April 13th 2018: Marvin 18.10.
Improvements
Editing
Ctrl+D shortcut and new Edit menu item have been added for Copy as OLE.
Bugfixes
Editing
NPE was thrown on the console when atom formatting was done.
Molconvert
April 4th 2018: Marvin 18.9.
March 13th 2018: Marvin 18.8.
Improvements
MarvinSketch
OLE format has been removed from the transferable list of Ctrl+c.
From this version on OLE format can be copied using the Copy as... (Ctrl+K) option.
API
February 28th 2018: Marvin 18.5.
Improvements
I/O
Data S group import from .CDX and .CDXML files has been improved.
Editing
'Discard existing formats' option has been introduced for atom and bond sets to the Document Style Settings dialog.
MarvinView
Structures were not centralized correctly when the window was resized.
Printing
Long Term Supported Release February 23st 2018: MarvinSuite - Argon 3. (17.24.3)
Bugfixes
Editing
Atomsets could not be discarded when changing the document style.
I/O
Long Term Supported Release February 16st 2018: MarvinSuite - Argon 2. (17.24.2)
Bugfixes
Editing
Copy as .MRV didn't work when Save/Load GUI Settings option was disabled.
Pasting rich text the sub/superscript formatting was lost.
Structures were not displayed in Marvin Services result window.
I/O
February 13th 2018: Marvin 18.4.
I/O
MRV import of abbreviated group failed if the file did not contain AttachmentPointArray.
OLE
Dimensions of EMF image was recalculated during generation in MarvinOLEPanel.
January 30th 2018: Marvin 18.3.
Improvements
Editing
Stereocalculation
I/O
Installer
January 18th 2018: Marvin 18.2.
January 12th 2018: Marvin 18.1.
MarvinView
I/O
NPE was thrown during the import of some tetrahedral stereo molecules containing explicit Hydrogens on the stereo centers.
December 8th 2017: Marvin 17.29.
Improvements
Editing
Shortcuts Alt+↑ and Alt+↓ for super- and subscript has been introduced for Atom Label Editor.
Editing
Structure cannot be seen in Marvin Services result window.
Zoom scale changed when a R group attachment point was added
Upon rich text pasting sub/superscript formatting was lost.
Escaping did not work for DataSGroup.
Copy as .MRV didn't work when Save/Load GUI Settings option was disabled.
I\O
November 9th 2017: Marvin 17.28.
No changes.
October 25th 2017: Marvin 17.27.
No changes.
Long Term Supported Release Oct 22nd 2017 MarvinSuite - Argon 1. (17.24.1)
Improvements
Editing
Stereo calculations
OLE
Bugfixes
Editing
Image IO
IO
October 19th 2017: Marvin 17.26.
No changes.
October 13th 2017: Marvin 17.25.
Editing
Sept 22nd 2017: Marvin 17.24.
Improvements
Editing
Analysis box handles pseudo formulas.
The size of textbox follows the changing in font type/size.
Stereo calculations
OLE
Editing
Charges were missing from the chemical formula in Analysis Box.
Opening new MarvinSketch window deleted the clipboard.
In some cases the bounding box of text box was active even in unselected state.
Image IO
IO
Names longer than 80 characters were saved in MOL v2000 files.
September 15th 2017: Marvin 17.23.
Editing
Sept 1st 2017: Marvin 17.22.
Improvements
Editing
Text box
Exception was thrown when pressing space key in one character long text box.
When a user copied a text which was a name of a chemical compound into an empty text box, the structure was displayed.
Image IO
August 18th 2017: Marvin 17.21.
I\O
Aug 9th 2017: Marvin 17.20.
Editing
In some cases the selection wasn't disabled by 'Esc'.
I\O
August 3rd 2017: Marvin 17.18.
No changes.
July 25th 2017: Marvin 17.17.
No changes.
July 21th 2017: Marvin 17.16.
Bugfixes
Editing
Atropisomerism for agents wasn't calculated.
In some cases aromatic rings were drawn incorrectly after canvas have been got increased
OS
Installer
I/O
MarvinView
Print to pdf using 'All option' gave warning..
High usage of CPU was observed upon scrolling.
July 14th 2017: Marvin 17.15.
Bugfixes
GUI
July 6th 2017: Marvin 17.14.
Editing
When changing Journal style the structure disappeared.
Atom font could not be set when "Apply for selection only" was selected.
Marvin crashed when MP stereo visibility option was on and a single arrow was placed on the canvas.
I\O
June 16th 2017: Marvin 17.13.
No changes.
June 15th 2017: Marvin 17.12.
2D clean
June 8th 2017: Marvin 17.11.
No changes.
June 1st 2017: Marvin 17.10.
Editing
Wirefame with knobs view option has been eliminated
.I\O
Bugfixes
Editing
May 26th 2017: Marvin 17.9.
Editing
I\O
Editing
Multiselection (Shift+selection) didn't work.
May 9th 2017: Marvin 17.8.
No changes.
May 5th 2017: Marvin 17.7.
Editing
Curved arrows imported from MRV file that was created by Marvin before version 16.5.2. were malformed.
April 26th 2017: Marvin 17.6.
No changes.
April 21th 2017: Marvin 17.5.
Editing
Only the atoms were highligted when colored bonds were selected.
Installing
April 6th 2017: Marvin 17.4.3.
Editing
I\O
Property of merged agent should is saved in MRV.
Bugfixes
Editing
March 29th 2017: Marvin 17.3.27.
Editing
The head of coordinate bond resizes with the length.
New R-group hit detection feedback has been introduced.
Stereo labels are not included in the selected structure.
Bugfixes
Editing
March 21th 2017: Marvin 17.3.13.
Editing
Editing
Disabled wedge bond tools after turning to 2D mode from 3D.
Mouse mode>Reset View was not synchronized with Zoom panel.
Dragging a structure replaced the structure in the center of the canvas.
Molecule was not centralized when changing the size of the editor.
Display
Fog effect was not visible.
I/O
Rich text from .SKC files in the canvas could not be modified.
Image generation
February 28th 2017: Marvin 17.2.27.
No changes.
February 21th 2017: Marvin 17.2.20.
No changes.
February 15th 2017: Marvin 17.2.13.
Editing
UIDs are not displayed
Editing
Molconvert
Molconvert did not take into account the colored atoms/bond.
Image generation
February 10th 2017: Marvin 17.2.6.
Editing
I/O
Editing
Display
I/O
February 1st 2017: Marvin 17.1.30.
Editing
TM/P notation for atropisomers has been revisited.
Editing
Naming - Name to Structure
January 24th 2017: Marvin 17.1.23.
No changes.
January 20th 2017: Marvin 17.1.16.
No changes.
January 11th 2017: Marvin 17.1.9.
Editing
January 3rd 2017: Marvin 17.1.2.
Editing
Some Linux environment the last file open location was not remembered.
December 27th 2016: Marvin 16.12.26.
No changes.
December 20th 2016: Marvin 16.12.19.
Editing
Marvin froze when one tried to aromatize a three-membered ring or imported this kind of structure.
Direct copy of EMF image in other applications resulted in poor quality picture.
Editing
API for image export parameters of Journal styles has been introduced.
Editing
November 29th 2016: Marvin 16.11.28.
Editing
November 23th 2016: Marvin 16.11.21.
Editing
Copy/Paste
I/O
November 15th 2016: Marvin 16.11.14.
No changes.
November 9th 2016: Marvin 16.11.7.
MarvinSketch
MarvinSpace
Core
November 2nd 2016: Marvin 16.10.31.
Editing
Editing
I/O
October 25th 2016: Marvin 16.10.24.
No changes.
October 20th 2016: Marvin 16.10.17.
Editing
Editing
Unmerge reactant/product deleting another component.
October 13th 2016: Marvin 16.10.10.
No changes.
October 4th 2016: Marvin 16.10.3.
No changes.
September 28th 2016: Marvin 16.9.26.
Bugfixes
Editing
Clicking on the canvas with the Atom assigning tool during directed merge painted a reaction +.
September 14th 2016: Marvin 16.9.12.
Editing
Services
September 6th 2016: Marvin 16.9.5.
Editing
Plus sign was not added in reaction when creating two structures from one via bond deletion.
Auto + sign cold be be deleted using the Eraser tool.
" +" symbol were not drawn automatically when adding a diatomic molecule to a reaction.
I/O
R-group attachment points were not imported properly from MDL Molfile.
September 1st 2016: Marvin 16.8.29.
Editing
August 23th 2016: Marvin 16.8.22.
I/O
August 15th 2016: Marvin 16.8.15.
No changes.
August 8th 2016: Marvin 16.8.8.
Editing
Editing
August 2nd 2016: Marvin 16.8.1.
Marvin GUI
Editing
OSRA
Import/export
2D Clean
Editing
Display
Import/export
Editing
Editing
The Analysis box was not updated properly in case of alias or pseudo atoms.
No changes.
No changes.
Editing:
No changes.
GUI
3D rotate (F6) mouse mode has been removed.
On atom format panel, atom label size can set instead of the former scale option.
Editing
Name of the items was displayed on the canvas even it they had been set off on the Preferences dialog or the Analysis box editing dialog.
The reaction arrow in single step reaction could not be copied using Ctrl+C, Ctrl+V.
IO
Editing
GUI
Editing
Editing
Editing
Editig:
No changes.
No changes.
Editing
Editig:
Editing
Rendering
Atom labels became much smaller using MolPrinter.
GUI
Editing
I/O
Duplicate -f options were ignored by molconvert
Editing
Circles in aromatic compounds was too small when the bond length was relatively short.
I\O
Number of explicit hydrogens of metals is exported in MRV format.
Marvin GUI
Editing:
I/O
Editing
Editing
I\O
Editing
Atom < Label Editor menu item did not work.
I/O
I/O
Editing
Editing
Editing
I/O
Marvin GUI
Editing
Known issue:
I/O
Editing
Clipboard
Editing
Image export
Applet
2D Cleaning
No changes.
Editing
OLE
I/O
Editing
Image export
Installation
No structure
Editing
Editing
Textbox
.NET
2DClean
Templates
Abbreviated groups
Customization
Editing
2D Cleaning
Customization
MarvinGUI
Editing
Journal styles
2D Cleaning
I/O
CXSMILES
Charge painting
Customization
Painting
Saving
2D Cleaning
Import
Editing
Import
Document styles
Charge painting
I/O
Exporting molecule with R-Group definition and scaffold gave a unscaled image.
Journal styles
Editing
No changes
.
April 29th 2015: Marvin 15.4.27.0Improvement
Editing
Before updating MarvinSketch please delete Userhome/Chemaxon/Styles folder (if exists).
Improvement
No changes.
Improvement
MarvinSketch
Bug
MarvinSketch
Editing
API
Bug
Editing
MarvinSketch
I/O
Improvement
Marvin GUI
Improvement
Editing
Naming
Marvin GUI
Bugfixes
Editing
Improvement
Editing
I\O
Marvin GUI
Naming
Bugfixes
Editing
Applet
Improvements
Editing
I\O
Marvin GUI
Bugfixes
Editing
I/O
Improvement
Editing
Marvin GUI
Bugfixes
Editing
I/O
Images with reaction arrow were exported incorrectly.
OLE
Improvement
Editing
Marvin GUI
I/O
Bugfixes
Editing
I/O
Improvement
MarvinGUI
Bugfix
MarvinGUI
Editing
I/O
Some cases Marvin saved null bytes (/empty bytes) to the end of the structure files.
Bugfix
Stereo calculation
Editing
Image export
Bugfix
bondLength
and image export parameter bondl
are also introduced.
The index of repeating unit polymers was not properly formatted.
Empty atom label could be created.
Attachement point(s) got erased upon placing an abbreviated group in its expanded form on the canvas.
MDL Molfile generated by Marvin JS could not be pasted into MarvinSketch.
2D clean of certain atropisomers resulted in chirality change.
Expanded amino acids got ungrouped when bond was drawn from one of their attachment point
Export
Hydrogen query properties of atoms within tetrahedral stereo configuration were not exported correctly to SMARTS.
Structure Representation
Alias, pseudo and abbreviated group labels are centered.
The size of circled charge labels was not considered during image export.
Structure Representation
Atom numbers and atom query properties are rendered outside ring in cyclic structures.
Edit < Preferences < OLE Server was removed.
Image import/export
Radical was displayed as electronpair after emf export.
InChi native libraries were not initialized on OSX systems since 14.7.21.
Aromatic "wedge down" bond can be drawn.
Bugfixes
Absolute label was partly missing from exported images.
Transparent png images were rendered with some artifact on java 7.
Image generation in applet did not work.
Copy as dialog always opened on the centre of the primary screen in a multi-display environment.
Joining points of graphical objects were considered even though one of them had been removed.
Bugfixes
Special query atoms M, MH, X, XH were given too much space during clean 2D.
New feature
Abbreviation groups have been revisited and formatted according to the IUPAC recommendation.
Bugfixes
H_hetero option in the Pdf export did not work.
Atom extra lables such as numbers, mapping, query properties etc. were displayed relatively far.
Bugfixes
Formatted text import was improved from SKC format.
Molecule properties with quotation marks and whitespaces were lost during export to Smiles/Smarts.
Chorene dioxide had false valence error.
No changes.
New Features and Improvements
Class chemaxon.struc.Sgroup.MulticenterSgroup is now public.
Bugfixes
Applet parameter "extraBonds" disabled the chain tool if the "Any bond" parameter was not set.
Decimal point was displayed at a wrong place and its relative place changed by zooming.
Dots representing electrons were displayed too far from the atom.
E/Z labels overlapped bonds.
Bonds were rendered incorrectly in "Ball and Stick" mode.
Image I/O
Position of atom labels was not correct in exported images.
MarvinSketch GUI
New template files could not be added to the default template.
Editing
Retrieving parity information could change the result of the CIP stereo recognition. Forum
Editing
Molecule representation
Clean 2D
Import/Export
MarvinSketch Menu
Calculator Plugins
Applet
MarvinSketch
MarvinGUI
Editing
Import/Export
Methods Deprecated or Removed in version 14.7.7.0
No changes.
Marvin JS 6.3.0 history of changes
d2s:osra
will request OSRA to be used.chemaxon.struc.MolBond.equals()
compares the bonds by reference and not by the end points.CHEMAXON_LICENSE_URL
environment variable or the chemaxon.license.url
java system property is set.NullPointerException
.NullPointerException
.java.lang.ArrayIndexOutOfBoundsException
when reading parallel bonds atoms. Now chemaxon.formats.MolFormatException
is thrown instead.d2s:-ole
format option, the optical structure recognition of images was disabled as well.
Import/Export
Marvin for JavaScript 6.2.3 history of changes
No changes
Marvin for JavaScript 6.2.2 history of changes
StackOverflowError
wrapped in an IOException
.Marvin for JavaScript 6.2.1 history of changes
Marvin for JavaScript 6.2.0 history of changes
atomNumbersVisible
parameter has been deprecated and has been replaced by the atomNumberingType
parameter. API DocumentationsetPiece(Molecule)
method did not work; it set the molecule on the canvas instead of putting it on the cursor. ForumMRecord.getMolString()
method returned null.java.lang.ArrayIndexOutOfBoundsException
was thrown when a multicenter atom being the only member of an S-group was removed.Deprecated and removed methods
No changes.
No changes.
Marvin for JavaScript 6.1.4 history of changes
Marvin for JavaScript 6.1.3 history of changes
setPiece(Molecule)
method did not work, it set the molecule on the canvas instead of putting it on the cursor. ForumMarvin for JavaScript 6.1.2 history of changes
Marvin for JavaScript 6.1.1 history of changes
Non-public version
Marvin for JavaScript 6.1.0 history of changes
java.util.Date
object instead of string.-ocr
format option. DocumentationcheckErrorCount
Chemical Terms function returns the number of errors/issues found by the checker(s) in the configuration. Documentation"abbrevgroup:excluded=Ph,Ala,Gly"
, "abbrevgroup:excluded='Ph,Ala,Gly'"
or "abbrevgroup:excluded="Ph,Ala,Gly""
.c
added 'CIS OR TRANS' stereo information to double bonds in small rings.insideTag
format option was not working for XML and XHTML documents.
Marvin for JavaScript 6.0.6 history of changes
Marvin for JavaScript 6.0.5 history of changes
Marvin for JavaScript 6.0.4 history of changes
Marvin for JavaScript 6.0.3 history of changes
No changes.
Marvin for JavaScript 6.0.2 history of changes
No changes.
Marvin for JavaScript 6.0.1 history of changes
extraBonds
did not work therefore the bond type menu appearance could not be changed. Forum topicosraTimeout
option has been added to configure the maximum time to wait for OSRA to convert an image to structure (the default is 20 seconds).sortableFormula()
function is introduced. The generated sortable formula can be used to sort formulas in alphabetical order. Documentation--correctionlibrarypath
to read custom training file.sortableFormula
option is introduced. The generated sortable formula can be used to sort formulas in alphabetical order.-p
, has been introduced to save the training result to custom path.com.chemaxon.mapper.Automapper
java.lang.RuntimeException
. Forum topicjava.lang.ArrayIndexOutOfBoundsException
during peptide import.name:source
returned an empty name for empty structures instead of the actual stored name. MoleculeGraph.VALENCE_CHECK_AMBIGUOUS,
MoleculeGraph.ValenceCheckState,
MoleculeGraph.setValenceCheckState(ValenceCheckState),
MoleculeGraph.getValenceCheckState()
MoleculeGraph.getPossibleAttachmentPoints(MolAtom)
SuperatomSgroup.getAttachAtoms(),
SuperatomSgroup.getLegalAttachAtoms(),
SuperatomSgroup.getFreeLegalAttachAtoms(),
SuperatomSgroup.isFreeLegalAttachAtom(MolAtom),
SuperatomSgroup.isLegalAttachment(MolAtom),
SuperatomSgroup.sortXBonds(),
MolAtom.getAttach(),
MolAtom.setAttach(int),
MolAtom.setAttach(int, Sgroup)
ElementalAnalyser.setMolecule(SMolecule)
Molecule.exportToFormat(String),
Molecule.exportToBinFormat(String),
Molecule exportToObject(String)
throws java.lang.IOException
.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. See https://www.chemaxon.com/marvin/help/formats/name-doc.html#export for all possible options.chemaxon.marvin.modules.AutoMapper
MolAtom.setMassnoIfKnown(String),
MolAtom.isNobleGas(),
MolAtom.isArrowEnd(),
MolAtom.valenceCheck(),
MolAtom.getEdgeCount(),
MolAtom.getEdge(int),
MolAtom.getEdgeTo(MolAtom),
MolAtom.haveSimilarEdges(MolAtom),
MolBond.ARROW(),
MolBond.isCoordinative(),
MolBond.isArrow(),
MolBond.getNode1(),
MolBond.getNode2(),
MolBond.getOtherNode(MolAtom),
MolBond.cloneEdge(MolAtom a1, MolAtom a2)
MoleculeGraph.AROM_CHEMAXON,
MoleculeGraph.AROM_DAYLIGHT(),
MoleculeGraph.setSetSeqs(int id),
MoleculeGraph.getAromrings(),
MoleculeGraph.getNonAromrings(),
MoleculeGraph.getAromrings(int),
MoleculeGraph.getNonAromrings(int),
MoleculeGraph.mergeFrags(),
MoleculeGraph.getFragIds(),
MoleculeGraph.getfindFragById(int fragId, MoleculeGraph frag),
MoleculeGraph.getNode(int),
MoleculeGraph.setNode(int, MolAtom),
MoleculeGraph.insertNode(int, MolAtom),
MoleculeGraph.removeNode(MolAtom),
MoleculeGraph.removeNode(MolAtom, int),
MoleculeGraph.removeNodeVector(),
MoleculeGraph.getEdgeCount(),
MoleculeGraph.getEdge(int),
MoleculeGraph.setEdge(int, MolBond),
MoleculeGraph.insertEdge(int, MolBond),
MoleculeGraph.insertEdgeInOrder(MolBond, MolBond[]),
MoleculeGraph.replaceEdge(MolBond, MolBond),
MoleculeGraph.removeEdge(MolBond),
MoleculeGraph.getEdgeArray(),
MoleculeGraph.getEdgeVector(),
MoleculeGraph.getAllEdges(),
MoleculeGraph.regenEdges(),
MoleculeGraph.sortEdgesAccordingTo(MolBond[]),
MoleculeGraph.mergeNodes(MolAtom that, MolAtom),
MoleculeGraph.mergeFrags(int, int)
Molecule.mergeFrags()
RgMolecule.setAbsStereo(boolean, int, int),
RgMolecule.createMol(String),
RgMolecule.getBtab()
RxnMolecule.getBtab(),
RxnMolecule.getStructureCount(int),
RxnMolecule.getStructure(int, int),
RxnMolecule.addStructure(Molecule, int),
RxnMolecule.removeStructure(int, int)
CEdge, CNode, CGraph
MDocument.setGUIProperyContainer(MPropertyContainer)
No changes.
No changes.
MolExporter.exportToObject()
added an extra newline to SMILES.+/-groups
" has been added to enable (+) or disable (-) the conversion of groups and fragments, such as "ethyl", "nitro", "phenoxy", etc.MolFormatException
.tpol
) calculation didn't interrupt when clean3D failed.structurechecker
command-line.cxcalc
and "Isoelectric Point" calculation in MarvinSketch threw "ArrayIndexOutOfBoundsException" in the reported cases. Forum topicjava.lang.IllegalStateException
is thrown.java.lang.ArrayIndexOutOfBoundException
.--pH
command line option did not work in hydrogen bond acceptor-donor calculation.structurechecker
command line tool.-g
(ignore error) option of evaluate
did not work when -x
(extract) option was used. Forum topicCXNSharedAddin
library has been introduced to handle tabular data transfer from/to Microsoft Office applications.imageImportServiceURL
has been added to the image importer module. The URL can be set on the "Preferences" dialog or as an import option.MolAtom.BRIDGEATOM_H
, is added to Hydrogenize.removeHAtoms(MoleculeGraph, int)
method to remove hydrogens connected to bridgehead atoms.MolImporter.close()
.Fsg
, has been introduced to ungroup superatom s-groups with more than two attachment points. DocumentationMolFileHandler.collectFileInfo()
returns molecule and reaction identifiers $MFMT $MIREG, $MFMT $MEREG, $RFMT $RIREG, $RFMT $REREG, $MIREG, $MEREG, $RIREG, $REREG as well.RgMolecule.fuse()
resulted inconsistent molecule when it was invoked on RgMolecules having SuperAtom S-group in its definition. SGROUP_H,
has been introduced, for remove such hydrogens. MulticenterTransform.transformMulticenters(Molecule mol)
and MulticenterTransform.restoreMulticenters(Molecule mol)
changed the number of implicit hydrogens of atoms. int[] getSSSRBondSet()
, was removed and, instead, BitSet getSSSRBondSet()
was introduced.structurecheck
commandline.No changes.
No changes.
No changes.
chemaxon.util.ImageExportUtil
did not calculate the size of the image properly in certain cases."evaluate --list-functions"
threw NullPointerException if the user's Evaluator configuration file was missing.No changes
markushEnumerations('random:true id:true', '1,2', 5)
.)celli_j
and the possibility to escape characters.
recogn
argument of the MFileFormat constructor. Deprecated Recognizer.getPriority(), use MFileFormat.getPriority(subformat) instead.Bugfixes:
license
command line scriptXYZ
files. See release notes.marvin.js
to get JVM and GUI ("awt" or "swing"): marvin_get_jvm()
and marvin_get_gui()
.true
. The molconvert program writes OS dependent end of lines always.MarvinPane.setBondSetColor()
bean method.true
(default).MarvinPane.setBondSetColor()
methods instead of setSetColor.true
settings instead of the deprecated "atomset" color scheme.noantialias
.labels
which became deprecated.MolConvert.convert()
cleans imported SMILES.MolAtom.SELECTED
and VALENCE_ERROR
constants are not public any more, they are replaced by the isSelected, setSelected, hasValenceError and setValenceError methods.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.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 valuemag
parameter).MarvinPane.setSetColor()
bean method.newInstance()
method of CGraph, Molecule, etc. became public.Molecule.getComment()
and setComment()
methodsgetReactionSupport()
, setReactionSupport()
.~/.mview
, ~/.msketch
) can be set using the setIniProps method.sketchPane.loadIni()
or viewPane.loadIni()
is called.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.Molecule.aromatize()
MViewPane.getCellCount()
returns the total number of cells, not just the number of visible cells.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.)chemaxon/marvin/util/MolExportModule
.T
) component for MView tables.Molecule.getProperty(key)
is not case sensitive.Optional spin vector.
marvinbeans/examples/sketch/chemaxon/marvin/Sketch.java
) for details.Molecule.getO()
and setO()
replaced by getLocation()
and setLocation()
Molecule.getCenter()
renamed to calcCenter()
, and it calculates center of mass instead of geometrical centerMolecule.moveTo(location)
CGraph.indexOf
changesindexOf(CNode atom)
and indexOf(CEdge bond)
MolAtom.ionChargeOf(Z)
MolAtom.negoxOf(Z, boolean)
removed, negOxOf(Z)
, posOxOf(Z)
created insteadMolecule.getProperties()
removedMolecule.clearForImport()
-> clearForImport(name)
MSketch.getMol("mol:b=XXX")
instead of <param NAME="bondlen" VALUE="XXX">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 insteadMolAtom.covalentRadiusOf(Z)
-> covalentRadiusOf(Z, bondOrder)
queryAtoms
, atomStrings
, and extraBonds
parameters.extraBonds
.cleanOpts
applet parameter.downWedge
parameter.getAtomCount(moleculeIndex)
to query the number of atoms in a molecule cellisSelected(moleculeIndex, atomIndex)
to query whether the specified atom is selected or notselectAtom(moleculeIndex, atomIndex, select)
to (un)select an atomselectAllAtoms(moleculeIndex, select)
to (un)select all atomslayout
and param
for the molecule cells, layoutH
and paramH
for the optional header.scroll
parameter ceased to exist.getCtab()
, getBtab()
, fragments()
, findFrag()
, getFragIds()
, getLock()
, getParent()
, etc.getLigand(i)
, getEdge(i)
, getEdgeCount()
CNode.findFrag()
and CGraph.fuseFrag()
removedCGraph.getEdge(i)
, CGraph.getNode(i)
, Molecule.getAtomArray()
created; CGraph.getEdges()
, CGraph.getNodes()
, Molecule.getAtoms()
, Molecule.getBonds()
removedMolecule.reuseAtom(Z, i)
and Molecule.endReuse(na)
created, MolAtom.reuse(Z, mol, i)
removedMolAtom.setCharge
method removed. Instead of a.setCharge(charge, false)
, use a.setCharge(charge);
a.setFlags(0, MolAtom.FIX_CHARGE);
CGraph.fuseFrag(CNode a)
has only one argument.null
in removeRef).MolBond.setFlags(int flags, int mask)
method introduced.colors=mono
, both in the sketcher and the viewer.labels
parameter.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.
chemaxon/marvin/templates/
(from templates/
)..t
(from .cssdf
).chemaxon/marvin/templates/generic.t
, so the firewall problem ceased for the generic template set.MolImport
module moved into marvin.jar because of the firewall problem.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
.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.ARCHIVE
option in the applet tag (Netscape 2 and MS Explorer 3). Reasons:marvin.jar
. The simplest way to keep Netscape from doing so is to remove the class files.ARCHIVE
is, and don't use it properly. The consequence is a significantly increased download time.ARCHIVE
option cannot be left unnoticed, because Marvin will simply not run. Much better than turning your user's hair gray.If you are absolutely sure that you want your Marvin page work with Netscape 2 and MS Explorer 3 too, you must unpack marvin.zip manually. However, we do not recommend this, because you will probably do something wrong. For example, once you will upgrade Marvin and forget to unpack the new marvin.zip. Mixing two different versions will result in malfunction.
Molecules in MarvinView are only editable if the editable applet parameter is set.
rescaling
parameter in MarvinSketch is changed to "mag
" because generally this value is the most useful.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).&{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.js:
action.In the past, JavaScripter was required because scripting applets are not cached by older browsers (namely Netscape 3). An applet that has the MAYSCRIPT attribute is loaded from the net for each page that contains it. In Netscape 4 and later, there is no such problem. On the other hand, a bug (or feature?) in Netscape 4.6 makes the use of JavaScripter impossible as a separate applet. That's why we merged the two applets now.
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
"explicitH=off
" (default: "all
"). setAtoms
, setNoatoms
, setNobonds
methods, and the atoms
, noatoms
, nobonds
applet parameters ceased to exist and replaced by elements
, anyatom
, queryAtoms
, and extraBonds
.Omitting the real newlines like in "... 000Wun+V70\ iuzV000W60\ iuzVGS2W60\ K72WGS2W60\ ...
000Wun+V70\iuzV000W60\iuzVGS2W60\K72WGS2W60\
", seemed to be safe so far, while the Marvin applets were tested only in Oracle, Netscape, Symantec, and Microsoft JVM's. The reason for discontinuing this practice is that the AppletViewer in Kaffe 1.0b3 has problems if you write more than one molfile lines in one HTML line.getMol()
and getM()
removed. It didn't work with MSIE anyway.In Marvin 1.1.4 and before, x
was a boolean variable specifying the format of the generated molfile: MDL mol (false
) or compressed mol (true
).
From version 1.2, x
is a format descriptor string to ease the introduction of new molecule file formats as Marvin evolves. MDL molfile format is denoted by the string "mol
", compressed mol is "csmol
", SMILES is "smiles
".
"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">
.
© ChemAxon Ltd.
anuary 18th 2018: Marvin 18.2.
When CDX/CDXML file was imported, the font size of text was smaller than the original one.