Changes, new parameters, upgrade problems
Bugfixes
- 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:
- File Open/Save preferences are implemented.
- Licenses:
- Environment variables and Java system property is introduced for
license install (See
details)
(forum topic).
Bugfixes
- 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:
- In the default configuration, the Explicit Hydrogens
option has been removed from the
View/Misc menu. (From now on the explicit Hydrogens are always
visible, but they can be added or removed using the corresponding options
of the Structure/Add and in Structure/Remove
menus.)
- API:
- New methods to control R-groups visibility in
chemaxon.marvin.beans.MarvinPane:
setRgroupsVisible(boolean),
isRgroupsVisible()
Bugfixes
- Molecule representation:
- Ungrouping of embedded S-groups threw IndexOutOfBoundsException.
- Import/Export:
- There was a slowdown in MView when loading molecules during scrolling.
- CalculatorPlugin:
- Calculator Plugins threw exception for molecules with pseudo atoms.
(forum topic)
- Random Markush enumeration generated larger link node enumerates than in definition.
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. (forum topic)
- 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()". (forum topic)
- 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).
- New calculation: randommarkushenumerations
Bugfixes
- 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 (forum topic).
- 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 (forum topic).
- 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:
- Bugfix: Reading compressed mol files from applet parameter was wrong
- Applet:
- Bugfix: Error by the initalization of the recent file list (forum topic)
- MarvinSketch:
- Atom > Stereo > R/S menu was missing
- Structure > Add > Position Variation Bond function is added
- Extended font support
- 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 (forum topic)
- Reading PDB files as simple Strings
- Import/Export
- Molecule file header and footer can be retreived using
MRecordReader.getHeaderAsString() and
getFooterAsString().
Related incompatibility: the MRV file header and footer are
not part of the record returned by
MRecord.getString() any more.
Prepend the header and append the footer to get an importable
molecule.
- Image export option to show E/Z labels.
(forum topic)
- East Asian character encoding support for applet parameters
(forum topic)
- The default behaviour 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.
- Bugfixes:
- Marvin applets did nothing by OLE copy (forum topic)
- MarvinSketch always dropped confirmation dialog when exiting in OLE mode (forum topic)
- UTF-16 character encoding fix in cell headers of MarvinView
- Fix on adding explicit H atoms to chiral centers (forum topic).
- Implicitize hydrogens bugfix.
- Fixed IUPAC name export failure involving spiro compounds.
- PDB import does better recognize connectivity and bond order of
hetero components, the assigment of superfluous hydrogen atoms is
fixed.
- 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 (forum topic)
- EMF and PDF exports uses the new version of Freehep API (2.1.1) (forum topic)
- Bugfix: Saving EMF and PDF in Marvin applets often gave emtpy or
corrupt file (forum topic)
- MarvinSketch:
- Toolbar drop-down list box is added
- Drag&Drop of templates works beside the template toolbar
- Bugfixes:
- tmpls, ttmpls, xtmpls parameters did not work
- setEnabled(false) function did not disable toolbars
- Help button did not work in the desktop application (forum topic)
- 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 (forum topic)
- Wedge arrangement around stereocenter having four ligands was improved
(forum topic)
- 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 (forum topic)
- 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 behaviour - reads in volumetric data by default
(former import option 'V'), skips it if
import option 'M' is specified
- UTF-16 encoding support for
MolInputStream
- API changes:
Related incompatibilities:
- MolImportIface and MDocumentImportIface interfaces are
replaced by the abstract class
MolImportModule.
Record skipping related methods removed
(isSkippingSupported, skipMol and skipToNext), use
MRecordReader.skipRecord
or
MRecordImporter.skipRecord
instead.
- MolExportModule:
the
open
method throws
MolExportException,
loadMarvinModule removed and replaced by
MFileFormatUtil.createExportModule,
getOptionSign removed.
Both MolExportModule and MolExportException moved to
chemaxon.marvin.io, the old versions in
chemaxon.marvin.util are deprecated.
- The canonical encoding name is returned by
MFileFormatUtil.getEncodingFromOptions
and stored by
MolExportModule.setEncoding,
MolConverter.createMolConverter and
the constructors of
MolImporter,
MolExporter
and
MolConverter.
These methods and constructors may throw
IllegalCharsetNameException or UnsupportedCharsetException.
- Import/export modules (not recommended to use directly!)
moved from chemaxon.marvin.modules to
chemaxon.marvin.io.formats and its subpackages.
- Calculator Plugins:
- Multiprocessor support in cxcalc
- Tautomerization:
- New tautomer generation rules were implemented
- Estimation of the tautomer distribution as function of pH was improved
- pKa, logP: Accuracy of the predictions were improved.
- Added EnumerationPlugin: enumerates Markush structures
- ElementalAnalyserPlugin:
- "Dot-disconnected isotope formula" calculation added
- "D" and "T" symbols can be used for "Deuterium" and "Tritium" in isotope formulas
- pKaPlugin: "Take major tautomeric form" option added
- logPPlugin: "Take major tautomeric form" option added
- logDPlugin: "Consider tautomerization" option added
- New surface area calculations in MSAPlugin:
- Water accessible surface area (ASA)
- Water accessible surface area of all atoms with positive partial charge (ASA+)
- Water accessible surface area of all atoms with negative partial charge (ASA-)
- Water accessible surface area of all hydrophobic atoms (ASA_H)
- Water accessible surface area of all polar atoms (ASA_P)
- GUI: "Restore defaults" button added to options panel
- Integration of user-developed calculations made easier (see developers guide)
- 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:
- 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:
- Incompatibilities:
- API:
- Fixed bugs:
- Import/export:
- There was a critical property based smiles export bug
- There was a NullPointerException in Parity (forum topic)
- 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.
(forum topic)
- Fix a small refreshing problem in MarvinSpace.
- Quick setting of component visibility on mouse drag in MarvinSpace.
- Calculator Plugins:
- Bugfix in the pKa plugin.
- Misc:
- Bugfix in the maximum common substructure search.
- API:
- Bugfixes:
- Change frames to dialogs to avoid focus problem of model dialogs.
(forum topic)
- "Any" bond was invisible in OS X.
(forum topic)
- ElementalAnalyser and ElementalAnalyserPlugin: scientifically correct rounding of molecular weight (mass)
- CleanUtil.arrangeComponents() bug for reactions containing Sgroups.
(forum topic)
- Bug in abbreviated group visibility.
- Correcting a bug of getting the most frequent natural isotope of Hydrogen. It returned 0, though the correct result is 1.
- Marvin Beans batch files accept 40 parameters.
(forum topic)
- 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.
- Bugfixes:
- 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:
- Bugfixes:
- IUPAC Naming: fixed timeout errors.
- Fixing bug "Phosphorus loses chirality after explicit-H-removal"
- Calculator plugins:
- Added dominant tautomer distribution calculation to Tautomeriztion plugin
- Maximum allowed lenght of the tautomerization path can be set in Tautomeriztion plugin
- Bugfix in displaying of pKa calculation results in command line (cxcalc).
- 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:
- IUPAC name generation improvements, in particular for ions.
- Bugfixes:
- Fixing arrow initialization problem in RxnMolecule clean.
- In PDB export, the -c option did not work properly.
- Empty field parsing bugfix in Smiles import.
- Import/export:
- Image export option ("noatsym") to hide atom symbols in
3D mode.
- SUBSTUCTURE 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:
- Bugfixes:
- LP chirality fix
- Bugfix in CleanUtil
- Minor bugfixes in calculation plugins
- IUPAC name generator, for
interactive and batch naming
- Bugfixes:
- In Graph invariant.
- Arrow mirroring bugfixes.
- Infinite loop fix in Parity.
- Converting to "base64:gzip:mrv" did not work.
- Exception by missing atom list definition fixed.
- ArrayIndexOutOfBoundsException in RxnMolecule.removeNode()
- Non-transformable polyline point highlighting fix
- InChi import/export works also in Java Web Start
- Import/Export:
- RDfile properties can be
hierarchized
or
flattened.
- Data sgroup improvements in MRV import/export.
- Bugfix in MRV export.
- Bugfixes in MolImporter.
- Bugfixes in Peptide import.
- Bad EOL (End Of Line) characters in the output of the InChi export was fixed.
- GUI:
- Double-clicking at selection unselects selected atoms.
- Bugfix in printing: Texts components covered each others on the printed view table.
- Removed unnecessary confirmation dialog by closing viewer detached sketch frame.
- Deleting problem of multiple is solved.
- Corrected the wrong location of plus sign in reactions.
- API:
- Bugfixes:
- Bugfixes in Clean 2D.
- Bugfixes in aromatization.
- Fix parity error during H removal.
- Potential deadlocks are fixed in MarvinSketch initalization.
- Bugfix in Parity.
- Bugfixes in calculator plugins (Tautomerization,pKa,Ionizer).
Bugfixes:
- Import/Export:
- EMF/PDF creating does not drop HeadlessException in headless
mode.
- Fix EMF export bug (structure was invisible if canvas contained
any text box).
- Problem with both super atom and data sgroups in mol import.
- ArrayIndexOutOfBoundsException in unique SMILES export.
- Plugins:
- In Tautomerization.
- In Charge.
- In pKa.
- In PolarGroups.
- Parity error during H removal.
- Abbrev group problem with Me3SiO.
- GUI:
- Fix endless loop by rings join.
- Exception in custom amino acid loading is fixed.
- API:
- Plugins:
- Bugfix in MSA calculation.
- Acceptor count and donor count is displayed on the plugin result window.
- Bugfix in Major Microspecies calculation.
- Minor bugfixes in pKa calculation.
- Improved canonical tautomer generation.
- Fixing broken peptide snake.
- Bugfix in peptide import/export
- Fixing minor bugs in clean 3D
- Minor bugfix in Parity
- API:
- Plugins:
- MarvinSpace
- Available in MarvinView as an optional 3D structure viewer.
- Enhanced secondary structure visualization
- Charmm pdb file support for both structures and crystals
- Charmm Slab visualization
- Import/Export:
- InChi import can load structures without AuxInfo.
- PDB import:
- multi model proteins
- nucleic acid backbone
- non-standard pdb file related changes (missing mandatory
blocks etc.)
- charmm pdb ATOm record support
- new class for Water molecules
- support for DOD and TIP3 water
- recognition of water H (even when it's denoted by O)
- H-O-H bonds
- GUI:
- Improved display performance for large structures.
- Bugfix in 3D rotation: Front atoms did not follow mouse movement.
- Atom/bond coloring bug for abbreviated groups is fixed.
- CxSmiles conversion in Edit Source window is fixed.
- Marvin applications uses user's home as default directory in the File Open dialog.
- New methods in API:
JMSketch.undo(),
JMSketch.redo(),
MSketchPane.undo() and
MSketchPane.redo()
- MarvinSpace 1.3.2:
- Charmm grid support
- Displaying bonds in water molecules
- Secondary structure visualization of nucleic acids
- Others:
- New S-group types: MIX (mixtures) and COM (components).
- Daylight style mapping, mapping style guessing
- Bugfix in Parity
- Changes
in MarvinSpace 1.3.1
- Bugfixes:
- Import/export:
- In SMARTS import
- In CxSmiles import/export
- In 3D cleaning
- Calculator plugins:
- In pKa calculation
- In logP calculation
- in logD calculation
- GUI:
- Bugfix in pseudo atom display
- Out of memory error by dearomatizing huge view tables
- Minor bugs in loading/saving journal styles settings
- Valence check bug
- Import/Export:
- EMF export
- Preliminary Mol2 import/export
- Image export: atom and bond
set colors,
wire thickness,
stick thickness
ball radius,
daylight down
wedge,
anybond style
and
atom mapping visibility
can be specified.
- Molecule and document properties
with special data types (not only strings) are exported and
imported in
MRV,
SDfiles and RDfiles.
Supported data types: boolean, int, double, int[],
Molecule, MDocument.
- molconvert: optionally skips
molecule on error and continues with the next molecule (option -g)
(default: as before, exits on error).
- R-groups:
- GUI:
- Integration of MarvinSketch and MarvinSpace:
- 3 Dimensional structure building: allows to modify ligand in the binding pocket.
- Visualization of plugin results: 3D structure display, colored molecular surfaces.
- Save options in viewer.
- Viewer handles huge SD files.
- Journal based drawing style templates
- Multipage molecular documents
- Plugins:
- License handling: added graphical license handler interface
- press the 'Manage license keys' button on the Edit / Preferences / Licenses tab,
in MarvinSketch or MarvinView, or else
- use the
license command line script
- MarvinSpace 1.3
- Ribbon representation of protein secondary structure
- Interactive editing of molecules/ligands in MarvinSketch
- Copy/Cut/Paste, Drag&Drop functions
- High resolution image export in various formats (PNG, BMP, Targa, JPG), arbitrary size
- New coloring types: secondary structure, rainbow, b-factor (temperature factor), SETOR residue colors, color palettes
- Interactive change of the isovalue of Gaussian Cube surfaces
- Enhanced selection tools: binding pocket, residues etc.
- Enhanced labels (colors, size, placement), more built in types (e.g. residue labels, secondary structure label)
- Improved error handling, out of memory does not terminate
- Progress bar, better feedback about processes
- API changes:
- Added
Molecule.cloneMoleculeWithDocument(): clones the molecule with its non-molecular data
(graphics objects: polylines, arrows; electron flows; text boxes).
- Added
Molecule.arrangeComponents(): avoids overlapping components (reaction components,
R-group definitions) by translations.
- Added
MolImporter.skipRecord(),
nextDoc(),
getRecordCount(),
getRecordCountMax(),
estimateNumRecords(),
seekRecord(int),
isRewindable().
- Sgroup.setGUIStateRecursively
returns true if the state was changed.
- CGraph became
abstract,
MoleculeGraph(parent)
and
Molecule(parent)
constructors removed to avoid confusion with copy constructors.
- The implementation of seeking in MolImporter required the extension
of the molecule/document import interfaces:
MolImportIface.isSkippingSupported(),
skipMol()
and
MDocumentImportIface.getGlobalProperties() must be implemented.
- The implementation of the sticky midpoints of MPolylines required
incompatible changes in the graphics classes:
MPoint.getX(),
getY(), getZ(), setLocation(DPoint3) and
setXYZ(double, double, double) are replaced by
getLocation(CTransform3D)
and
setLocation(DPoint3, CTransform3D),
MObject.calcCenter(DPoint3),
transform(CTransform3D, int) and getPointRef(int) are replaced by
by calcCenter(DPoint3, CTransform3D),
transform(CTransform3D, int, CTransform3D)
and
getPointRef(int, CTransform3D).
- Applet/bean parameter changes:
- 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:
- AWT applets have been removed from Marvin Applets package.
- .NET support in Marvin Beans.
- Bugfixes:
- Molecule.calcHybridization() assigns HS_S to hydrogen atoms.
- Fixed potential memory leaks in Marvin applets.
- Bugfixes:
- In aromatization.
- In ionizer.
- In Marvin Beans installer.
- NullPointerException at refreshing empty cells in view table
- Import/Export:
- Minor bugfixes in SMILES and in SMARTS import.
- Atom value in molfile.
- Bugfix in PDB import.
- Fix RXN incompatibility in MDLCompressor and in MolImporter.
- GUI:
- Speed-up slow viewer/sketcher performance on very large structures.
- Shortcut for clear screen.
- Plugins:
- Adding the dot-disconnected molecule formula calculation to Elemental Analysis.
- MarvinSpace:
- Proper handling of H and LP on hetero groups.
- Bond order perception.
- Import/Export:
- Non-ASCII characters are escaped in MRV import/export.
- SMILES fields can be separated with TAB separators.
- Slow image export bug fixed.
- Minor bugs fixed in CML import.
- Bugfixes in PDB import. Note, that PDB import is no longer
compatible with the original implementation which is still
applied for
XYZ files. See
release notes.
- Bugfix in the SMILES import of aromatic bonds.
- Minor CxSmiles import/export bug.
- API:
- Skin parameter/menu is denied in MViewPane and in
MSketchPane. It is available ony in Marvin applets/applications.
- Giving of the encoding in MolConverter was changed. Both input and output
encoding can be specified.
- GUI Bugfixes:
- Link node drawing problem.
- Copy from R-group definition did not work.
- Last page of the view table was not printed if there were empty
cells.
- PropertyChangeEvent was not invoked when molecule was changed.
- Down wedge looked like Up wedge on the toolbar.
- Pseudo atom exception in sketcher.
- Missing attachment point option in popup menu.
- Right click raises exception for reactions with abbrev. groups.
- Opening molfile with embedded groups caused exception.
- Other Bugfixes:
- 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.
- Bug in Molecule.clone().
- Bugfixes:
- Minor bugfixes in MarvinSpace
- In mol file export
- Import/Export:
- IUPAC InChi
- MDL Molfiles, RGfiles etc.:
Implicit H is stored as attached data when needed.
- Improved PDB import.
- Hydrogenize bug fixed: tetrahedral geometry of alcohol Oxygen atom is now maintained.
- Volumetric data import/export for CUBE files
(not processed by Marvin)
- Implemented trivalent doublet and quartet.
(RAD3_DOUBLET,
RAD3_QUARTET)
- Applets:
- New methods:
MSketch.getSelectedMol,
MSketch.getMolMass,
MSketch.getMolExactMass,
MSketch.getMolFormula,
MView.getMolMass,
MView.getMolExactMass,
MView.getMolFormula,
JMSketch.getMolMass,
JMSketch.getMolExactMass,
JMSketch.getMolFormula,
JMView.getMolMass,
JMView.getMolExactMass,
JMView.getMolFormula
- New sketcher parameter:
undetachByX.
- MarvinSpace beta, includes public
API:
- Dynamic loading of JOGL libraries.
- Better handling of PDB files including not standard complient variants.
- Save graphic scene as PNG image file.
- Basic Gaussian Cube file support.
- Improved User Interface.
- Bugfixes.
- Plugin:
- Sgroup names can contain almost any ascii character.
- Bugfixes:
- Hydrogenize bug fixed: tetrahedral geometry of alcohol O is now
maintained.
- Minor bugfixes in aromatization, in 2D cleaning and in
molconverter.
- Trivalent radicals are displayed and their
MRV import is fixed.
- Bugfixes in cxsmiles, in 2D cleaning and in parity calculation.
- MarvinSpace 1.0-alpha
is released as part of Marvin 4.0.
MarvinSpace is a 3D molecular structure visualization tool for
displaying macromolecules, protein-ligand complexes as well as small
molecules.
Release notes: At present MarvinSpace is available as standalone desktop
application and as Java Applet.
Java Beans and the public API will be released later.
See also Known Issues.
- 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:
- 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
- Improved aromatization
- Svg export gives UTF-8 encoded output.
- Bugfixes:
- In CmlImport
- In 3D cleaning
- In dearomatization
- Bugfixes:
- In plugin calculations.
- In parity.
- In 3D cleaning.
- In displaying of implicit hydrogens
- Minor bugfixes in plugin calculations.
- R/S and canonical smiles calculation speedup.
- 3D:
- Improved 3D cleaning efficiency.
- New Clean3D options. Time limit in the 3D cleaning process.
- Bugfixes:
- 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.
- Bug fix in cxsmiles export.
- Plugins: logP calculation is supplemented with metal fragments.
- Bugfixes:
- 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].
- Bugfix: 3D cleaning can cause Java 1.4.2_06 VM to crash.
- Bugfix: Import of SMILES containing atoms with "unspecified atomic
number" (*) is fixed.
- Colored MarvinView labels at celular level
- Bugfixes:
- Error in extended SMILES export
- NullPointerException at adding new structure to My Templates
- Error in drawing multiple groups
- Extended SMILES export: d
option to write C/T info for ring double bonds.
- API:
- Plugins:
-
TopologyAnalyserPlugin is available: calculates molecule properties from topology like number of various ring types, rotatable bonds.
- Calculation of molecular polarizability is available in
PolarizabilityPlugin.
- Improved pKa and logP predictions.Test Results
- Added calculation of aromatic system and aromatic ring total charges in
ChargePlugin.
- Import/export:
- 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:
- New applet parameter: molChanged0
to evaluate a JavaScript code when the molecule is loaded.
- Bugfixes: NullPointerException in shapely color mode,
deadlock in MarvinSketch applet.
- Bugfixes: memory leak and deadlock in sketcher bean.
- Import/Export
- New formats:
ChemAxon Extended SMILES
and SMARTS,
Gaussian Cube.
- Full support of SMARTS.
Added features:
- Recursive SMARTS $()
- Logical expressions in atom and bond: high and low priority "and"(& and ;), "or" (,) and "not" (!).
- Degree atom query property (D)
- Implicit hydrogens atom query property (h)
- Chiral or unspecified atoms @?, @@?
- Ring bond query property (@)
- Conditional directional bonds: /?,\?
- CML and
Marvin Document Format fix:
atom aliases and query strings are imported and exported.
- MDL Molfiles:
S-group parent list (M SPL in V2, PARENT in V3) and expansion
information (M SDS EXP in V2, ESTATE in V3) are stored.
- Incompatible API change in the
MolImportIface
interface: molecule import modules must implement the
createMol()
method.
- MolConverter
and
MolExporter
fix: created text files are in the local text format (instead of
unix) if the useSysEOL boolean argument is
true.
The molconvert program writes OS dependent end of lines always.
- S-groups
- Embedded S-group support (in MDL Molfiles and Marvin Document
Format).
- API changes in
Sgroup,
SuperatomSgroup,
and
MultipleSgroup:
the copy and the newInstance methods are replaced by copy
constructors and cloneSgroup.
- Other
- 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 pKa, logP, logD calculation.
- New methods in MolPrinter:
getChiralitySupport(),
getExplicitH(),
isAtomSymbolsVisible(),
isEzVisible(),
setAtomSymbolsVisible(),
setChiralitySupport(),
setExplicitH(),
setEzVisible().
- Marvin Applets: Workaround for browsers without
Java - JavaScript communication.
- Mac friendly shortcuts for Cut, Copy and Paste.
- Bugfixes:
- In MolConverter
- In the opening of the edit source window.
- Bugfixes: in SMILES import.
- Mac OS X: MarvinSketch and MarvinView applications use the
screen menu bar.
- Bugfix in the drawing of R-group attachment points.
- Atom and bond sets
- Colorable bond sets are introduced, see the
bondSet and
bondSetColor
applet parameters, the
MView.setBondSetColor()
applet method and the
MarvinPane.setBondSetColor() bean
method.
- Atom and bond set coloring can be used together with other color
schemes. Atoms and bonds in set 0 are displayed in Monochrome,
CPK, Shapely or Group color scheme, but other sets are displayed
with atom/bond set colors if the value of the
setColoringEnabled
applet parameter is
true (default).
- Deprecation:
- Use the
atomSet
applet parameter instead of set,
atomSetColor
instead of setColor and the
MView.setAtomSetColor()
and
MarvinPane.setBondSetColor() methods instead of
setSetColor.
- Use
colorScheme="mono"
and
setColoringEnabled=
true
settings instead of the deprecated
"atomset" color scheme.
- Import/export:
- Marvin Document file format
- Multiple Sgroup support for
MDL molfiles
- New image export
option to switch off antialiasing:
noantialias.
- CML improvements:
support of CML2 atom/bond attributes (instead of the deprecated
builtins), reactions, stereochemistry, residues.
Because of efficiency reasons, deprecated CML-1 data types are
not supported any more.
- Base64 encoding/decoding.
- Import options for input files are specified in braces instead of
parentheses ("file{options}") to avoid conflicts with
ugly SMILES strings ending with a branch specification.
For backward compatibility, parentheses still work after
filenames (but not after SMILES strings).
- 3D:
- 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 logP and logD calculations.
- Concentration of K, Na and Cl ions can be adjusted in the range of 0 - 0.25 mol/l.
- logP calculation of zwitterionic compounds also have been improved with considering distance correction
factors.
- pKa calculation have been extended to carbon-bases. Now basic pKa estimation of Indole derivatives available.
Both acidic and basic pKa values are displayed.
Microspecies distribution is shown on chart.
- Accuracy of pKa calculations is improved for heterocyclic compounds.
-
Calculation of polar surface area (PSA) based on 2D topological (TPSA) information of molecules are available.
- Others:
- Recognition of more than four hundred chemical abbreviations.
- Help documents can be specified by applet parameters:
sketchHelp,
sketchQuickHelp,
viewHelp,
viewQuickHelp.
- Molecule.draw
paints the molecule to a graphics context.
- Standard residue names returned by
MolAtom.residueSymbolOf(int)
are not all upper case, only the first letter ("Ala"
instead of "ALA").
- Marvin GUI: Set the visibility of the atom chirality (R/S) labels from
View/Misc menu.
- Double click in Windows operating systems opens chemical files with
the MarvinView application.
- Deprecation: SketchMolecule (replaced by MDocument),
SuperAtom.updateSgroupCrossings() (replaced by
Sgroup.findCrossingBonds())
- Incompatible change: chemaxon.struc.sgroup.Contractable
interface removed,
Expandable
changed. This change was required because MDL's incomplete
multiple group expansion had to be simulated for proper
molfile export.
- Bugfixes: in MViewPanel.setParams, in Dreiding forcefield, PDB import,
atom lists in V3 molfiles, resize of MViewPanel and MSketchPanel,
R-logic, etc.
- RDfiles containing internal and external regnos: the first molecule
or reaction type property is supposed to be the main structure.
- API changes
- Removed the broken RxnMolecule.moveReactionArrow method.
- 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.
- In calculation of third order amins strain is considered.
- 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.
- clean2dOpts and
clean3dOpts
parameters.
- MDL import/export improvements:
- S-groups: automatic contraction after import in sketcher and viewer.
- API changes:
- Bugfixes: R-logic bug.
- JRE bug workaround (inappropriate lines were drawn on the Marvin panel).
- Applets
- Java 1.0 compatibility is no longer maintained.
The minimum Java VM version required to run the applets is 1.1
(Netscape 4.06, MSIE 4 or later version).
- The Swing version of the unsigned applets are no longer
available. Use the signed applets instead. To unsign signed
jar files, see the FAQ.
- The deprecated installer for Marvin Applets is no longer maintained.
The set of downloadable Marvin Applets packages has been reduced.
- Plugins:
- New plugin: Atom polarizability
- Chart display in logD plugin
- Molecule import/export improvements:
- SMILES:
- PDB:
residues are imported as Sgroups,
Sgroups are exported as residues.
- Molfiles:
- Sgroups are also imported as (PDB) residues. As a consequence,
the PDB-specific coloring styles, "shapely"
and "group", are also applicable to molfiles
containing Sgroups.
- Extended (V3) molfile
export.
- Changes in V2 format:
- 3D molecule coordinates are stored in
Angstrom units. The unit can be specified as an
import
option.
- Illegal atom map values (from molfiles generated by the
IDBS ChemXtra data cartridge) are not considered to be
error at import.
- API changes
- New RgMolecule method:
RgMolecule.addRgroupsTo.
- New flag
RxnMolecule.RGROUPED
for the
getStructure(flags, f)
method.
- New methods related to explicit Hydrogen removal:
MoleculeGraph.calcDehydrogenizedGrinv,
implicitizeHydrogens,
MolAtom.isImplicitizableH.
- The protected removeNode(..., boolean changeNodes) and
removeEdge(..., boolean changeNodes) methods in CGraph,
MoleculeGraph, Molecule, etc. are replaced by
removeNode(int i, int cleanupFlags),
removeNode(CNode node, int cleanupFlags),
removeEdge(int i, int cleanupFlags),
removeEdge(CEdge edge, int cleanupFlags).
- Removed the malfunctioning RxnMolecule(parent) and
RgMolecule(parent) constructors.
- Bugfixes:
contracted S-groups are automatically expanded before exporting in
molecule file formats (PDB, SMILES, XYZ, ...)
- RGfile
import/export:
root structure can be a reaction.
Note that mixing RGfiles and Rxnfiles is not possible in
a standard way so these files can only be imported by Marvin.
- PDB import:
HETATM records are recognized.
- Bugfixes:
Invisible atom symbols at image export in
Molecule.toObject(String), Sgroup export in MDL formats,
Sgroup-related NullPointerException in viewer.
- 3D cleaning.
- New applet paremeters and bean properties
- API improvements and simplifications:
- chemaxon.struc:
- CGraph and
Molecule
are not thread safe any more but their methods became 20-30%
faster.
- Created the
SelectionMolecule
class for molecule selections, removed the CGraph.selection field.
- Created the
MoleculeGraph
class as the direct ancestor of SelectionMolecule and Molecule.
- RgMolecule and RxnMolecule
changes:
- Nodes and edges are only stored in subgraphs (root structure,
R-groups, product/reactant/agent structures).
- The graph union is returned by the
MoleculeGraph.getGraphUnion()
method.
- Methods like getNodeCount(), getEdgeCount(), getNode(i),
getEdge(i) call the root structure's corresponding
method in RgMolecule or the graph union's method in
RxnMolecule.
- CGraph.findFrags() and CGraph.findFrags(boolean) are replaced by
CGraph.findFrags(Class)
and
Molecule.findFrags()
- CGraph.cloneNodes() and cloneEdges() renamed to
getNodeVector,
getEdgeVector.
- CGraph.reallyContains(CEdge) and countRealEdges() removed.
- CGraph.getSSSR()
returns an int[][] array instead of CEdge[][]
- The MolAtom.flags, MolAtom.countFlags and MolBond.flags fields
became private.
- Molecule import/export:
- Initialization file saving:
- Other bean related changes
- Template button title is specified using the abbreviation
SDF property instead of title.
- Bugfix: in Rxnfile import
- atomMappingVisible
is a new applet/bean parameter and property.
- Bugfixes:
Copy and Copy as smiles bugs under Mac.
Hotkey bug in swing version of Marvin applets at Java 1.4.
- skin applet/bean parameter and new menu option (only in SWING).
- Improved SD file import (DTn fields).
- Bugfix:
NoSuchMethodError at drawing R-group definition in AWT mode (if Java version is earlier
than 1.2).
- grinv is a
new applet/bean parameter and property.
- Bugfix: in SDfile import.
- Bugfixes:
- Improved printing layout of MView tables.
- Improvements in Copy / Paste of reactions.
- Fixed calculation of molecule bounds.
- Molweight calculation.
- Handling agents of reactions.
- Bugfix:
MolConvert.convert() cleans imported SMILES.
- 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.
- Stereochemistry
- Other new applet/bean parameters and properties
- 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
- bondWidth applet
parameter and setBondWidth bean method.
- API changes
- Molecule.toFormat, toBinFormat, toObject, MolExportModule.open and
MolExportModule.parseOption throw IllegalArgumentException instead
of IOException if bad format string was specified
- "mag" property renamed to "scale",
setMag, getMag, maxMag methods became deprecated (MSketchPane,
MSketch, JMSketch, MolPrinter) and replaced by setScale, getScale,
maxScale
- Fixed: delayed printing, image export option parsing, cml:A, etc.
- Occassional NullPointerException in MolInputStream.canBeJTF() fixed.
January 28, 2002: Marvin 2.9.9
- 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".
- MolExportModule.getOptions() became protected
December 20, 2001: Marvin 2.9.8
- Apache Batik 1.1.1 classes needed for SVG export are included with
Marvin Beans and Applications
December 19, 2001: Marvin 2.9.7
- Image export:
- MViewPane.applyRotationMatrix, applyRotationMatrixes: methods to
apply the viewing transformation on the atomic
coordinates appearing in the molfile
November 26, 2001: Marvin 2.9.6
- No autoscale is the default in the sketcher.
November 12, 2001: Marvin 2.9.3
- MView applet: atom sets can be selected for different coloring, using
the setN.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.
- Bug fixes.
October 13, 2001: Marvin 2.9.2
- New applet and bean methods:
getTabScale(i) to query the magnification in a cellgetBestTabScale(i) to query the best magnification value for a
cellgetBestTabScale() to query the smallest best scale value
- MViewPane bean only:
- autoTabScale
property enables automatic uniform scaling of cells.
September 21, 2001: Marvin 2.9.1
- MarvinView improvements
- JavaScript code can be called at image click in the applet
using the "js:javascript" syntax.
- Use tabScale to set
the magnification in the molecule cells (instead of automatic
scaling), use
winScale to set
the magnification in the zoom windows (same as the old
mag
parameter).
- Many molecules in one cell. Molecules coming from multi-molecule
files are merged into one molecule object containing
atom sets if MULTISET is specified as the first import
option in the mol
parameter. To display only the specified sets, use the
showSets applet
parameter, the
MView.setSetVisible()
applet method or the MarvinPane.setInvisibleSets bean method.
- Atom set colors can be changed using the
setColor applet
parameters, the
MView.setSetColor()
applet method or the
MarvinPane.setSetColor() bean method.
- "Shapely" and
"Group" color schemes (for PDB input).
- Class library changes
- MULTISET can also be passed to the MolImporter constructor
through the option string
- The
newInstance() method of CGraph, Molecule, etc.
became public.
- PDB
- 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.
August 20, 2001: Marvin 2.9
June 25, 2001: Marvin 2.8.4
- Default value of the "format" property is "DEFAULT"
instead of null
June 22, 2001: Marvin 2.8.3
- 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.
June 18, 2001: Marvin 2.8.1
- New bean methods and applet parameters for customizing 3D rendering:
stickThickness,
ballRadius.
- java.awt.Image objects can be created from
molecules using
mol.toObject("image");
- API for import module
creation (MolImportIface).
- Import file format can be specified, by writing
"filename(format:)" or "filename(format:options)" in the
mol applet parameter,
or in the command line of molconvert,
