(forum topic).
- 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
- Customizable applet splash screen which is displayed while the applet is loading (live example).
- Import/Export
- Allows aromatic boron in cxsmiles.
- cxsmarts format stores attachment point data.
- Support for atom values in cxsmiles.
- Keep wedge arrangement in cxsmiles
(forum topic).
- 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
- CGraph.cloneCopy() copies all relevant cached calculated data.
Bugfixes
- MarvinSketch
- The first alteration of the structure couldn't be undone in MarvinSketch opened through MarvinView.
- The .H+/.H- buttons could not be used in some cases.
- Do not show carbon atoms when charge is on bracket.
- Bold font is used for superscripts in case of charge for better visibility.
- Missing bond problem after OLE copy: reimplementing bond-crossing drawing.
- Missing bond crossing visualization when crossing a bond with a bond vertically.
- The Insert > Groups dialog contained some empty elements.
- MarvinView
- MarvinView hid the right side of text boxes.
- MarvinView did not display SD file property when first entries are missing the value.
- MarvinView freezing when molecule subset start index set to invalid value.
- MarvinSpace
- MSpace debug printout is removed.
- Import/Export
- Rdf conversion lost the reaction number
(forum topic).
- Fixed fusion bridge wrong lettering in name export
(forum topic).
- 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
- New option for adding an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.
- 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") (forum topic).
- "Take major tautomeric form" option in MajorMicrospeciesPlugin.
- 23 new ring related functions in TopologyAnalyser.
- Resonance Plugin was moved to "Other" plugin group, and it can be used without license key (free)
(forum topic).
- Chemical Terms
- Flexible plugin parameter setting in Evaluator: "name1:value1 name2:value2 ...". (Example:
markushEnumerations('random:true id:true', '1,2', 5).)
- hasRadical(), radicalCount(), and hasIsotope() functions in Chemical Terms.
- fragments() function in Chemical Terms
(forum topic).
- CT Editor is available in Marvin API.
- API
- Transfer button: optional button to send the molecule to the specified target after closing MarvinSketch window.
- Specify own background color separately for each cell in MarvinView via (applet) parameter.
- New metal types can be specified in Periodic system.
- Structure checker core classes and functions are implemented.
- MViewPane enhanced table support.
- PluginFactory creates new plugin and display instances
for each getPlugin() and getDisplay() call in case of multimol display; added MOLECULES result domain type and
canRepeat() in CalculatorPlugin
Bugfixes
- MarvinSketch
- Disabled tooltips in menus.
- The copied and generated structure with Data S-group is much bigger than needed (forum topic).
- 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.
(forum topic
- SMILES export of SuperAtom S-group in SuperAtom S-group did not work (forum topic).
- Molecule representation
- Calculator Plugins
- Double bond stereoisomers of molecules containing wiggly type double bonds are generated correctly
(forum topic).
- 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.
What's new in Marvin 5.2?
- 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.
- A splash screen image is shown during the initialization of the standalone version.
- 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.
- MolConverter:
- Option -m produces multiple output files from multi-molecule input.
- Applet:
- The loading of MSketch Applet is sped up: the total size of the files
downloaded during the first initialization has been reduced by more than 20% between 5.2.0 and 5.2.3.
- New applet parameters for setting license files.
- 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).
- InChiKey can be exported. New export option: inchi:key.
- Partial charges are saved in mol2 file format based on the calculation
result of the charge plugin.
- Molecule representation
- New option for adding an explicit hydrogen atom to chiral centers
having no terminal atoms when 2D cleaning is performed.
- 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.
- The major tautomer generation has been sped up.
- Total charge calculation in cxcalc ("totalcharge").
-
- "Take major tautomeric form" option in MajorMicrospeciesPlugin.
- New ring related functions in TopologyAnalyser.
- Resonance Plugin was moved to "Other" plugin group, and it can
be used without license key (free).
- Added average microspecies charge calculations to cxcalc (averagemicrospeciescharge)
and Chemical Terms (averageMicrospeciesCharge()).
- Chemical Terms
- Flexible plugin parameter setting in Evaluator.
- New functions: hasRadical(), radicalCount(), hasIsotope(), fragments().
- CT Editor is available in Marvin.
- 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.
- 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.
- Named constants for applet and bean parameters are available.
- New MolRenderer API available.
