History of changes: New features and improvements, Bugfixes

May 4th, 2012: Marvin 5.9.4

Bugfixes

• Calculations
  • Marvin Services did not return string result in some cases.
• Backend / Core
  • Import/Export
    • MolImporter.importMol(String) returned null when no molecule was recognized from the input document.
• Structure Checker
  • Custom checker implementation related fixes.

April 20th, 2012: Marvin 5.9.3

Bugfixes

• Molecule representations
  • S-groups
    • The relative position of multiple data S-groups on an object during clean was not kept.
• Import/Export
  • MOL, SDF, RXN, RDF
    • File format "molV3000" was recognized only when it was imported from a file having "mol" extension.
  • Load/Save handling in UI
    • Image export did not use the color scheme setting. See forum.

April 6th, 2012: Marvin 5.9.2

Bugfixes

• Aromatization/dearomatization
  • Aromatic ring count returned zero in those cases, where the aromatic ring contained charged carbon with two aromatic and one single bond.

March 22nd, 2012: Marvin 5.9.1

New features and improvements

• Import/Export
  • CXSMILES import/export handles every special atom available in the Periodic System dialog window in MarvinSketch.
  • DNA/RNA sequences are imported in their acidic form (i.e., instead of negative charge, an implicit hydrogen is added to the phosphoric acid ester group).
• Calculations
  • Accuracy of pKa calculation for amides has been improved.
  • Tautomerization of molecules containing nitroso group results in chemically more feasible isomers.
  • Speed of standard tautomer generation has been improved significantly. (On average about one hundred times faster.)

Bugfixes

• MarvinSketch GUI
  • Painting
    • Displaying proteins was very slow in some cases.
• Import/Export
  • CDX/CDXML
    • Coordinates of graphical objects were incorrectly imported from CDX files. Currently, imported "Anonymous Alternative Groups" are placed next to the imported molecule; "Anonymous Alternative Groups" with no bonds are imported as textboxes.
    • MRV attributes that contain line breaks were not exported correctly: \n, \r, \r\n were not escaped.
  • SKC
    • Atom and bond colors, font types, and bond thickness in SKC import and export were incorrect.
    • SKC import was failing on some structures containing built-in abbreviations.
  • PDB
    • Element type in some non-standard PDB file was not recognized properly. Forum topic
  • VMN
    • Charge and implicit hydrogen information was not read from VMN files.
  • Document to Structure (d2s)
    • Reactions embedded in documents were not extracted.
    • When OSRA was installed, a failure of OSRA prevented the rest of the document to be processed.
  • Peptide
    • DNA sequence import resulted in RNA sequence representation because of ambiguous one letter abbreviations. Currently, abbreviations dA, dC, dG, and dT are used to import DNA, while A, C, G, and U are used to import RNA sequences.
    • A peptide sequence containing custom amino acids was only imported when the custom amino acid was the last one in the sequence.
• Aromatization/dearomatization
  • Aromatic ring count returned zero in cases where the aromatic ring contained negatively charged carbon with two aromatic and one single bond.
• Calculations
  • Protonation (pKa, etc.)
    • CH acid type structures might have caused errors during pKa calculation.
  • Isomers (tautomer., reson.)
    • Wiggly bonds were changed to single bonds during standard canonical tautomer generation.
    • Resonance structure calculation of nitrogen containing molecules has been reconsidered: 10 valence electrons around a nitrogen are only allowed for nitro groups.
• Backend / Core
  • Import/Export
    • NullPointerException was thrown by MoleculeImporter if "d2s:+cas" or "d2s:-cas" format string was specified.
  • Character encoding
    • Some special characters were converted incorrectly from UTF.

March 2nd, 2012: Marvin 5.9.0

New features and improvements

• MarvinSketch GUI
  • Drawing electron flow arrow in a reaction has been enabled.
• MarvinView GUI
  • Document to Structure on PDF documents can display the first structures without waiting to process the whole document.
• Import/Export
  • CML, MRV
    • New option to MRV and CML export, :CN, is introduced, where 0 < N ≤ 9 and N is the length of the decimals of the exported coordinates. For example, mrv:C5
  • Name to Structure (n2s)
    • Conversion of systematic names has been increased by about 5%, and increased accuracy of the generated structures.
    • Prefix "nor" has been implemented (e.g., 17-Hydroxy-19-norpregn-4-ene).
    • Name with stereo-markers "r" or "s" where such stereoconfiguration cannot be present are now interpreted as "R" or "S". This allows names that have been completely lowercased to be converted correctly.
  • Document to Structure (d2s)
    • Document to Structure supports the following common office document formats: doc, docx, ppt, pptx, xls, xls, odt in addition to pdf, xml, html and txt.
    • Format options have been added to d2s, to specify what input formats should be converted (for CAS, SMILES and inchi). Format option "insideTag=<tag>" to restrict conversions to the content of a specific tag (for instance in HTML).
    • The type of source text used for the conversion is included in generated structures. Possibly values: systematic, generic, common (for names), smiles, InChI, CAS# (for text formats), cdx, mrv, symyx (for embedded structures in office documents).
    • Processing speed has been increased: doubled on typical documents including chemical names, and tripled on documents with few chemical names.
• Molecule Representation
  • Molecule/atom/bond properties
    • ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
  • Valence Check
    • A new option is provided which enables to turn off the valence check of nitrogen, phosphorus, or boron atoms in those cases when they are in aromatic compounds.
• Calculations
  • Isomers (tautomer., reson.)
    • Tautomerization can take into account the possibility of ring closure when "All tautomers" function is selected.
  • NMR Predictor Beta
    • "Copy to Clipboard" and "Export Prediction to PDF" actions have been implemented.
• cxcalc
  • Advanced logging in cxcalc: logging errors and execution times is available.
• Structure Checker
  • Chiral flag error checker options have been improved.
  • Custom fixers use annotations replacing property files. Backward compatibility is ensured for both custom checkers and fixers. Documentation
  • Pattern based report file generation is available as a new option in structurecheck commandline.
• MarvinSpace
  • Default aromatization method in MarvinSpace is the Basic aromatization (the same as in MarvinSketch).

Bugfixes

• MarvinSketch GUI
  • MarvinView 3D window could not be opened from the sketcher if MarvinView 2D window had been opened before.
• Applet
  • Applet settings could influence the client side desktop application settings.
• Painting
  • The query properties were wrongly painted in some cases and covered the atom labels.
  • 3D rotate action activated automatically when joining a structure in hand to a bond of a 2D structure on the canvas.
  • Double bond was not painted in centered position in case of terminal bonds when the label of the connected atom was displayed or both of the atom labels were displayed.
  • Single arrow type brackets were not painted.
  • The orientation of explicit hydrogens was incorrect when explicit hydrogens were added to the (selected) upper methylene C atom of a cyclohexane.
• Import/Export
  • MOL, SDF, RXN, RDF
    • Handling of special characters (-, ", space) in extended MDL MOL format IO was wrong.
    • RDF file exported by Instant JChem was not imported correctly to ISIS/Base.
  • SMILES, SMARTS
    • In some rare cases, the unique SMILES of a molecule depended on the numbering of the atoms.
  • CML, MRV
    • Parity value in CML format was stored the opposite way as the CML standard defines it. Now the correct value is stored which leads to backward inconsistency with CML files generated by ChemAxon applications in previous versions, but correct values are read from standard CML files. To avoid running into similar problems in the future, now a version information is stored both in CML and MRV formats. This information contains a version number of the file format and the application version by which the file was generated. The parity value is changed to opposite in MRV format as well to be consistent with the CML format but it does not lead to backward inconsistency in this case: parity values stored in not versioned MRV files are converted to their opposite while parity values from versioned MRV files are not.
  • PDF
    • View settings were not applied in exported pdf file.
  • VMN
    • VNM format sometimes was recognized wrongly as mol2.
  • Image I/O
    • The molecule source was generated in unnecessary cases.
    • javax.imageio left temp files open if the ImageOutputStream was not closed properly.
  • Structure to Name (s2n)
    • The generated names for bridged and spiro ring systems were missing E/Z stereodescriptors for double bonds in large rings.
    • Some unconventional names were generated with suffixes such as amido, sulfonyl, carbonyl, ... mentioned as prefixes. For instance 2-[(2-chlorophenyl)amido]benzoate for [O-]C(=O)C1=C(NC(=O)C2=C(Cl)C=CC=C2)C=CC=C1. The generated names is now 2-(2-chlorobenzamido)benzoate.
  • Name to Structure (n2s)
    • Stereochemistry was not indicated in the displayed structure when cis or trans is used to specify the configuration of the two substituents of a ring system.
    • Cycloalkane substituents of fused ring systems were aromatized.
    • The stereochemistry of chiral atoms in subsitutents was sometimes inverted.
    • Name to Structure was blocked on some very long names with unbalanced parentheses.
  • Document to Structure (d2s)
    • Some types of smiles strings were not recognized by Document to Structure, in particular those with stereochemistry or acyclic structures with two-letter heteroatoms.
  • Peptide
    • Numbers or sign "-" in the name of custom aminoacids were not accepted during the import of peptides (exception was thrown).
• Molecule Representation
  • Molecule/atom/bond properties
    • ArrayIndexOutOfBoundsException was thrown in the Parity.generateDigraph method in special circumstances.
    • Molecule.implicitizeHydrogens() threw "java.lang.IndexOutOfBoundsException" after fragmentation if the molecule contained information in MDocument field.
  • Valence Check
    • Valence Check gave false valence error for aromatic oxygen having +1 charge.
• Structure Checker
  • Aromaticity Error checker options could not be set.

Known issue

• Structure Checker
  • R-group Reference Error Checker cannot find circular and selfreferring R-atoms and R-groups.

February 20th, 2012: Marvin 5.8.3

Bugfixes

• Stereochemistry
  • Bicyclostereo information was calculated on symmetric ligands.
• Structure Checker
  • External fixers could not be applied properly in MarvinSketch.

February 8th, 2012: Marvin 5.8.2

New features and improvements

• MarvinSketch GUI
  • Standalone mode of OLE can be set on the preferences dialog if the application is launched in administrator mode.
• Import/Export
  • Molconvert has a new option, :D, which is important if the molecule has parity information and has 0 dimension. By default during the export, a clean method is invoked on the structure and the generated coordinates and wedge information are exported into MRV format but NOT the parity information. However, using this option coordinates and wedge information are not generated but parity information is exported.
  • Mrv files can be validated by using the XSD schema containing the description of the mrv format.
  • Export options of cml and mrv formats can be used in molconverter application.

Bugfixes

• MarvinSketch GUI
  • The tooltip of template groups was displayed incorrectly in some cases.
• Import/Export
  • Starting the OSRA utility failed on Unix and Macintosh platforms.

January 30th, 2012: Marvin 5.8.1

Bugfixes

• MarvinSketch GUI
  • Dialogs
    • Subscripts and superscripts (\s, \S, and \n) were not enabled in Group names in version 5.7.x and 5.8.0.
• Import/Export
  • MOL, SDF, RXN, RDF
    • The line break in the Sgroup Attachment Point information section of the Extended MOLFile (MOL V3000) format was wrongly inserted in case of longer peptide sequences containing Cysteine.
  • CML, MRV
    • From version 5.8.1, molecules having parity information are exported in 2D form instead of 0D form in order to avoid incorrect parity representation.
• Molecule Representation
  • Valence Check
    • The aromatic nitrogen handling in case of pyridine-oxide was incorrect.
    • In release 5.8, all amino acids of an amino acid chain were detected to have valence error if it was imported from the Edit > Source menu of MarvinSketch.
  • S-Groups
    • Hydrogens attaching to sgroups were not treated as special ones and from version 5.8.1, their removal is optional.
• Data Transfer
  • OLE
    • Symyx content conversion (by redirecting) crashed Marvin OLE.
• Calculations
  • The hydrogen count was incorrect in case of position variation and metallocene-like structures.
• Structure Checker
  • "neutralize" fixer did not work in structurcheck command line application; "null" output was generated.

January 11th, 2012: Marvin 5.8.0

New features and improvements

• MarvinSketch GUI
  • Group types on "group creation" dialog can be configured.
  • The icon of manual atom mapping has been changed.
  • A new radical electron setting and the corresponding toolbar icon group has been introduced, solely for educational purposes: Up to four radical electrons can be defined for an atom, and it is arranged evenly in the empty space around the atom label.
  • Recent file list length has been increased up to 50. (The default is 25.)
• MarvinView GUI
  • Atom mark and atom highlight display can be enabled/disabled.
• Import/Export
  • Structure to Name (s2n)
    • New name format option: "source" has been introduced to print the names present in the source molecule data. For instance, molconvert name:source input.sdf.
  • Name to Structure (n2s)
    • n2s handles stereochemistry of cyclic monosaccharides.
    • Extended support for common names: n2s can convert 123 thousand common names – including synonyms – corresponding to 34 thousand structures instead of the previous 63 and 28 thousand, respectively.
  • Document to Structure (d2s)
    • Automatic text OCR (optical character recognition) has been added to support document to structure conversion of scanned (non searchable) PDF documents.
  • MRV
    • The information on the selected atoms and bonds can be stored in MRV format.
    • MRV format has been changed: there is no indentation, there are line-breaks only after the header and after the documents. The original format (including line-breaks and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications. See export options here.
  • SMARTS
    • ChemAxon Extended SMARTS represents R-group (Markush) structures.
  • CML
    • CML bondStereo implementation has been completed with atom references.
    • CML format has been changed: there is no indentation, there are line-breaks only after the molecules and after the header. The original format (including line-breaks and indentation) can be achieved using the -P option; this previous format is displayed – for easier reading – in the Edit > Source window in Marvin graphical applications. See export options here.
• Calculator Plugins
  • New integrated component: NMR Predictor Beta has been implemented.
  • "Consider tautomerization" option has been renamed to "Consider tautomerization/resonance" in logP and logD calculator plugins.
  • "Tools" menu content has been moved to "Calculations" menu.
• Data transfer
  • Native PDF format as the default image pasteboard format is used on MAC systems. It allows the user to copy a structure (which was originally created by either Marvin or ChemDraw) from a Microsoft Office 2011 document and to paste it to Marvin.
  • More verbose logging from OLE .NET panel (catching managed bridge exceptions via COM) has been introduced.

Bugfixes

• MarvinView
  • Sometimes molecules were lost when switching from "Spreadsheet mode" (Table>Options>Table Type) to "Molecule matrix" mode.
  • When a zero length structure file was opened, the content of the previous file remained in the viewer until the first repainting.
  • Scrolling up and down increased the number of molecules and changed their orders.
• Painting
  • Until the first repaint, textbox was smaller than required, and the content was cropped to its size.
• Import/Export
  • Structure to Name (s2n)
    • Incorrect name was generated for chiral allenes, for instance: (2M)-1,3-dichloropropa-1,2-diene, the correct is 1M. (The locant was previously in the middle of the cumulated double bond system, but is now at the beginning of it, as prescribed by IUPAC.)
    • Fixed generation of names in the case where a radical marker "yl" was missing, for instance "...(4-methylbenzene)sulfonyl..." instead of the correct form "...(4-methylphenyl)sulfonyl..."
    • Name generation was sometimes failing on fused ring systems with a spiro connections or adjacent fusion bonds. Conversion rate of fused ring systems goes up from 99.83% to 99.95% on the NCI database set.
    • The numbering of fused ring systems was incorrect in about 1% of the cases both in s2n and n2s.
  • Name to Structure (n2s)
    • Automatic name format recognition failed for names containing unicode prime characters.
    • CAS number cache could get corrupted and created failures.
  • Document to Structure (d2s)
    • The total length (getEstimatedTotalCharacters) was not available to progress listeners during Document to Structure conversion of PDFs using the API.
  • SMILES
    • CXSMILES IO error due to non-escaped characters appeared.
    • The name imported from SMILES format was wrong in rare cases, when special characters (e.g., |) were in the fields part of the extended SMILES.
• Calculator Plugins
  • logP and pKa calculations threw error at heavy atom count 300.
  • Generic tautomer generation might have threw an error if the molecule contained Hydrogen isotopes.

January 25th, 2012: Marvin 5.7.2

No changes.

December 12th, 2011: Marvin 5.7.1

Bugfixes

• Molecule Painting
  • Valences higher than nine were wrongly displayed if the valence property visibility was turned off.
• Calculator Plugins
  • Some property calculations threw ArrayIndexOutOfBoundsException when the input molecule contained multiple fragments.
• Build/Installation
  • OLE defect occurred during side-by-side installations.

November 4th, 2011: Marvin 5.7.0

New features and improvements

• MarvinSketch GUI
  • New bond type: "Hashed bond" has been introduced.
  • "Coordinate" Bond Line Style – in the Edit>Preferences>Bonds menu – allows changing the type of coordinate bonds between the default ones (arrow for single atom and hashed for multicenter) and solid.
  • Selected structures can be aligned or distributed relative to each other horizontally or vertically. The Align&Distribute function aligns and distribute the objects at the same time.
  • New chain drawing tool: Curved chain tool. Instead of creating a straight chain it modifies the direction of the last bond of the chain based on the mouse movement. Curved chains or macrocycles can be created that way.
  • The chain drawing direction is mirrored based on the direction of the mouse movements.
  • Selection can be moved in greater units with SHIFT + arrow keys.
• Import/Export
  • Structure to Name
    • Traditional name for known class names (e.g. acylcholine) is generated.
  • Name to Structure
    • "Name to structure" converter supports more systematic names (6% to 50% measured on various sets of names extracted from patents). For instance, names representing esterification with locants (e.g. 1,4-di-tert-butyl piperazine-1,4-dicarboxylate).
    • Optional support for CAS numbers in Document2Structure.
    • Faster loading of PDFs by Document to Structure (from 25% to 75% speedup in most cases). Names can be extracted from more types of PDFs.
  • CDX/CDXML
    • Hashed bond type has been implemented in Marvin. "Hashed to Down Wedge" conversion has been changed to "Hashed to Hashed" conversion.
• Clean 3D/optimization
  • Verbose mode has been added to Generate3D. Use option "[verbose]" to switch on; use "molconvert -H3D" for detailed help.
• Data transfer
  • Native pasteboard for Macintosh has been implemented. It solves general copy/paste issues, e.g. copy/paste between Marvin and other chemical sketcher programs (e.g., ChemDraw).
  • Marvin supports conversion of other Vendors (currently ISIS and Symys) embedded OLE objects to Marvin OLE.
• Structure Checker
  • New checkers are available:
    • R-atom Checker: detects R-atoms (all, disconnected, generic, linker, nested).
    • R-group Attachment Error Checker: detects attachment differences between R-atoms and R-group members. A new fixer corrects the attachment bond types and adds missing attachments in unambiguous cases.
    • R-group Reference Error Checker: detects missing R-atoms, missing R-groups, self or circular references of nested R-atoms.
  • Checker and fixer classes implemented by the user are loaded from given jar file.
• API
  • chemaxon.marvin.util.ColorGenerator class provides an easy way to generate the required number of different colors.
  • Several core functions are deprecated. See this table for details.
  • API support for running checkers and fixers multiple times automatically.

Bugfixes

• MarvinSketch
  • The Java beans and applet parameter for switching the valence property visibility OFF was missing.
• MarvinSketch GUI
  • Scrolling with mousewheel or arrow keys enlarged Marvin Sketch canvas.
  • Moving selection with arrow keys could not be undone.
  • Attachment points were not highlighted by green when they were selected.
  • Sugar templates: D-furanoses had S label on carbon 5.
  • Double click selection did not work when it pointed to an atom.
• MarvinView
  • MViewPane did not refresh when UserSettings changed.
• MarvinView printing
  • Several MarvinView display property was missing in MolPrinter
• Painting
  • Error highlight was partially visible and often disappeared on mouse move.
• Molecule Painting
  • Positive charge of hydrogen was not scaled properly in case of small magnification.
• Import/Export
  • Structure to Name
    • Incorrect names where generated when the parent structure has identical substituents orientated differently, for instance: 4-formamido-1H-pyrazole-3-carboxamide
  • Inchi Key
    • Inchi slowdown with inchikey call for 10000s of structures.
  • PDF
    • OSRA did not work in Marvin unless its library was set in the PATH.
  • SMILES/SMARTS
    • A molfile or sketch is carrying an 'rb*' flag on any atom(s) was translated incorrectly to SMARTS ('x' atomic primitive).
    • cxsmiles IO of Data sgroup was incorrect.
    • mol format from smarts which contained "[C,!N]" (representing "Carbon , not Nitrogen") was converted incorrectly.
• Molecule representation
  • Connecting an additional bond to an abbreviated group freezed Marvin Sketch.
• Stereochemistry
  • Allene parity lost by removing explicit hydrogens.
• Aromatization/dearomatization
  • Aromatization of an aromatized structure created new aromatic ring
• Elemental analysis
  • The Elemental Analyzer did not support Position-Variation bonds in formula calculation. Known issue: Dot-disconnected formula calculation is not working correctly in case of Position-Variation bonds.

December 13th, 2011: Marvin 5.6.0.5

No changes.

October 25th, 2011: Marvin 5.6.0.4

Bugfix

• Import/Export
  • Importing Molfile which starts with "BM" failed with OSRA related error message.
  • SD files started with "P3" was recognized as PPM file instead of SDF. This bug was a result of changes in Marvin version 5.5.

October 18th, 2011: Marvin 5.6.0.3

No changes.

October 5th, 2011: Marvin 5.6.0.2

Bugfix

• Import/Export
  • Sgroups handled implicit hydrogens incorrectly depending on file formats. The bug could prevent matching in case of duplicate search.

September 25th, 2011: Marvin 5.6.0.1

Bugfixes

• Import/Export
  • Data Sgroup was converted incorrectly to cxmiles.
  • Opening PDF files, NullPointerException occured in some cases.

August 31st, 2011: Marvin 5.6.0

New features and improvements

• MarvinSketch GUI
  • New mouse cursors have been introduced.
  • New structure templates have been added (Alpha D sugars, Beta D sugars, Deoxynucleosides, Flavonoids, Nucleobases, Nucleosides, Protoalkaloids, True Alkaloids, Vitamins, Functional Groups).
• MarvinView GUI
  • Atoms can be marked in Marvin View by hovering the cursor over it. This also works even if another atom has already been selected. A property change event is sent on every atom mark (Documentation).
• Applet
  • New parameters have been introduced:
    • onError (Documentation).
    • alertError (Documentation).
• Import/Export
  • Str2Name
    • New option has been added to generate all common names for a structure, e.g.: molconvert "name:common,all" -s viagra.
    • Less brackets are generated in names in traditional mode. For instance, instead of "{1-[(tert-butoxy)carbonyl]-1H-indol-2-yl}boronic acid" the generated traditional name is now "1-(tert-butoxycarbonyl)indol-2-ylboronic acid".
  • Name2Str
    • MolImporter can now process a PDF file as input and convert the chemical names in the text into structures. Structure images are also converted if OSRA is installed on the computer.
    • Increased support for name to structure conversion (measured between 6% and 30% on certain datasets).
• Calculator Plugins
  • "Marvin Services" has been introduced: Web/local services client, which provides seamless integration of third-party calculations into Marvin Sketch, cxcalc, and via Chemical Terms into Instant JChem or JChem for Excel. Industrial standard solutions like SOAP with WSDL are supported, along with the more lightweight XML-RPC or JSON-RPC protocols. Java based calculations can be called without server, directly from the jar file.
  • A new type of fragmentation has been implemented where the fragments contained in the same S-group are not separated. Fragmentation methods now have fragmentation type as parameter. The three types of fragmentation are:
    • Basic: no S-groups are considered, fragments are separated even if they are in one S-group. Broken S-groups are not added to the fragments.
    • Keeping multicenters: multicenter S-groups are kept in one fragment, other types of S-groups that contain more than one fragment are not added to the fragments, those fragments are separated.
    • Keeping S-groups: all S-groups are kept, fragments in the same S-group are not separated.
    Previous fragmenting methods which did not indicate the type of fragmentation are deprecated; they do the same as before (keep multicenters), but now – correctly – without generating inconsistent molecules with broken S-groups. These methods will be removed in later releases.
• Markush enumeration
  • There is a significant speedup of sequential and random Markush enumerations. (Hundreds of times speedup for average patent Markush structures. Speedup depends on the complexity of Markush structures.)
• Structure Checker
  • New checkers are available:
    • Unbalanced Reaction Checker: reports if there is difference in the total number of atoms or atom types on the two sides of the reaction arrow.
    • Atom Query Property Checker: detects atoms having query properties. A new fixer can remove the identified query properties.
  • New feature: "3D checker" detected issues can be fixed by "Remove Z-Coordinate Fixer". It flattens molecules by setting the z-coordinates of atoms to zero.
  • Structure Checker command line application has greatly improved. See the documentation for details.
  • Improvements in substructure checker: multifragment molecule handling, implicit hydrogen handling, improved command line access. "Transform" fixer for substructure errors: modifies substructures.
• API
  • New function to get the enantiomer of a molecule has been implemented: chemaxon.calculations.stereo.Stereochemistry.getEnantiomer(MoleculeGraph m).
  • Applet API has been improved with validateMoleculeStr(String str) and validateMoleculeStr(String str, String format) methods.

Bugfixes

• MarvinSketch GUI
  • The double-click selection action did not work after rotating the view in 3D, and then moving/rotating the structure in 3D.
• MarvinView GUI
  • Scale factor was not updated on rescale in MarvinView.
• MarvinView printing
  When multiple structures were printed in PDF with molecule matrix rendering, structures with crossing bonds in the second or further cells were just partially drawn.
• Applet
  • Marvin Applet failed to load changes in a file if the same file url was loaded before and applet started from the legacy cache.
  • Legacy_lfecycle related initialization (parameter loading, event listening, etc.) was fixed in applets.
• Molecule Painting
  • The shadow painting of the sprout drawing feature removed the error highlight of Structure Checker.
  • Atom label was shifted in case of terminal double/aromatic bonds at the end of chains. Double bond was not painted in the centered position when there were no substituents on either sides.
• Import/Export
  • MOL and SDF files including pipe character in the first line were recognized as Chemaxon Extended SMILES.
  • MOLFiles including a caret symbol in the Alias or Sgroup label fields were displayed incorrectly (the caret symbol was not hidden).
  • MOL/SDF files starting with "BM" characters in the first line were recognized as BMP file.
• SMILES/SMARTS
  • ArrayIndexOutOfBoundsException did not work in case of SmilesImport and Chirality calculation.
• Data transfer
  • Copy/paste of Marvin OLE objects from MSOffice applications back to Marvin did not work.
  • OLE image was not updated consistently after editing structure in MsOffice applications on 64 bit environment.
• 2D clean
  • Bad 2D cleaning in case of fused ring system.
• Aromatization/dearomatization
  • Aromata.isDaylightAromatic considered (O=[N+]1C=CC=C1) incorrectly.
• Calculator Plugin
  • logP calculation threw ArrayIndexOutOfBoundsException in some cases.
  • There were incorrect systematic names generated in case of sulfur-based groups with non-standard valence (for instance dihydroxy-lambda6-sulfanone).
  • FindAllRings failed with OutOfMemory error.
• Structure Checker
  StructureCheck command line application did not generate report field in output if checker options are set (e.g. "explicith:isotopic=true").
• Build/Installation
  Marvin Beans installer could not start with 64bit Java 1.6 under OS X 10.5.

July 8th, 2011: Marvin 5.5.1.0

New features and improvements

• Import/Export
  • molconvert: The -T option works with pipes using the fields of the first molecule.
  • Name to structure: Document to Structure also extracts smiles and InChI from the text.
  • CML: CML files now passes the validator at http://validator.xml-cml.org.

Bug fixes

• MarvinSketch
  • Pressing the Shift key when the mouse cursor was on an atom threw an ArrayIndexOutOfBoundsException.
• Chemical structure painting
  • Bond coloring was wrong in 2D if the colors of the neighboring atoms were different.
  • Quick rotation of the 3D view of 2D structures sometimes resulted in the disappearance of the structure.
  • The Java beans and applet parameters for switching the valence property visibility OFF was missing.
• Import/Export
  • MOL/SDF: The coordinate bonds in R-group definitions were wrongly exported.
  • Name to structure: Traditional naming export failed in applet.
  • Name to structure: Document to Structure failed to extract names from PDF documents .
• Calculator Plugins
  • pKa prediction threw ArrayIndexOutOfBoundsException in case of oximes.
  • Tautomerization threw ArrayIndexOutOfBoundsException in case of a few complex aromatic systems.

May 12th, 2011: Marvin 5.5.0.1

Bugfixes

• Calculator Plugins
  • Improved pKa prediction of the "OH" acid in oxim group.
• Structure Checker
  • SubstructureChecker did not work (requires JChem).

May 3th, 2011: Marvin 5.5

New features and improvements

• Marvin Sketch
  • Bold Tool is intended to be used for graphical presentations of molecules. Activate the tool, click on a bond and it will be changed to bold. Bold Tool is located in the Bond Menu, Tools toolbar, and bond PopUp menu by default. Read more about its application in (documentation).
  • The explicit valence setting display (v#) can be switched off (forum topics: #1, #2; documentation).
  • Ctrl + Mouse Wheel zooms in and out on the canvas, while the geometric center of the zoom is defined by the current position of the mouse pointer.
  • To scroll the canvas you can use the mouse wheel or the arrow keys on the keyboard.
  • If there is a selection on the canvas, you can either move the selected object using the arrow keys or move the canvas with Ctrl + Arrow Keys. (See documentation: Marvin Sketch GUI, shortcuts, canvas, snapshoot.)
  • MarvinSketch canvas is centered to the scaffold after opening R-Group molecules.
  • Atom List and Atom Not List can be entered by simple typing (without opening the Periodic Table).
  • Symbols can be inserted into textboxes. An Insert Symbol dialog with recent symbol list is accessible from the Textbox toolbar.
  • Error messages, warnings, warning details, and error stack trace can be copied to the clipboard.
  • Version and Copyright info can be found in Marvin splash screen.
• Marvin View
  • Printing the molecule matrix view of a multirecord file containing data fields has been improved:
    • Instead of cropping the content of the data fields when the cell is too narrow, they are wrapped into multi-line texts automatically.
    • A minimal size is provided for the molecule structure, so it is visible even if the data fields want to occupy more space than the cell size.
  • The explicit valence setting display (v#) can be switched off.
  • Molecule matrix view is scrollable with mouse wheel.
  • R-groups are visible in MarvinView by default.
• Marvin Space
  • Visualization of aromatic rings and triple bonds have been improved.
• Compatibility
  • Minimum Java requirement of Marvin is 1.6.
• Data Transfer
  • If a selection is made on the structure in the MSketch window that has been opened from the MView pane, the closing of the MSketch window (or clicking on the transfer button) transfers the selection back to the MView pane.
• Chemical structure painting
  • Drawing 2D projected views of 3D aromatic rings (forum topics: #1, #2).
    • Aromatic rings have ellipses in 3D view as well.
    • Bold bonds and Aromatic Up bonds can be displayed.
    • The display quality of the junctions of Bold and Up bonds with other bonds has been improved.
  • The electron flow arrow display has been improved: Radicals, lone pairs, and negative charges are considered now. If the source is an atom, the electron flow automatically starts from the lone pair, the radical or the charge when they are displayed.
  • The automatic attachment point placement in R-group lists has been improved.
• Electron flow arrow
  • Electron flow arrows are redesigned. It is now separated to logic and display part.
• Import/Export
  • Image Export:
    • JPG, SVG and PNG formats contain the molecule source, so when opening or pasting these images, the molecule source is used (instead of trying to convert the image using OSRA).
    • PNG image color-depth can be specified as bitrate: 1-, 2-, 4-, 8-, 24- and 32-bit PNG image can be created.
  • Syn/Anti and Endo/Exo stereoisomer information is exported into ChemAxonExtended SMILES and SMARTS format.
  • Data fields are exported into SMILES format.
  • Improved SMART representation of generic query atoms (Q, QH, X, XH, etc.).
  • IUPAC Name
    • Major rewrite of the name to structure converter. Higher precision (around 50% improvement) and support for additional names.
    • Import of sulfide has been improved in Name To Structure.
    • Dictionary format improvement in IUPAC naming.
    • Name To Structure supports Alpha and Beta sign in names.
    • Automatic format recognition for CAS numbers. (This feature uses a Web service.)
  • IUPAC InChI
    • Inchi converter now uses the IUPAC software API via the jni-inchi instead of the executable. Now it can handle stereochemistry information in 0D.
    • Marvin now uses inchi 1.03.
    • The conversion is much faster now.
    • InChI export does not clean in 0d any more.
• 2D clean / aromatization
  • Keep stereo information at aromatization.
  • Query aromatization considers single/aromatic and double/aromatic.
  • Converting to aromatic form keeps the Bold property of the bond.
• Stereochemistry
  • Syn/Anti and Endo/Exo stereoisomers are recognized.
  • Proper chirality detection in case of topographical differences.
  • Define chirality for adamantane structures (forum topic).
  • New standardizer action: add implicit parities of bridged systems.
  • NEMA features: atrop isomers, allenes.
• Structure Checker
  • New Checkers:
  • SubstructureChecker detects user defined substructures (requires JChem);
  • RacemateChecker detects tetrahedral stereo centers without specific stereochemistry defined.
  • Improvements:
  • AromaticityErrorChecker searches for aromatic systems that can't be dearomatized or rearomatizing with the given method does not reproduce the initial molecule.
  • Tooltip improvements.
  • Checker status bar indicator can display warning and error icon as well.
  • Rename of specific checkers is supported (affects SubstructureChecker).
• Calculator Plugins
  • Molecular volume calculator plugin has been introduced.
  • Generic tautomer generation ignores all options except "Protect all tetrahedral stereo centers".
  • Preserve exocyclic groups in BMF.
• Chemical Terms
  • Improving initialization speed of Chemical Terms Editor.
  • Enhanced integration of BMF in Chemical Terms.
  • New Chemical Terms function: markushLibrarySize(), markushLibrarySizeAsString(), markushLibraryMagnitude(), matchFirst(), booleanToNumber().
• Automapping
  • Integrate new MCES algorithm into AutoMapper.
• API
  • Implementation of MoleculeGraph.getAtomCount(int atomicNumber). It returns number of atoms in the molecule with the given atomic number (forum topic).
  • Let user to insert new action into MarvinSketch popup menu.

Bugfixes

• Marvin Sketch
  • A bond to the second attachment point of an Sgroup could not be drawn if it was created by changing a terminal atom of a previously drawn structure.
  • The BzOM group has to be renamed to PhOMe, and its left name should be MeOPh (forum topic).
  • Selecting every atom and using the "Ungroup" function from the menu caused ArrayInedOutOfBoundsException.
  • Edit source dialog could not be opened after importing SKC.
  • After setting of "Save/Load-default location - Startup directory" in Preferences dialog, Marvin did not navigate to the Startup directory by saving or loading a molecule.
  • The canvas was not scrollable with mouse wheel.
  • When Ala was ungrouped in the R1 definition, the attachment point (which was both an Sgroup and an Rgroup attachment) disappeared.
  • When a reagent was placed over the reaction arrow in abbreviated form, Marvin Sketch became unresponsive.
  • When drawing electron flows to multicenter, Marvin stopped doing anything.
  • Electron flows could cross double and triple bonds when starting from bond.
  • The exception frame was not scrollable when the message was too long.
  • Atoms from periodic table modified bond length when the atom in hand was attached to the end of a bond on the canvas.
  • The aromatization/dearomatization did not run during Directed Merge, therefore if the double bonds were not located at the appropriate positions in case of two aromatizable rings, 5-valence carbon atoms were created.
• Marvin View
  • Scrolling and cleaning 2D in the same time caused CuncurrentModificationException.
  • After clean 2D, Marvin View cells in molecule matrix view were not repainted automatically. You had to click on each cell to refresh them.
• OLE support
  • StandAlone mode could not be set for all users.
• Molecule representation
  • QueryBond cloning did not preserve bond type.
  • Exception related to expanding Sgroups in RgMolecules
  • SuperatomSgroup.attachAtoms was not set automatically during SuperatomSgroup creation.
• Chemical Structure Painting
  • 3D rotation of fragments started to wrong direction.
  • Valence count displayed ugly: on the top of the atom label.
  • The COCl group was not connected through the Carbon label when it was on the left side of a structure (forum topic).
• Import/Export
  • Smiles did not set arrow for reaction because of it RXNMolecule threw NullPointerException.
  • Molecule.toFormat("smarts") changed the state of Molecule: getAtomCount(), getBondCount() and the unifiedStructure properties of query were null value.
  • Certain MRV files could not be imported where tag included a line break.
  • R-group queries could not be exported to SMARTS as recursive SMARTS in 5.4.x.
  • ArrayIndexOutOfBoundsException was written on System.out by parsing SMILES.
  • IUPAC Name
    • By parsing 2-(o-Toluidino)ethanol IUPAC name, the 'o' was ignored.
    • IUPAC name import did not support correctly poly spiro in the simple case (numbers, not structures).
    • Those IUPAC name could not be parsed from HTML where an &nbsp; preceded the name.
    • By importing certain IUPAC names, the stereo center missed on the created molecule.
    • All IUPAC names with "hydrazon" were wrongly imported.
    • dicarbonimidic diamide and imidodicarbonimidic diamide were not supported.
    • Generate correct name for hydrides of elements in group 1 to 12, for instance "sodium hydride".
  • IUPAC InChi
    • There was a memory leak in the native call, now in the jni-inchi interface it is resolved.
    • InChI failed to export stereochemistry on 0D molecules.
  • Certain CDX files that included graphical arrows and dashed rectangles could not import properly.
• 2D cleaning / Aromatization
  • General aromatization put single-or-aromatic and double-or-aromatic bonds when it shouldn't.
  • Molecule.partialClean(int, int[], String) removed stereo info from molecule when the input was in mrv format.
  • At first attempt, the aromatization did not work after creating a ring with bold double bonds in it.
  • The 2D clean of a molecule with position variation bond caused an error dialog: "Error in module Clean2D".
  • Five membered rings were not converted to aromatic form with single_or_aromatic and double_or_aromatic bonds respectively.
• StereoChemistry
  • Superfluous wedges appeared by importing of certain SMILES.
  • The Phosphorus in phosphines was not recognized as stereo center (forum topic).
• 3D alignment
  • MCS based alignment bug: bad similarity score was returned for CCC1CCCCC1.CCCCCCC1CCCCC1.
• Calculator Plugins
  • Elemental Analyser result window did not display text fields in single fragment mode.
  • In Naming Plugin result window, the IUPAC name disappeared after scroll down and scroll up by those compounds whose name included special characters (like lambda).
• Chemical Terms
  • When a chem terms column was added in IJC that generated InChI, it occurred a lots of errors and JVM could crash (forum topic).
• API
  • Molecule.getBondTable() threw exception when a bond with atom index higher than atom count was get.
  • MoleculeGraph.getFormula getMass and getExactMass were not thread-safe.
  • When a new bond with a new end-atom was added to a SelectionMolecule, it was not cloned properly.
  • Serialization threw an EOFException when it was used from MolImporter/MolExporter.

April 8th, 2011: Marvin 5.4.1.2

• Marvin Sketch
  • In the Save As Image dialog, there was a typo in the file type filter list.
  • ArrayIndexOutOfBoundException in template parameter handling.

February 16th, 2011: Marvin 5.4.1.1

Bugfix

• MarvinSketch
  • Fix generic template toolbar removal ability throught ttmpls parameter. Avoid warnings in template related code.

February 9th, 2011: Marvin 5.4.1

New features and improvements

• MarvinSketch
  • Public database search in chemicalize.org.
  • Possibility to change ligand order in MarvinSketch.
• Molecule Painting
  • Fog-effect can be controlled in various ways:
    • There is a slider on the Display tab of the Preferences dialog in the Sketch/View GUI to set the strength of the fog-effect and a checkbox to switch off the automatic fog-effect.
    • Applet and beans parameters are introduced: fogFactor, automaticFogEnabled. (forum topic).
• Molecule Representation
  • Attaching to a group attachment point does not automatically ungroup the Sgroup anymore.
  • Determination of S-group content: multiple and generic S-groups have to contain the whole subgraph between the bonds crossing the brackets.
  • Update of S-group content if bracket positions change: either brackets or the structure is moved.
  • S-group embedding and overlap are checked at molecule consistency checks.
• Import/Export
  • SMARTS import supports aliphatic carbons with double bond (forum topic).
  • SMILES import/export supports allenes.
  • IUPAC name
    • Generate traditional name for fragments inside a larger compound (e.g. "dextromethorphan hydrobromide").
    • Support for CAS number conversion.
    • Improved OCR error correction in DocumentExtractor (missing commas, misrecognized parenthesis type, extra spaces, ...).
    • Document Extractor on PDF documents now gives the page number of hits.
    • Improved support for common names in structure-to-name and name-to-structure. The general support for name import increased by around 5% for common and 10% for systematic names. Conversion speed is increased by about 20%.
• Installers
  • JChem and Marvin Beans installers for Windows also extract shell script for cygwin.
• Calculator Plugins
  • Preserve exocycyclic groups in Bemis-Murcko frameworks.
• Markush Enumeration
  • Halogen can have more than one connection during enumeration.
  • Aromatic bonds are considered during calculating the number of double bonds for homology property checking.
• API
  • Lasso selection mode can be set to be the default in MSketchPane (forum topic).
  • A new function, isChiral has been added to TopologyAnalyzer.
  • New Chmical Terms functions: isQuery(), fieldAsString().

Bugfixes

• MarvinSketch
  • Name box was not updated after group creation because creating a group did not increase graph invariant change count (forum topic).
  • MarvinSketch application did not understand "-{name}" command line parameter.
  • When the Structure > Find structure online menu was invoked under Linux, the default browser could not be detected to display result (forum topic).
• Applet
  • The loading of the isotopes.data file from the java cache failed if its uncompressed version was stored in the cache (i.e. if the uncompression was done automatically by the webserver, and not by Marvin). Forum topic, documentation.
• Molecule Painting
  • Graphical objects were not displayed in the Geometry Plugin result window.
  • On the electron-flow arrow, the blue box for highlighting was missed (forum topic).
  • Ligand order was not displayed on the scaffold if the definitions were deleted, even if the "Always" display option was set for "Ligand Orders" on the preferences dialog.
• Import/Export
  • Index of the multicenter atom became corrupt after exporting into MDL Mol format if it was connected to an R-group.
  • Arrow stuck to rectangles was damaged during Mrv import/export (forum topic).
  • Import of 1-letter peptide failed at a single Histidine (forum topic).
  • Implicit hydrogens were missing by importing from skc.
  • Null property value of MolAtom was not exported/imported in Mrv format.
  • By importing certain SMARTS, wrong bond type was determined instead of single or aromatic bond.
  • Certain brackets imported from Cdx files drawn in ChemDraw were displayed in the wrong direction.
  • SMARTS export: 1-atom single bond neighbor of an aromatic ring was exported as single bond instead of single/aromatic.
  • Exporting queries with link node and R-groups in SMARTS format were incorrect.
  • The H atom handling was ambiguous in SMARTS expressions.
  • Mol file comment field import failed.
  • Importing of certain SMILES was wrong (forum topic).
• Clean 2D
  • If the template contains a chain part which can be located in the target as a part of a ring (or ring system) we should ignore that part of the template.
• Molecule Representation
  • The Fine with Hydrogenize option of Clean3D did not ungroup S-groups automatically (forum topic).
  • Molecule.contractSgroups() messed up the molecule coordinates (forum topic).
• Stereochemistry
  • Explicit hydrogens were not properly taken into account in Cis/Trans stereochemistry calculation.
• Calculator Plugins
  • Tautomer generator threw ArrayIndexOutOfBoundsException in some cases.
• Markush Enumeration
  • Homology enumeration produced inconsistent molecules for some VMN input.
• Structure Checker
  • Incorrect charge count after applying CovalentCounterion fixer.
  • The log output format of StructureChecker command line differed from output format of the wizard.
  • ChiralFlagErrorChecker did not handle chirality correctly. Instead of calculating chirality from parity data, it used an implementation based on the isChiral method of TopologyAnalyser.

December 17th, 2010: Marvin 5.4.0.1

Bugfixes

• MarvinSketch
  • Highlighting of electron flow arrows was wrong when the base or end point was a bond (forum topic).
• Applet
  • Serialized menu configuration did not work.
• Import/Export
  • MDL MOL and SDF
    • The index of the multicenter atom was incorrectly created during MDL MOLFile export in case of structures where the R-group was connected to the multicenter atom (position variation bonds).
  • SKC
    • Implicit hydrogens were missing from the atoms after the import or paste of structures in ISIS/Symyx Sketch file format (SKC file format).
  • CDX
    • CDX files including rotated graphical objects exported from old versions of ChemDraw could not be imported.
• Calculator Plugins
  • Tautomer calculation
    • Generic tautomer was not unique enough in some cases. Due to the fix, the generic tautomer is provided aromatic form.
    • Canoncical tautomer calculation has been improved due to the fix of dearomatization.
• cxcalc
  • Certain structures with explicit hydrogens connected with wedge bond gave an exception during generic tautomerization.
  • Volume calculation was missing from cxcalc.
• Structure Checker
  • Structure Checker threw NullPointerException instead of ignoring incorrect configuration file.
• API
  • chemaxon.struc.Molecule.implicitizeHydrogens(MolAtom.ALL_H) did not remove hydrogens.

November 25th, 2010: Marvin 5.4.0

New features and improvements

• MarvinSketch GUI
  • Multiple, ordered R-group attachment points in Markush structures. It is possible to define bond types on the ligands, and change the order of the attachment points as well.
  • PubChem substructure search from Marvin.
  • New 3D transformation options: rotate around various axes, group rotation, horizontal/vertical/group Flip, horizontal/vertical/canvas/group Mirror, and Inversion (Documentation: Move and rotate, Flip, Mirror, Inverse).
  • 3D Plane option: upon three selected atoms it rotates the structure to have the selected atoms in the drawing plane (Documentation).
  • Directed Merge option: It merges a fragment (Substituent) to another (Template or Scaffold) based on atom pairs assigned by the Atom Assigner tool (Documentation).
  • New Substituent option: Opens a separate MSketch window to sketch a new fragment, and transfers it back to the main window (Documentation).
  • Context based, configurable attached data editing (Documentation: Attached Data and Attach Data Config).
  • Delete actions have been uniformized, and the Delete tool work differently on terminal atoms when holding the Alt key. The default behaviour of delete can be configured on the Preferences dialog (forum topic).
  • Atom editing procedures have been improved, so the "feature" that automatically deleted a bond when an atom was dragged over it has been removed.
• Applet
  • New parameters have been introduced:
    • disablePluginsLookup (Documentation).
    • defaultDatatransferPolicy (Documentation).
    • isMyTemplatesEnabled (Documentation).
• Molecule Painting
  • Aromatic and double bond display improvements: now it follows the IUPAC recommendation in each case (forum topic).
  • Ellipses are drawn in asymmetric aromatic rings in 2D.
  • The R-group attachment point display has been changed to follow the IUPAC recommendation. The order of the attachment points is visualized both at the Scaffold and the substituents.
  • R-logic can optionally be displayed on the sketch.
  • The degree of rotation is displayed during rotations having specified axis.
• Molecule Representation
  • S-groups are validated at creation based on the selected (sub)structure: only the chemically meaningful types can be created. How to draw S-groups. The option can be switched off on the Preferences dialog.
  • R-group attachment point representation has been redesigned.
• Import/Export
  • IUPAC Naming
    • Major upgrade of Name To Structure. Reduces wrong conversions by 50% to 70%, and supports about 10% more names.
    • Significant speedup (around 100%) in structure to name generation.
    • Local relative stereo (R* and S*) is supported in name to structure.
    • Pseudo-asymmetric stereo descriptors (r) and (s) are generated.
    • The generated names for salts have been improved.
    • Name generation detects new cases of very complex structures and aborts quickly instead of timing out or locking. All known cases are handled well now.
  • MRV
    • The S-group and the R-group storage has been changed.
  • MOL/SDF
    • The S-group and the R-group storage has been separated: the APO tag stores only the R-group attachment points, and the SAP tag is used for storing the S-group attachment points. The new storage format is not imported properly by older versions of Marvin.
    • A new option, called "skipAtomValues" has been introduced in MolImporter and molconvert to avoid importing lines containing atom values (Documentation).
    • SDFiles (incorrectly) having an empty line between the CTAB block and the properties block are accepted at import.
  • SMILES/SMARTS
    • SMARTS representation of X (forum topic).
  • CDX/CDXML
    • CDX/CDXML import has been improved: TLC plates, table objects and r-logic are imported now.
• Datatransfer
  • Configurable clipboard handling in applets: the file formats available for copy and paste can be customized. Documentation.
  • Marvin OLE object: 64-bit support for windows natives (OLE, EMF generator).
  • Traditional name has been added to the Copy as dialog formats.
• Stereochemistry
  • Graph invariant calculation uses local parity instead of local chirality.
  • Improved stereochemistry (r, s, M, P descriptors).
• Aromatization
  • New aromatization option for ambiguous 5-membered rings. Linking documents: Basic Export Options, Aromaticity Detection.
  • Query aromatization changes single bonds to single_or_aromatic, double bonds to double_or_aromatic in a ring which contains _or_aromatic bond. Linking document: Aromaticity Detection.
• Calculator Plugins
  • logP and logD plugins support multiple logP training parameter files.
  • pKa and logD plugins support multiple pKa correction library files.
  • Fused output option on Markush enumerator GUI (forum topic).
  • Industry standard MMFF94 forcefield options in Conformer Generator and 3D Molecular Properties.
  • Atrop isomers are detected during conformer generation.
  • Canonic tauotomer generation was improved.
  • Performance and accuracy improvements of 3D molecular alignment.
  • Structure Checker functions in Chemical Terms. Documentation.
  • Chemical Terms uses a new file format for storing predefined molecules. The new format contains also the R-group representation of the molecules, which can be used for visualization.
  • Training and Prediction
    • A new plugin called Predictor enables to train and run the users' own molecular property prediction. Documentation.
    • A command line trainer tool has been introduced, called cxtrain.
    • LogP and General (Atomic Contribution Based) Training and Prediction has been refactored (performance improvement and structural changes).
• Structure Checker
  • New checkers are available:
    • Empty Structure Checker
    • Explicit Lone Pair Checker
    • Star Atom Checker
    • Metallocene Checker
    • Covalent Counterion Checker
    • OCR Error Checker
    • Ring Strain Error Checker
    Read about available checkers
  • A command line tool called structurecheck is available for checking files in batch mode.
  • Application based structure checker configuration support has been added to the API. It is also available in the applications that are integrating Structure Checker.
  • Several improvements have been made in the Overlapping Atoms and the Overlapping Bonds checkers: The accuracy of the overlap detection has been improved to avoid fault warnings.
• Licenses
  • All Topology Analysis functions require a valid license.
• Installer
  • Full 64 bit support: 64-bit installers are available for all platforms.
  • Registration of file associations can be turned-off with one checkox.

Bugfixes

• MarvinSketch GUI
  • Delete action sometimes had undesired effect from atom context menu.
  • On Mac OS X, Drag and Drop of names to the canvas did not work (forum topic).
• Marvin Space GUI
  • The screen flickered and an empty canvas was displayed sometimes (forum topic).
  • There was a frame closing problem when MarvinSpace was launched for MarvinSketch (forum topics: 1, 2).
  • The pull-down menus were not displayed properly (forum topics: 1, 2, 3, 4, 5, 6, 7).
• Applet
  • On Mac OS X, in Safari, the opening of the Periodic Table (or other modal) dialog caused freezing the MarvinSketch applet.
• Molecule Painting
  • Charges disappeared on carbon atoms if carbon labels were hidden and lone pair painting was turned off (forum topic).
  • Certain MEflow object disappeared when display properties were changed (forum topic).
  • The second data attached to the same selection using absolute placement overlapped with the first one.
• Molecule Representation
  • RgMolecule.addRgroup(int rl, Molecule m) did not change the grinvCC, therefore the graph union was not updated and had not contained the newly added Rgroup.
  • The bond table representation of the MoleculeGraph has been changed to avoid OutOfMemoryError.
  • There were a few S-groups related bugs: in creating a reaction from a molecule with S-groups, in creating S-groups in reactions, and in merge/unmerge of reaction components containing S-groups.
  • When deleting multiple groups, n-1 occurrences of its content remained.
• Import/Export
  • 0D molfiles can not contain stereo information, therefore Marvin applications apply a 2D clean to 0D molfiles in the future.
  • SMILES/SMARTS
    • Certain SMARTS was imported wrongly.
    • Explicit bond appeared where it was not needed in SMARTS.
• Datatransfer
  • InChi with AuxInfo failed to paste in into Marvin.
• Stereochemistry
  • If only one explicit Hydrogen is attached to one side of the double bond, then it incorrectly got E/Z stereo information.
  • The calculation of chirality/parity for phosphanes was incorrect in some cases (forum topic).
  • Remove explicit hydrogen removing some stereochemistry (forum topic).
• Clean 2D
  • Cleaning of ferrocenes created some extremely long bonds.
• Calculator Plugins
  • Moieties (Repeating Units without crossing bonds) were ignored in Markush enumeration.
  • HBDAPlugin threw ClassCastException in some cases.
  • Some bugs were fixed in the tautomer generation (forum topic).

September 3rd, 2010: Marvin 5.3.8

Bugfixes

• MarvinSketch
  • Lone pair placement wrong in some case.
  • Simple arrows could not be deleted at enpoints.
• Import/Export
  • molconvert.bat cxsmarts:qh failed with explicit H (forum topic).
  • Exporting of Single Electron Flow Arrow to Mrv failed.

August 13th, 2010: Marvin 5.3.7

Bugfixes

• Applet
  • Marvin applets did not start with Turkish default locale.
• Molecule representation
  • Small brackets were displayed looking like a box when reading polymer Sgroups from MOL V2000 format.
• Painting
  • When a reactant contained Sgroup, reaction arrow was not drawn.
  • If an Sgroup was a single reactant in a reaction, it could not be ungrouped.
• Data transfer
  • Clipboard operation hanged with an error in ExecutorService if legacy_lifecycle was off and two applets were started in the same JVM (forum topic).
  • OLE copy fail-over mechanism did not work.
• Calculator Plugins
  • PluginFactory threw NullPointerException on applet loading.

July 15th, 2010: Marvin 5.3.6

New features and improvements

• Molecule representation
  • Warning message on incorrect s-group selection in reactions.
• Calculator Plugins
  • Markush enumeration: valence filter is set off by default.
• Import/Export
  • IUPAC Name
    • Name generation has been improved and handles more traditional names.
    • Shorter names are generated in more cases, for instance "pentamethylhydrazinium" instead of "1,1,1,2,2-pentamethylhydrazinium".
    • Name generation for large structures succeeds with a systematic, Von Baeyer name instead of failing with a timeout.

Bugfixes

• MarvinSketch
  • Scaffold zoom was not working.
• MarvinSpace
  • MSpace did not start on various platforms or OS versions: the installation of native OpenGL libraries failed in some cases.
  • MSpace menus were displayed behind the canvas (forum topic).
• Editing
  • When trying to open the Format dialog from contextual menu over the corner point of a bracket, the Format dialog was empty.
  • Uniformization and bug fixes in delete actions.
• Painting
  • R group sign was misplaced when inserting a graphical object into the sketch.
• Import/Export
  • MDL MOL import of incorrect bracket information caused AIOB (forum topic).
  • InChI failed to export stereochemistry on 0D molecules.
  • InChI export silently ignored unknown options.
  • SRU was read as repeating group with repetition ranges.
  • ReaxysGenerics were not imported from Extended MOLFile.
  • In IUPAC Name export, generation of E/Z stereo descriptors was missed in certain cases.
• Molecule representation
  • The implicit H was not correct after importing cxSmarts string with radical information.
  • Changing group type to MultipleSgroup produced inconsistent molecule.
  • Changeing a type of a non-expandable s-group to SRU didn't change bracket type from double to single.
  • MarvinSketch had a problem with valence calculation after removing explicit hydrogens.
  • Rubber tool was not working for attached data.
  • On terminal groups the Repeating unit with repetition ranges group type had only a single bracket.

June 24th, 2010: Marvin 5.3.5

Bugfixes

• MarvinSketch GUI
  • Setting "Automatic Lone Pair Calculation" off does not work after restarting MarvinSketch.
  • The Save as image menu action did not update the save directory.
• Applet
  • Marvin Applets could not load-in resources from out of jars.
  • Improve Java Plugin detecting mechanism in marvin.js to print warning when required Java is missing.
• Import/Export
  • Certain generics from extended molfile that had saved by Marvin 5.2.x could not be loaded.

June 15th, 2010: Marvin 5.3.4

New features and improvements

• IUPAC Name2Structure
  • Non standard capitalization of names in the custom dictionary are also accepted.
• Marvin OLE support
  • It is possible to change the default editing mode of Marvin objects in MS Office applications to Stand Alone mode (i.e. upon double click the object is opened in a separate office document) by excecuting the corresponding registry setting (.reg) files (documentation).

Bugfixes

• MarvinSketch
  • Loading predifined styles in format dialog threw an exception.
  • Structure checker dialog was displayed behind the main sketcher window in OS X.
• Applet
  • There was a false request to download chemaxon/marvin/dict.class.
  • Template files that were out of jars could not be accessed.
  • In the student examination example, newer Java Plugins (1.6.0_19 or higher) could not load resource bundles of customization.xml from outside jar.
  • RejectedExecutionException was thrown by module loading.
  • IUPAC name recognition system could not load functional groups dictionary in case of newer Java Plugins (1.6.0_19 or higher).
• Compatibility
  • In Safari, under OS X 10.6, the default value of "legacy_lifecycle" applet parameter has been changed (to false) to avoid hanging by concurrent applet loading and insufficent delay at the closing of applet pages.
  • In the default configuration of Marvin applets, the "codebase_lookup" Java Plugin parameter has been set to false to avoid insufficent search of certain localization files in applet codebase.
• Import/Export
  • If a MOL/SDF file contained incorrect bracket coordinates info, an exception was thrown. Now the proper coordinates for the corresponding Sgroup are automatically generated in these cases (forum topic).
• Molecule Representation
  • There was a valence check problem with NC4-radicals and C-C4radicals (forum topic).
• Calculator plugins
  • Tautomerization of certain SMILES with explicit hydrogens failed (forum topic).
• API
  • Periodic system modality problem inside MSketchPane on a dialog or frame.
  • The Periodic System dialog was not displayed properly in Instant JChem.
  • Structure Checker dialog stuck under MSketchPane when it was in a modal dialog under Mac OS X.
  • chemaxon.util.ImageExportUtil did not calculate the size of the image properly in certain cases.
  • ChiralityFlagErrorChecker got wrong result when molecule contained a stereo with no enhanced stereo property.

May 14th, 2010: Marvin 5.3.3

New features and improvements

• MarvinSketch
  • A new option for direct structure search in a public database has been introduced: Find Structure in PubChem.
• Applet
  • A message dialog containing a progress bar is displayed if the loading of a module takes more than 100 milliseconds, which automatically disappears when the module is loaded.
  • New applet parameters ahve been introduced to control pre-loading of modules: preload,bgloadEnabled and bgloadPriority.
• Molecule representation
  • A new method has been introduced that returns MolAtom: MolAtom.getLigands() (forum topic).
• Calculator Plugins
  • Tautomers: dominant tautomers are returned by default, instead of all tautomers (cxcalc, Chemical Terms, GUI).
  • Markush enumeration: New homology example definitions are used, which are based on matching statistics from a large data base.
  • TPSA: Sulfur and Phosphorus atoms optionally can be excluded from calculation (forum topic).

Bugfixes

• MarvinSketch
  • The "extraBonds" parameter value was missing for Single Bold Bond, therefore the Bold Single Type could not be removed from the Bond menu.
  • Joining two multicenters threw an exception in some cases.
• MarvinView
  • After opening a file in MView by adding the file name as a parameter, the "Save Selection" menu did not worked in some cases.
• Applet
  • Certain resources (like template files) could not be loaded-in with Java 1.6.0_19 and above versions. Since Java blocked loading resources from untrusted content. (forum topic).
• Painting
  • The lone-pair placement was incorrect in some cases (forum topic).
• Import/Export
  • Mrv: Reaction arrow parameters exported into Mrv files with Marvin 4.1.13 or older versions were not imported properly.
  • Name to Structure: The stero information was lost during the conversion of Name to some other formats (inchi, mol, sdf, ...).
• Molecule representation
  • Deleting atoms in reactions raised exception, did not ungroup the superatom s-group and could split content of one s-group into several reaction components.
  • During setting bond array in Sgroup constructor, an exception was thrown when calling mol.clonecopy(int[], MoleculeGraph).
  • The attachment point information was missing when creating abbreviated group in MarvinSketch.
  • Markush enumeration failed on repeating unit with repetition ranges (forum topic).
• Calculator Plugins
  • StereoisomerPlugin returned wrong stereoisomer count via API (forum topic).
  • Random Markush enumeration was very slow for highly complex Markush structures.
• Chemical Terms
  • "evaluate --list-functions" threw NullPointerException if the user's Evaluator configuration file was missing.

April 14th, 2010: Marvin 5.3.2

New features and improvements

• MarvinSketch
  • New parameter "abbrevgroupsAllowed" is introduced to be able to disable abbreviated groups on key types (documentation, example, forum topic).
  • New parameter "toolbarFloatable" is introduced that can be used to make the toolbars immovable (documentation, forum topic).
  • Changes in the Structure > Aromatization menu of MarvinSketch: renaming menu elements, the default aromatization method is changed to Basic.
  • Change in the behavior of the Custom Property buttons on the Periodic System dialog window. (The buttons are not toggled automatically any more. If the Value cannot be represented in the given Type, the Value text field is highlighted.) (Forum topic.)
• Import/Export
  • ISIS (Symyx) sketch file (skc) format import and export.
  • CDXML import.
  • InChI is now available on windows 64 bit.
• Licenses
  • Arbitrary license file names are supported under the user's home directory (documentation).
  • It is possible to define multiple license file locations using environment variables or Java system properties (documentation for desktop applications | servers).
• Calculator Plugins
  • ElementalAnalyser and ElementalAnalyserPlugin can accept molecular formula input, so mass, atom count, etc. calculations can be performed on molecular formula.
  • New option for excluding halogens from acceptors in HBDAPlugin. Halogens are excluded from acceptors by default.
  • Molecular volume calculation (forum topic).
  • Projected surface area calculation: new implementation, speedup and enhanced accuracy (forum topic #1, #2).
  • The import of traditional names supports greek letters, salts, sulfonamides and bi/tri/... phenyl groups.
  • Name import supports mixture names with proportions, for instance 'Methanol, bismuth(3+) salt (3:1)' (forum topic).
• API
  • New MolPrinter API method to display valence errors MolPrinter.isValenceErrorVisible().

Bugfixes

• MarvinSketch
  • After adding a Multicenter to a structure, the menu item did not become disabled, and a second invocation threw an AIOOB exception.
  • Sometimes an NPE was thrown at initialization of Abbreviated groups (forum topic).
  • Switching from 3D to 2D mode using the button on the statusbar caused loosing stereo information.
  • It was impossible to resize a textbox created by mouse-click (forum topic #1, #2).
  • It was impossible to create ladder-type repeating unit with repeatition ranges in sketcher.
  • Adding bonds in bond drawing mode sometimes damaged the molecule.
  • It was possible to create too small textboxes by drag-drawing; a minimum size was intorduced for graphic objects to avoid that (forum topic).
  • The hydrogen number was not updated after creating position variation bond.
• MarvinView
  • The MarvinView parameter "tabScale" did not work properly (forum topic).
  • Unnecessary hourglass cursor was displayed in MarvinView's spreadsheet view when selecting a structure.
  • MarvinView did not display associtated file in OS X. Dragging molecule file into MarvinView did not work either (forum topic).
• MarvinSpace
  • Transparent surface drawing artefact in MarvinSpace.
• Import/Export
  • Mol2 export did not export fragment count properly and there was a multifragment charge problem (forum topic).
  • There were OSRA errors on some Linux and Macs machines.
  • IJC and JCman crashed when using inchi chemical terms expressions.
• Molecule Representation
  • Bold bond type remained set when changing the bond type to single/double/triple from menu.
  • Mrv import of two contracted embedded abbreviated S-groups was not working.
  • There was an endless loop in MolSearch on a structure having a Multicenter S-group.
  • The E/Z stereo information was incorrectly displayed after S-group expansion (forum topic).
  • Attachment points were mixed after copy and then paste or export and then import.
  • Ungroup function of Sketcher didn't remove the empty S-groups.
• Template Handling
  • Template parameters (tmpls, ttmpls) did not work properly.
  • Moving template sets up or down in the Template Library did not have affect on the toolbar.
• Calculator Plugins
  • Molecule with homology atoms and undefined R-atoms threw ExpansionException during markush enumeration.
  • JavaDoc on MarkushEnumerationPlugin.setEnumerateHomology and setMolecule order dependency was not up-to-date.
  • Markush enumeration was not working on ladder-type repeating unit with repeatition ranges structures.
  • The MarvinView result window of the 3D Aligment calculation in MarvinSketch contained the coordinate info of the removed Hydrogen atoms, which sometimes resulted in not enough space for the display of the aligned structures.

February 22th, 2010: Marvin 5.3.1

Bugfixes

• MarvinSketch
  • Manual mapping did not work.
  • The bond between the two atoms of the multicenter part of a position variation bond was deleted when a new bond was added to the position variation bond by click drawing
• Applet
  • Applet could not be reffered from JavaScript in Chrome.
• Calculator Plugins
  • Avoid NullPointerException in logPFragmentCreator.
  • logP calculation in cxcalc did not produce output under Linux.
  • pKa training threw ArrayIndexOutOfBounds exception

January 29th, 2010: Marvin 5.3.0.2

Bugfixes

• MarvinSpace
  • MarvinSpace could not be launched without a valid conformer license.
• Applet
  • The unix2local method converted string by wrong way under Mac.
• API
  • chemaxon.struc.StaticMolecule.getExplicitHcount() returned with null value instead of zero when no explicit hcount was defined for any atoms.
• Marvin OLE
  • An empty molecule was returned by the first invocation of the getMol method of Marvin OLE server after setMol.
• Documentation
  • Complete apidoc for Structure Checker API
• Installer
  • The Marvin installer did nothing in silent mode (-q command line parameter) if an earlier version of Marvin was already installed previously.

January 21th, 2010: Marvin 5.3.0.1

Bugfixes

• Marvin Sketch
  • Structure Checker Progress bar remained on the screen during structure fixing.
• Applets
  • Chemical terms calculation did not work from MarvinSketch applet.

January 15th, 2010: Marvin 5.3

New features and improvements

• MarvinSketch GUI
  • Structure Checker add-on, a tool for detecting molecule features or drawing errors is integrated.
  • The Template Library is redesigned. It allows hierarchic template structure and custom locations to be set in the library. Templates are loaded dynamically (documentation).
  • OLE anti-aliasing is improved: enhanced embedded object quality in MS Office documents.
  • "Sprout" drawing: attaching templates and abbreviated groups by automatically inserting a bond. Using the SHIFT button the rings are attached as spiro, while the abbreviated groups are attached in expanded form. Rotation by 15 degrees is possible before releasing the mouse button.
  • Bracket drawing tool: simple group creation without the need of preselection; the targeted substructure just have to rounded by the bracket tool.
  • Bracket editing: group type can be changed in Edit > Group (no need for recreation of group).
  • Data can be attached to brackets.
  • Possibility to load up to 100 molecules from multirecord files to the canvas. Ranges can be defined during the opening process.
  • Importing images by converting them to structures (using OSRA in the background).
  • The Copy As dialog is redesigned to contain explicit formats. At the same time, the Copy tab of the Edit > Preferences dialog has been removed.
  • Copy/Paste: single line text formats (name, inchi, ...) can be pasted even if they contain extra newlines.
  • New bond type: bold bond.
  • Ellipse drawing and circle drawing.
  • Rectangle with rounded corners drawing. Square drawing.
  • Direct structure search in public database: ChemSpider.
  • Web links are detected in attached data, and opened in browser by Ctrl-click.
  • The layout of the Attach Data dialog is improved, new data types are introduced and listed by default in "Name" field: [DUP], REAGENT. See the documentation.
  • Copying Marvin Objects to MS Office documents is sped up.
  • CDX format is placed on the clipboard by default copy action and automatically recognized during paste.
• MarvinView GUI
  • Text search in molecule tables.
  • Marvin View can now open name files even when not all names are supported.
  • Save layout in MarvinView.
• MolConverter
  • New parameters: -U for union output (fuse) and -I for processing input molecules in index range (forum topic).
• Marvin Space
  • 3D molecular alignment is integrated into Marvin Space.
  • Save structure in Marvin Space.
• Applets
  • Move Marvin applets (JMSketch, JMView) into the chemaxon.marvin.applets package.
• Chemical Structure Painting
  • Electron flow arrows start at closest lone pair electron.
• Molecule Representation
  • Annotating with URLs.
  • New bond type: bold bond.
  • Atoms with three similar wedge had no parity value.
  • A bracket button for S-group bracket drawing.
  • Valence check of alkali metals has been changed. (Alkali metals are not imported as alkali hydrides: Na is imported without implicit hydrogen atom instead of NaH.)
• Import/Export
  • Concurrent processing in molecule import/export.
  • CDX Export.
  • VMN file import.
  • Usage of S-group bracket coordinate info (BRKXYZ tags) and style info (SBT) in MDL MOL formats.
  • Import and paste images via OSRA.
  • SMILES/SMARTS
    • Aliphatic explicit H is written as [H] instead of [#1A]
    • SMILES export default behaviour to check graph invariants at CIS TRANS export.
  • IUPAC Name
    • Concise names generated for acyl-CoA (coenzyme A) derivatives.
    • Dictionary of common and traditional names have vastly improved and augmented.
    • Structure to name generates many more common names with the "traditional" option.
• Clean 2D
  • Use the template wedges in PartialClean.
  • Clean of adamantane structures is nicer.
• 3D Alignment
  • Alignment by pharmacophore types.
  • Alignment by Maximum common substructure.
• Calculator Plugins
  • Tooltips with help messages are displayed on Calculator Plugins options panels.
  • Some Calculator Plugin options panels have been redesigned, to fit small resolution displays (forum topic).
  • Tautomerization Plugin: ester groups are not considered as tautomerizable region by default but you can switch it on.
  • In HBDA Plugin, sulfur atoms are not hydrogen bond acceptors by default (optional) (forum topic).
• Documentation
  • MarvinSketch and MarvinView documentation (JavaHelp) supports Favorites, which allows help topics to be saved and reused.
• Licenses
  • License files can be merged with the command line tool (See merging license)
• API
  • MarvinBeans.jar has been devided into several small jars.
  • New methods in Marvin Applets API: JMSketch.clean2D(), JMSketch.clean3D().
  • API to add custom file formats to clipboard functionalities in Marvin.

Bugfixes

• MarvinSketch
  • Fixing compatibility problem of structure templates with a file named custom.t.
  • Some of the tooltips in the Reaxys Generics dialog were mixed.
  • Undoing the deletion of a reaction arrow was not working in case of there was nothing more on the canvas.
  • Anti-aliasing was not working in OLE objects if atom labels were present in the structure.
  • The multipage function buttons were missing on statusbar.
  • NullPointerException in Marvin Sketch when opening a recent file.
  • E/Z labels display option was not saved in MarvinSketch.
• Applet
  • URL of java download pages in marvin.jar have been modified (forum topic).
  • Security errors in applet when it called from JavaScript (forum topic).
• Import/Export
  • SMILES/SMARTS
    • Clean2D not called from molconvert cxsmiles:+c
    • SMILES export: elements in the "organic subset" is considered more seriously.
    • SMILES export without stereo info.
  • IUPAC Name
    • Add missing chiral modifiers in the name of pure hydrocarbons.
• Clean2D
  • Stereochemistry error during 2D clean.
  • Badly cleaned molecules in JWS example.
  • Improvement of multicenter bonds' 2D cleaning.
  • The Hydrogenize Chiral Center option in 2D clean changed the stereochemistry.
  • Clean2D threw exception for graph containing only hydrogen atoms.
• Generate 3D
  • 3D coordinate generation stereo critieria handling has been improved.
  • Bugfix in clean 3D parallel execution.
  • General improvement in conformer generation (forum topic).
  • Forcefield (Dreiding) patch: correct geometry fo hydrazine (CNNC) like substructures.
  • ChemAxon force-field enhancement: planar geometry of aniline nitrogen is ensured (forum topic).
• Molecule Representation
  • StereoChemistry: CIS TRANS interpretation fix.
  • Add explicit H should not move the original atoms (forum topic).
  • Chirality fix for symmetrical molecules.
• Installer
  • Batch files failed if its path was C:\Program Files (x86)\ChemAxon (forum topic).
  • Installer did not upgrade the previously installed OLE server to newer version.
• API
  • MolPrinter.paint(Graphics2D,Dimension) threw NullPointerException if clip was not set for the graphics.

September 11th, 2009: Marvin 5.2.5

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
  • MarvinBeans for .NET snapshot version is available (download, documentation).

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.

August 11th, 2009: Marvin 5.2.4

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).

July 29th, 2009: Marvin 5.2.3.2

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.

July 15th, 2009: Marvin 5.2.3.1

No changes

July 8th, 2009: Marvin 5.2.3

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).

May 27th, 2009: Marvin 5.2.2

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:
  • Named constants for applet and bean parameters are available in the API: chemaxon.marvin.common.ParameterConstants.
  • New MolRenderer API available: chemaxon.marvin.beans.MolRenderer.
  • Deprecated methods in chemaxon.formats.MolImporter: parameterless constructor, setOptions(String), setFileName(String).

Bugfixes

• MarvinSketch:
  • Undo sets viewport to lower-right corner/Undo-Redo scaling.
  • Number of missing from menu label AND1 and AND2 in Atom > Stereo > Enhanced menu.
• MarvinView:
  • 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.

April 14th, 2009: Marvin 5.2.1

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.

March 10th, 2009: Marvin 5.2

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
  • Clean 2D improvement (forum topic).
• 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.

March 26th, 2009: Marvin 5.1.7

New features and improvements

• MarvinSketch
  • Customizable behavior of the "Close" option of Sketcher window.
  • The isotope list can be modified by the user (editing the isotope list).
• Applet
  • A custom image can be used with the java splash screen displayed while the applet is loading (live example).

Bugfixes

• Import/Export
  • The "Double Cis or Trans" bond ("Double Either" bond) was improperly imported from / exported to extended MOL (V3000) format.

March 23rd, 2009: Marvin 5.1.6

New features and improvements

• MarvinSketch
  • New template group: the generic groups that are used in searches in Beilstein.
• Import/Export
  • MOL and extended MOL import and export of Belstein Generics.
• Applet
  • A java splash screen ("Applet is loading...") is displayed while the applet is loading.
  • Load on-demand modules in background thread.
  • Display wait icon when loading on-demand modules.

February 14th, 2009: Marvin 5.1.5

New features and improvements

• MarvinSketch
  • Explicit valence setting of atoms is available from menu (forum topic).
• MarvinView
  • Large file viewing improved and lots of bugs fixed with both table types.
• Applet
  • New MarvinView applet parameter: celli_j and the possibility to escape characters.
• Import/Export
  • Text format import from cdx.
• Installer
  • Marvin Beans installer for Linux with Java.
• API
  • Save/load MSketchPane toolbar and menu configuration : reset active configuration fix.
  • New method in MolAtom (getLonePairCount()) that returns the same value as MoleculeGraph().getLonePairCount(int i) is implemented. (forum topic).

Bugfixes

• MarvinSketch
  • Keyboard shortcuts did not work properly (forum topic).
• MarvinView
  • Print All accessed only cached molecules from the table.
  • Save As did not save all molecules.
• Applet
  • Width of HTML label components fixed in MarvinView applet.
  • Marvin applets did not accepted inline CML/MRV files that were given in applet parameter.
• Calculator Plugins
  • Stereo isomer plugin: Enhanced stereo information was cleared before generating the stereoisomers.

December 19th, 2008: Marvin 5.1.4

New features and improvements

• MarvinSketch
  • Arrows group is restructured in the toolbar and in the menubar (forum topic).
  • The Insert > Groups menu is replaced by a more convenient dialog.
• Import/Export
  • Unique SMILES should implicitize plain Hydrogens (forum topic).
• Calculator Plugins
  • Unique Markush code can be generated for each enumerated structure.
  • logP and logD calculations are significantly faster.
• API
  • New methods in chemaxon.beans.MViewPane: isViewWindowOpened(int), isSketchWindowOpened(int) and closeSketcher(int).
  • PDBReader and related classes were moved from chemaxon.modules to chemaxon.marvin.io.formats.pdb.
  • MacroMolecule and related classes were moved from chemaxon.modules to chemaxon.struc.

Bugfixes

• MarvinSketch
  • The layout of the Copy As... dialog is polished.
  • Periodic System button remained pressed on the toolbar even after the dialog was closed.
  • The Atom > Stereo > Enhanced, Atom > Charge, Atom > Map, Atom > R-group menus are replaced by more convenient dialogs. (forum topic)
  • Ctrl+Del in MarvinSketch did not delete properties.
• Licenses
  • The command license -l produced bad output, not listing properly installed licenses.
• Calculator Plugins
  • When using Calculator Plugins, the result window of a previous calculation sometimes reappeared (forum topic).
  • Huckel Analysis Plugin threw exception if the input molecule contained explicit hydrogens.

November 13th, 2008: Marvin 5.1.3_2

Bugfixes

• MarvinView
  • Thread conflict while scrolling in huge SDfiles. (forum topic)
  • ArithmeticException in progress monitor.
• Import/Export
  • The implicit hydrogen setting option did not work in image generation.
  • Molfile import bug: pseudoatom names in atom block were not trimmed. (forum topic)

November 7th, 2008: Marvin 5.1.3

New Features and Improvements

• MarvinSketch
  • Slight improvement in multimolecule file opening, the index of the stucture in the preview is automatically offered.
• MarvinView
  • New helper API (chemaxon.marvin.beans.MViewParams) that generates the value to the molecule table parameters of MarvinView.
  • Support MDLCT format in OLE Object.
• Licenses
  • Important change in the licensing of calculator plugins: all plugins work in evaluation mode without a license.
• Import/Export
  • Encoding detection when the default system encoding is not suitable for the input file. It tries to recognize UTF-8, UTF-16, EUC-JP and Shift_JIS. If all fails, then it also tries ISO-8859-1 and windows-1252. The guessed encoding can be printed using molconvert query-encoding.
  • Energy is stored in the second line of XYZ files.
  • MDL formats
    • Import of SDfiles without structure fields.
    • Energy is imported from the header line, the "Energy" SDF property is removed.
    • Format recognition optimized: other recognizers are not called any more if the first 12 lines match at least one MDL format.
  • API
    • PositionedInputStream.skipLine() method is created to speed up pre-reading of huge multi-molecule files. It should be called in MRecordReader.skipRecord() implementations instead of readLine() if the line contents are unimportant.
• Clean 2D
  • Clean 2D considers electron flow arrows (forum topic).
• Calculator Plugins
  • Huckel orbital coefficient calculation in HuckelAnalysisPlugin (forum topic)
  • Markush enumeration ID can be generated for enumerated molecules.
  • logP calculation methods were introduced; available methods: "VG", "KLOP", "PHYS", "user defined", "weighted".
  • logP calculation is trainable, the "user defined" logP calculation method can be trained with experimental logP values provided by the user.
  • cxcalc can be used for training the plugin calculations (currently only logP is trainable).

Bugfixes

• MarvinSketch GUI
  • Correction in geometric transformation when placing SMARTS with the help of the Periodic System dialog window.
  • Help menu opened very slow on Mac (forum topic).
  • MarvinSketch web start application did not launch with Java 1.5.0_16.
• Import/Export
  • UTF-16 encoding is recognized and imported correctly if the file starts with a byte order mark (BOM).
  • Reaction arrow did not display (from rxn file) with exporting to image (forum topic).
• Clean 2D
  • Minor partial clean fix in case of rings.
• Calculator Plugins
  • HuckelAnalysisPlugin: numbers in arrays returned by cxcalc are separated by semicolons (forum topic).

October 1st, 2008: Marvin 5.1.2

New Features and Improvements

• MarvinSketch/View
  • New option/parameter to display the label of carbon atoms in structures.
• Moleculear representation
  • Get smallest set of smallest ring bond indexes (forum topic).
• API
  • chemaxon.marvin.io.MDocSource and chemaxon.marvin.io.MFieldAccessor are added to public API.
  • New abstract method in chemaxon.marvin.io.MDocStorage.Listener: storageSizeFinalized(MDocStorage).
• Documentation
  • chemaxon.util.iterator.IteratorFactory is added to apidoc and to the documentation.
  • Improved MarvinSketch applet examples for molecular property calculations.

Bugfixes

• Import/Export
  • SMILES import removed parity from rigi N stereo (forum topic).
  • Cxsmiles export generated unimportable output.
• Molecule Representations
  • Adding a bond to terciary N did not add + charge automatically and displayed valence error.
  • Reaction arrow head missed after import steps in mview and molconvert.
  • Adding and then removing explicit hydrogens created stereo bonds.
• Clean 3D
  • Bug caused parity error for certain strained structures fixed (forum topics:#4092, #4089, #3594).
• Calculator Plugins
  • If only scaffold coloring was set in Markush Enumeration plugin, link node bonds in scaffold were not correct.

September 1st, 2008: Marvin 5.1.1

New Features and Improvements

• MarvinSketch
  • New, explicit way of defining lone pair and radical electrons on atoms (live example).
  • The following menus were (temporarily) removed from the Template Library: File > Close, Options menu (the functions are out of order).
  • The Structure > Clean 3D > Select Conformer menu option is renamed to Display Stored Conformers.
• Applet
  • New applet parameter (templateToolbarCustomizable) to remove the on-the-fly customizability of the Advanced Template Toolbar.
• Import/Export
  • The lone pair and radical electrons can be exported to cxsmiles format.
  • Also recognize names that are part of the traditional dictionary (now that name recognition should only be tried when most others have failed, it is not as problematic to load the dictionary during recognition).
• Chemical Terms
  • Evaluator config files defined by the user are read from .chemaxon/MARVIN_MAJOR_VERSION (UNIX / Linux) or chemaxon/MARVIN_MAJOR_VERSION (Windows) directory.
• API:
  • Renderer (chemaxon.marvin.beans.MViewRenderer) and editor (chemaxon.marvin.beans.MViewEditor) components for JTables are part of the public API.

Bugfixes

• MarvinSketch
  • Explicit hydrogen was added automatically to newly placed atom after adding explicit hydrogen from the Structure menu.
  • Explicit lone pairs disappeared when editing the molecule with the sprout function (mouse drag).
  • Source window sometimes failed to open from plugin result dialog.
  • Extra selection of the radical atom was invoked.
• Import/Export
  • Add missing structures to nameimport dictionary, fix suffix and stereo handling on esters.
  • Molfile recognition failed if first line includes only spaces.
• Clean 2D
  • Some certain structures cleaned ugly (forum topic, forum topic).
• Template Handling
  • The nitro abbreviation template has been changed from neutral to the ionic form.
• Calculator Plugins
  • Changed default SDF tag names of cxcalc calulations acceptorsitecount (ACCEPTOR_SITE_COUNT), acceptorcount (ACCEPTOR_COUNT), donorsitecount (DONOR_SITE_COUNT) and donorcount (DONOR_COUNT) (forum topic).
  • Calculation result list often disappeared when the result display window was resized.
  • Parameter files of several plugins included invalid xml syntax.
• API
  • New methods to close streams in MolExporter: flush(), close(int).
  • F6 and F7 did not work if MViewPane was a JTable cell.

August 7th, 2008: Marvin 5.1.0

New features and Improvements

• MarvinSketch:
  • Converting IUPAC Names to structure:
    • from .name files
    • through the Edit > Enter IUPAC Name option
    • when pasting IUPAC names to the canvas of MarvinSketch
  • OLE 2 support: improved support of pasting MarvinSketch objects into MS office documents, and ability to edit the inserted object inside the Office document. More memory efficient, stable on Vista. JNI-based communication, multi-document server.
  • Accelerated initialization of MarvinSketch and MarvinView at startup, both as standalone version, and as implemented component in other applications.
  • Flip Group option: Flip a selected group in the molecule around the bond connecting this group to the rest of the structure.
  • Recent file list length is configurable in the Save/Load tab of Edit > Preferences
  • The save and load of GUI properties can be set only with one checkbox at the preferences Save/Load tab in the future.
  • The magnification (zoom factor) of a molecule is now saved in MRV format if it is enabled on the Save/Load tab of Edit > Preferences.
• MarvinView:
  • (Batch) conversion of IUPAC Names to structure when opening .name files.
  • Printing is redesigned. New options: Print to PDF and Print Preview.
• Applet:
  • New applet parameter to listen for mouse events: example (forum topic).
  • Calculator Plugins are accessible from JavaScript via Chemical Terms.
• Import/Export:
  • IUPAC name import (converting IUPAC names to structures):
    • opening .name files
    • batch conversion of names (in .name files) by molconvert
    • direct conversion of names to structures through the Edit > Enter IUPAC Name option
    • on-the-fly conversion of IUPAC Names to structure when pasting IUPAC Names to the canvas of MarvinSketch
  • IUPAC name export: improved support for amino-acids and peptides.
  • Compressed base64 encoded (cx)SMILES/(cx)SMARTS output.
  • UTF-8 character encoding support for applet parameters (forum topic).
  • Unique SMILES export has been changed because of the modification in aromatization.
• Molecule Representation:
  • Allow N with valence 5 in aromatic rings (forum topic).
  • Aromatization to accept all atom types in aromatic rings.
• Clean 3D:
  • Major Clean 3D core modifications: the fragment-fragment fuse code is rewritten. The new version places greater effort to avoid situations where excessive coordinate generation time is elapsed. The performance of multiple conformer generation is also improved.
  • New Dreiding force field implementation introduced.
  • Hyperfine parameters tuned: excessive runtime when invoked with looser optimization limit fixed.
• Calculator Plugins:
  • Tautomerization Plugin
    • Generic tautomer generation.
    • New tautomerization options: protect double bond stereo, protect all tetrahedral stereo centers, protect labeled tetrahedral stereo centers only.
  • Topology Analyser Plugin (forum topics: 1, 2)
    • New calculations: fragment count, ring system count, largest ring system size, smallest ring system size, aromatic ring count, aliphatic ring count, size dependent ring counting functions (ring count of given size, aromatic ring count of given size, aliphatic ringcount of given size, ring system count of given size). See also the list of cxcalc calculations and the Chemical Terms Reference Tables.
  • Geometry Plugin
    • Molecule projection calculations in GeometryPlugin: minimal projection area, maximal projection area, minimal projection radius, maximal projection radius. See also the list of cxcalc calculations and the Chemical Terms Reference Tables.
  • Markush Enumeration Plugin
    • Structure coloring and scaffold aligning options in Markush enumeration.
    • Position variation bonds in Markush enumeration.
    • New Markush enumeration options: orienting scaffold uniformly and coloring enumerated structures.
    • Speeding up random enumeration.
  • Huckel Analysis Plugin (forum topic)
    • Eigenvalue and eigenvector calculations (cxcalc: "huckeleigenvalue" and "huckeleigenvector").
    • Some cxcalc calculations have been renamed: "energy" to "localizationenergy", "pichargedensity" to "electrondensity", "totalchargedensity" to "chargedensity".
    • Removed aromatic restriction from Huckel E/Nu order calculations (forum topic).
  • logP plugin
    • The calculation algorithm has been improved using approximately 13,000 experimental logP values collected from the PhysProp database. Nevertheless, the original unique algorithm that makes possible to accurately predict novel compounds still provides the basis of the calculation.
• Chemical Terms:
  • Chemical Terms is available from Marvin in command line (Evaluator command line application) and API (until now it was available only in JChem).
  • It can also be used in JavaScripts (in applets). Examples for usage:
    • MarvinSketch Example - Calculating molecular properties on the fly
    • MarvinView Example - Molecular property calculations with Chemical Terms
  • New functions: abs(), fragmentCount(), ringSystemCount(), smallestRingSystemSize(), largestRingSystemSize(), ringCountOfSize(), ringSystemCountOfSize(), aliphaticRingCountOfSize(), aromaticRingCountOfSize(), minimalProjectionArea(), maximalProjectionArea(), minimalProjectionRadius(), maximalProjectionRadius(), genericTautomer(), mostStableTautomer(), markushEnumerationsDisplay(), randomMarkushEnumerationsDisplay().
  • New (optional) parameters are available for enumerations() and randomEnumerations() functions.
  • Functions available only in JChem: match(), matchCount(), disjointMatchCount(), dissimilarity().
  • AND, OR, NOT boolean operators in Chemical Terms (alternatives for &&, ||, ! operators).
  • Option to set output format in Evaluator command line application if result is molecule.
  • Evaluator command line application can list available Chemical Terms functions.
• API:
  • Both aromatization methods aromatize query atoms if they have double and single bonds in the ring.
  • Atoms belonging to the following atom groups can be recognized by the name of the group: alkali, alkaline earth, other metal, transition metal, lanthanides, actinides, metalloids, halogens.
  • Calculator Plugins:
    • New calculations in TopologyAnalyser and TopologyAnalyserPlugin (see the list of calculations above).
    • New calculations in GeometryPlugin (see the list of calculations above).
    • New calculations and options in TautomerizationPlugin (see the list of calculations and options above).
    • New calculations and options in MarkushEnumerationPlugin (see the list of calculations and options above).
    • New and renamed calculations in HuckelAnalysisPlugin (see the list of calculations above).
  • Molecule file format recognizers are called in the priority order defined by the recogn argument of the MFileFormat constructor. Deprecated Recognizer.getPriority(), use MFileFormat.getPriority(subformat) instead.
  • MoleculeIteratior interface moved to chemaxon.util.iterator.
• Documentation:
  • Updated developer's guide and examples.

Bugfixes

• MarvinSketch:
  • Atom > Stereo > R/S menu was missing.
  • MarvinSketch always dropped confirmation dialog when exiting in OLE mode (forum topic).
  • In MarvinSketch, scale factor was loading in an improper time.
  • Zooming after atom font changing shouldn't delete the set atom font.
  • Atom font changes from Format dialog disappeared when scrolling.
  • Automatic mapping of long chain substituents was incorrect (forum topic).
• MarvinView:
  • UTF-16 character encoding was incorrect in cell headers of MarvinView.
• Applet:
  • Marvin applets did nothing by OLE copy (forum topic).
• Molecule representation:
  • Wedge bonds were displayed incorrectly after adding explicit H atoms to chiral centers (forum topic).
  • Implicitization of explicit hydrogens was sometimes incorrect.
  • Clean2d placed wedge on symmetric atoms.
  • Planar ligands in 3D returned 0 instead of EITHER in parity.
  • There was a minor bug in the valence check algorithm (forum topic).
  • MRV export of the molecule in reaction editor threw NullPointerException.
  • A valence error was given to pyridine oxide drawn with aromatic bonds (forum topic).
  • The head of the reaction arrow disappeared after 2D or 3D clean.
  • The reaction arrow overlapped a reactant upon hit coloring of reactions.
  • Atom coloring didn't work after subsequent molecule loads.
  • ArrayIndexOutOfBoundsException was thrown when drag&dropping expanded S-groups from the canvas to MyTemplates.
  • The reaction arrow was duplicated after 2D clean.
  • Replacing atom in S-group with Asp caused ArrayIndexOutOfBoundsException.
  • In SMILES format, double bond lost cis/trans info after aromatization.
  • M, MH, X, XH are not aromatic query atom.
• Import/export:
  • Double bond stereo information was sometimes lost during SMILES import (if a double bond was between two stereo double bonds).
• Clean 3D:
  • There were errors in gradient calculation. The fix also improves the optimization performance for some deformed initial structures.
  • Possibly corrupted stereochemical requirements caused a bug when invoked directly from the sketcher.
  • Using chirality when invoked from the sketcher sometimes failed. (forum topic)
  • Hyperfine produced unpredictable results. Now MD parameters are modified (lower initial temperature) and very strict optimization limit is used. (forum topic)
  • Energies calculated by the building process and the dreidingenergy plugin were slightly different (forum topic).
  • Optimization limit error message fixed (forum topic).
• Calculator Plugins:
  • An exception was thrown during enumeration of structures with multicenter S-group.
  • Random Markush enumeration generated larger link node enumerates than in definition
  • Random enumeration hasn't thrown exception in case of invalid input structures (R-group in the variable part of multiposition bond).
  • NullPointerException was thrown in some cases of random enumeration when molecule contained possible valence error. Now a more informative RuntimeException is thrown.
  • Random Markush enumeration has returned null for non-generic structures instead of the structure itself.
  • DotForumla functions of Elemental Analyser threw exceptions on empty molecules.

July 28th, 2008: Marvin 5.0.7

New features and Improvements

• Applet:
  • Introducing new parameters (maxscale, detach) to control the maximum magnification of exported images and applet canvas (forum topic).
• API:
  • Calculator Plugins: New methods in pKaPlugin: getMacropKaValues(int, double[], int[]) and getMacropKaValues(int) (forum topic).

Bugfixes

• Molecule representation:
  • ArrayIndexOutOfBoundsException when drag and dropping expanded S-groups from the canvas to MyTemplates.

June 30th, 2008: Marvin 5.0.6

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.

June 20th, 2008: Marvin 5.0.5

New features and Improvements

• MarvinSketch GUI:
  • Default file location can be set in the Save/Load tab of Edit > Preferences.
• Licenses:
  • Environment variables and Java system property is introduced for license install (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).

May 24th, 2008: Marvin 5.0.4

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.

April 21st, 2008: Marvin 5.0.3

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.

March 20th, 2008: Marvin 5.0.2.1

• MarvinView:
  • Bugfix: Reading compressed mol files from applet parameter was wrong
• Applet:
  • Bugfix: Error by the initalization of the recent file list (forum topic)

March 18th, 2008: Marvin 5.0.2

• MarvinSketch:
  • Position variation bond. It is available under the Structure > Add menu.
  • Extended font support: Texts (atom labels and text box content) can be formatted using any font that is available in the operating system.
  • Global IME support in Textboxes (allows entering East Asian characters).
  • Recent file list added to file menu.
• MarvinView:
  • Recent file list added to file menu.
  • "Print All" and "Save As" options are enabled in "File" menu, and they work properly
• MarvinSpace:
  • Displaying coordinate system (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. PDB import does better recognize connectivity and bond order of hetero components.
• Bugfixes:
  • Atom > Stereo > R/S menu was missing in MarvinSketch GUI
  • Marvin applets did nothing by OLE copy (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.
  • Superfluous hydrogen atoms were assigned during PDB import (forum topic).
  • 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.

February 18, 2008: Marvin 5.0.1

• 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)

January 9th, 2008: Marvin 5.0

• 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:
    • Metadata for file formats handled by Marvin is represented by class MFileFormat. File formats can be found using MFileFormatUtil.findFormats. User defined formats can be registered with registerFormat.
    • Metadata for import or export options is represented by class OptionDescriptor. Export options for a given format can be retrieved using MolExportModule.getOptionDescriptors.
    • Record reading. MRecordReader implementations can be used to parse records without creating Molecule objects. An MRecordReader can be created using MFileFormat.createRecordReader or MFileFormatUtil.createRecordReader.
    • Only narrow ends of wedge bonds are considered in 2D representation of the molecules, following IUPAC recommendations. To convert your existing 2D molecules created with the both-end interpretation to the new convention, use the ConvertWedgeInterpretation Standardizer action.
    Related incompatibilities:
    • MolImportIface and MDocumentImportIface interfaces are replaced by the abstract class MolImportModule. Record skipping related methods removed (isSkippingSupported, skipMol and skipToNext), use MRecordReader.skipRecord or MRecordImporter.skipRecord instead.
    • MolExportModule: the open method throws MolExportException, loadMarvinModule removed and replaced by MFileFormatUtil.createExportModule, getOptionSign removed. Both MolExportModule and MolExportException moved to chemaxon.marvin.io, the old versions in chemaxon.marvin.util are deprecated.
    • The canonical encoding name is returned by MFileFormatUtil.getEncodingFromOptions and stored by MolExportModule.setEncoding, MolConverter.createMolConverter and the constructors of MolImporter, MolExporter and MolConverter. These methods and constructors may throw IllegalCharsetNameException or UnsupportedCharsetException.
    • Import/export modules (not recommended to use directly!) moved from chemaxon.marvin.modules to chemaxon.marvin.io.formats and its subpackages.
• Calculator Plugins:
  • Multiprocessor support in cxcalc
  • Tautomerization:
    • New tautomer generation rules were implemented
    • Estimation of the tautomer distribution as function of pH was improved
  • pKa, logP: Accuracy of the predictions were improved.
  • Added EnumerationPlugin: enumerates Markush structures
  • ElementalAnalyserPlugin:
    • "Dot-disconnected isotope formula" calculation added
    • "D" and "T" symbols can be used for "Deuterium" and "Tritium" in isotope formulas
  • pKaPlugin: "Take major tautomeric form" option added
  • logPPlugin: "Take major tautomeric form" option added
  • logDPlugin: "Consider tautomerization" option added
  • New surface area calculations in MSAPlugin:
    • Water accessible surface area (ASA)
    • Water accessible surface area of all atoms with positive partial charge (ASA+)
    • Water accessible surface area of all atoms with negative partial charge (ASA-)
    • Water accessible surface area of all hydrophobic atoms (ASA_H)
    • Water accessible surface area of all polar atoms (ASA_P)
  • GUI: "Restore defaults" button added to options panel
  • Integration of user-developed calculations made easier (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:
    • MBracket class, supports parentheses, square brackets and chevrons.
    • New MTextBox attributes "halign" and "valign" for aligning the text, see setHorizontalAlignment and setVerticalAlignment.
    • Incompatible change: java.awt.Graphics2D is used as the first argument of MObject.paint() and its implementations.
  • GUI:
    • Invoking Paste action from API: MarvinPane.doPaste()
    • Removed MarvinPane.addSaveImageMenu and MViewPane.makeSaveImageMenu because the menu of multiple image formats is replaced by only one "Save Image(s)" menu item. It can be added to a custom "File" menu using MarvinPane.getCommonActions().getSaveImageAction().addTo(menu).
  • Applet Parameters:
    • New: listenpropertychange.
    • Deprecated: preload, background.
  • Incompatibilities:
    • MProp. convertToString(String) became a final method calling the abstract convertToString(String, int) with 0 second argument.
    • fuse(CGraph graph) and fuse0(CGraph graph) have been made final. Subclasses should implement fuse(CGraph graph, boolean check) and fuse0(CGraph graph, boolean check) instead.

December 11, 2007: Marvin 4.1.14

• API:
  • MDocument.simplifyMolecule()
• 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.

September 18, 2007: Marvin 4.1.13

• API:
  • Background color settings for MolPrinter: MolPrinter.setBackgroundColor(java.awt.Color). (forum topic)
• 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.

August 17, 2007: Marvin 4.1.12

• 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.

July 23, 2007: Marvin 4.1.11

• GUI:
  • Text box improvement: its highlighting color is lighter than other highlighting colors because dark colors obscured the text for short strings.
• API:
  • Clear undo queue: MSketchPane.clearHistory().
  • New property to set default save format: defaultSaveFormat
• Bugfixes:
  • IUPAC Naming: fixed timeout errors.
  • Fixing bug "Phosphorus loses chirality after explicit-H-removal"
• Calculator plugins:
  • Added dominant tautomer distribution calculation to Tautomeriztion plugin
    • cxcalc: dominanttautomerdistribution calculation
    • Related changes in TautomerizationPlugin API
  • Maximum allowed lenght of the tautomerization path can be set in Tautomeriztion plugin
    • See options of the tautomers calculation in cxcalc
    • New method in TautomerizationPlugin API: setMaximumTautomerizationPathLength(int)

July 6, 2007: Marvin 4.1.10

• Bugfix in displaying of pKa calculation results in command line (cxcalc).

June 26, 2007: Marvin 4.1.9

• GUI:
  • Remove small blue corners in MarvinView (except in tables).
  • Hide dashed line in bond forming electron flow arrows.
  • Fixing undo and copying error in reactions.
• API:
  • New image export option to display atom numbers.
  • New PropertyChangeEvent to indicate when selection changes.
  • New method in the MolPrinter class to set display options.
  • In the chemaxon.marvin.util.MolExportModule class, the optionSign2 field is replaced by getOptionSign() method.
• IUPAC name generation improvements, in particular for ions.
• Bugfixes:
  • Fixing arrow initialization problem in RxnMolecule clean.
  • In PDB export, the -c option did not work properly.
  • Empty field parsing bugfix in Smiles import.

May 17, 2007: Marvin 4.1.8

• Import/export:
  • Image export option ("noatsym") to hide atom symbols in 3D mode.
  • SUBSTRUCTURE section is also generated in mol2
  • Bugfix in MRV import: absolute stereo flag could not be set.
  • Fix superatom S-group export bug in MRV export.
• GUI:
  • Fix NullPointerException by displaying MViewPane with menubar.
  • Graphical reaction arrows.
  • Bugfix in arrow drawing.
• API:
  chemaxon.marvin.util.MPainterUtil is deprecated, use chemaxon.marvin.MolPrinter
• Bugfixes:
  • LP chirality fix
  • Bugfix in CleanUtil
  • Minor bugfixes in calculation plugins

April 13, 2007: Marvin 4.1.7

• 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

March 14, 2007: Marvin 4.1.6

• Import/Export:
  • RDfile properties can be hierarchized or flattened.
  • Data sgroup improvements in MRV import/export.
  • Bugfix in MRV export.
  • Bugfixes in MolImporter.
  • Bugfixes in Peptide import.
  • Bad EOL (End Of Line) characters in the output of the InChi export was fixed.
• GUI:
  • Double-clicking at selection unselects selected atoms.
  • Bugfix in printing: Texts components covered each others on the printed view table.
  • Removed unnecessary confirmation dialog by closing viewer detached sketch frame.
  • Deleting problem of multiple is solved.
  • Corrected the wrong location of plus sign in reactions.
• API:
  • MarvinPane.setEnabled(boolean) is implemented.
  • MViewPane.setDraggable(boolean) allows or denies drag operation in cells.
  • New property change event in MarvinView: selectedIndex
  • Molecule.draw is deprecated, use chemaxon.marvin.util.MPainterUtil instead of that.
  • New MarvinSketch applet parameter: buttonmenubar
  • Text Box improvements
• Bugfixes:
  • Bugfixes 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).

January 9, 2007: Marvin 4.1.5

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.

December 7, 2006: Marvin 4.1.4

• GUI:
  • Fix endless loop by rings join.
  • Exception in custom amino acid loading is fixed.
• API:
  • MarvinView drops events by opening/closing detached sketcher/viewer.
  • New methods: ConformerPlugin.getEnergy(), ConformerPlugin.getEnergy(int).
• Plugins:
  • Bugfix in MSA calculation.
  • Acceptor count and donor count is displayed on the plugin result window.
  • Bugfix in Major Microspecies calculation.
  • Minor bugfixes in pKa calculation.
  • Improved canonical tautomer generation.
• Fixing broken peptide snake.
• Bugfix in peptide import/export
• Fixing minor bugs in clean 3D
• Minor bugfix in Parity

November 17, 2006: Marvin 4.1.3

• API:
  • implicitizeHydrogens(int) is final. Subclasses should implement implicitizeHydrogens(int, MolAtom[]) instead.
• Plugins:
  • New option added to conformer plugin to set the conformer diversity limit. API: setDiversity(double)
  • New option added to pKa plugin to handle the acid/base state depending on the submitted micro state. API: setpKaPrefix(int), getpKaValues(int, int)
• MarvinSpace
  • Available in MarvinView as an optional 3D structure viewer.
  • Enhanced secondary structure visualization
  • Charmm pdb file support for both structures and crystals
  • Charmm Slab visualization

October 16, 2006: Marvin 4.1.2

• 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

September 8, 2006: Marvin 4.1.1

• 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

August 4, 2006: Marvin 4.1

• Import/Export:
  • EMF export
  • Preliminary Mol2 import/export
  • Image export: atom and bond set colors, wire thickness, stick thickness ball radius, daylight down wedge, anybond style and atom mapping visibility can be specified.
  • Molecule and document properties with special data types (not only strings) are exported and imported in MRV, SDfiles and RDfiles. Supported data types: boolean, int, double, int[], Molecule, MDocument.
  • molconvert: optionally skips molecule on error and continues with the next molecule (option -g) (default: as before, exits on error).
• R-groups:
  • the maximum R-group number is increased to 32767 (from 32), the minimum is decreased to 0 (from 1). R0-R32767 are saved in MRV and V3 Molfiles. In V2 Molfiles, only R1-R999 are saved. The values of following constants are changed: MolAtom.RGROUP_MAX=32767, RgMolecule.RG_ID_MASK, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH.
  • RgMolecule.indexOf(CNode), indexOf(CEdge), getNode(int) and getEdge(int) are applied to the graph union instead of the root structure.
• GUI:
  • Integration of MarvinSketch and MarvinSpace:
  • 3 Dimensional structure building: allows to modify ligand in the binding pocket.
  • Visualization of plugin results: 3D structure display, colored molecular surfaces.
  • Save options in viewer.
  • Viewer handles huge SD files.
  • Journal based drawing style templates
  • Multipage molecular documents
• Plugins:
  • Plugins are grouped
  • Added OrbitalElectronegativityPlugin to Charge group
  • Added StereoisomerPlugin to Isomers group
  • Added ConformerPlugin and MolecularDynamicsPlugin to Conformation group
  • Added GeometryPlugin and MSAPlugin (3D molecular surface area calculation - methods: van der Waals, solvent accessible) to Geometry group
  • Improved calculation methods in several plugins (pKa, logP, logD, etc.)
  • Possibility to save multimolecular plugin results from GUI (e.g. conformers)
• License handling: added graphical license handler interface
  • press the 'Manage license keys' button on the Edit / Preferences / Licenses tab, in MarvinSketch or MarvinView, or else
  • use the license command line script
• MarvinSpace 1.3
  • Ribbon representation of protein secondary structure
  • Interactive editing of molecules/ligands in MarvinSketch
  • Copy/Cut/Paste, Drag&Drop functions
  • High resolution image export in various formats (PNG, BMP, Targa, JPG), arbitrary size
  • New coloring types: secondary structure, rainbow, b-factor (temperature factor), SETOR residue colors, color palettes
  • Interactive change of the isovalue of Gaussian Cube surfaces
  • Enhanced selection tools: binding pocket, residues etc.
  • Enhanced labels (colors, size, placement), more built in types (e.g. residue labels, secondary structure label)
  • Improved error handling, out of memory does not terminate
  • Progress bar, better feedback about processes
• API changes:
  • Added Molecule.cloneMoleculeWithDocument(): clones the molecule with its non-molecular data (graphics objects: polylines, arrows; electron flows; text boxes).
  • Added Molecule.arrangeComponents(): avoids overlapping components (reaction components, R-group definitions) by translations.
  • Added MolImporter.skipRecord(), nextDoc(), getRecordCount(), getRecordCountMax(), estimateNumRecords(), seekRecord(int), isRewindable().
  • Sgroup.setGUIStateRecursively returns true if the state was changed.
  • CGraph became abstract, MoleculeGraph(parent) and Molecule(parent) constructors removed to avoid confusion with copy constructors.
  • The implementation of seeking in MolImporter required the extension of the molecule/document import interfaces:
    MolImportIface.isSkippingSupported(), skipMol() and MDocumentImportIface.getGlobalProperties() must be implemented.
  • The implementation of the sticky midpoints of MPolylines required incompatible changes in the graphics classes:
    MPoint.getX(), getY(), getZ(), setLocation(DPoint3) and setXYZ(double, double, double) are replaced by getLocation(CTransform3D) and setLocation(DPoint3, CTransform3D), MObject.calcCenter(DPoint3), transform(CTransform3D, int) and getPointRef(int) are replaced by by calcCenter(DPoint3, CTransform3D), transform(CTransform3D, int, CTransform3D) and getPointRef(int, CTransform3D).
• Applet/bean parameter changes:
  • Toolbar templates are not handled together with the other templates appearing in their own window. Toolbar template sets can be specified using the new ttmpls parameter, the old tmpls parameter is used only for other template sets.
• Deprecation:
  • bondWidth property/applet parameter is replaced by bondSpacing
  • RxnMolecule.getStructureCount, getStructure, addStructure, removeStructure methods are replaced by getComponentCount, getComponent, addComponent and removeComponent.
• AWT applets have been removed from Marvin Applets package.
• .NET support in Marvin Beans.
• Bugfixes:
  • Molecule.calcHybridization() assigns HS_S to hydrogen atoms.
  • Fixed potential memory leaks in Marvin applets.

May 25, 2006: Marvin 4.0.6

• Bugfixes:
  • In aromatization.
  • In ionizer.
  • In Marvin Beans installer.
  • NullPointerException at refreshing empty cells in view table

March 24, 2006: Marvin 4.0.5

• 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.

January 23, 2006: Marvin 4.0.4

• 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().

November 10, 2005: Marvin 4.0.3

• Bugfixes:
  • Minor bugfixes in MarvinSpace
  • In mol file export

November 4, 2005: Marvin 4.0.2

• Import/Export:
  • IUPAC InChi
  • MDL Molfiles, RGfiles etc.: Implicit H is stored as attached data when needed.
  • Improved PDB import.
  • Hydrogenize bug fixed: tetrahedral geometry of alcohol Oxygen atom is now maintained.
  • Volumetric data import/export for CUBE files (not processed by Marvin)
• Implemented trivalent doublet and quartet. (RAD3_DOUBLET, RAD3_QUARTET)
• Applets:
  • New methods: MSketch.getSelectedMol, MSketch.getMolMass, MSketch.getMolExactMass, MSketch.getMolFormula, MView.getMolMass, MView.getMolExactMass, MView.getMolFormula, JMSketch.getMolMass, JMSketch.getMolExactMass, JMSketch.getMolFormula, JMView.getMolMass, JMView.getMolExactMass, JMView.getMolFormula
  • New sketcher parameter: undetachByX.
• MarvinSpace beta, includes public API:
  • Dynamic loading of JOGL libraries.
  • Better handling of PDB files including not standard complient variants.
  • Save graphic scene as PNG image file.
  • Basic Gaussian Cube file support.
  • Improved User Interface.
  • Bugfixes.
• Plugin:
  • New parameter in ResonancePlugin: take major contributors (-m, --mcontrib).
  • New parameter in TautomerizationPlugin: take dominant tautomers (--d, --dominants).
  • Bugfix in TautomerizationPlugin.
• Sgroup names can contain almost any ascii character.
• Bugfixes:
  • Hydrogenize bug fixed: tetrahedral geometry of alcohol O is now maintained.
  • Minor bugfixes in aromatization, in 2D cleaning and in molconverter.

August 19, 2005: Marvin 4.0.1

• Trivalent radicals are displayed and their MRV import is fixed.
• Bugfixes in cxsmiles, in 2D cleaning and in parity calculation.

August 8, 2005: Marvin 4.0

• 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:
    • Dynamical loading of plugins and parameter panels based on configuration by PluginFactory
    • Separated graphical plugin result display: CalculatorPluginDisplay
    • Graphical parameter panels are generated from XML: <plugin class name>Parameters.xml if exists, otherwise asked from the display class: CalculatorPluginDisplay.getParameterPanel()
    • Configuration files calc.properties (Calculator) and plugins.properties (MarvinSketch, MarvinView) together with the parameter panel configuration XMLs and custom plugin JARs are placed in the xjars directory under Marvin root.
    • CalculatorOutput used by Calculator is renamed: CalculatorPluginOutput (and subclasses are found automatically by the following naming convention: output class name = <plugin class name>Output)
    • CalculatorPlugin API is slightly changed.
    • A custom plugin example with test application is added.
  • Added MRV result molecule output to cxcalc.
  • Added options JPEG / PNG image save and copy & paste image to chart result display in MarvinSketch / MarvinView.
  • Changes in specific plugin calculations:
    • Added IsoelectricPointPlugin.
    • Added TautomerizationPlugin and ResonancePlugin.
    • Added microspecies distribution calculation (msdistr) to cxcalc.
    • New topological properties in TopologyAnalyser and TopologyAnalyserPlugin:
      asymmetricAtomCount(), balabanIndex(), carboRingCount(), carboaromaticRingCount(), cyclomaticNumber(), distanceCount(int atom, int distance), distanceDegree(int atom), eccentricity(int atom), hararyIndex(), hyperWienerIndex(), isAsymmetricAtom(), isConnected(), isConnected(int atom1, int atom2), plattIndex(), randicIndex(), shortestPath(int atom1, int atom2), stericEffectIndex(), szegedIndex(), wienerIndex(), wienerPolarity().
• API
  • PeriodicSystem: new radius functions getAtomicRadius(int z), getCovalentRadius(int z), getVanDerWaalsRadius(int z).
  • MSketchPane: new methods isCloseEnabled(), setCloseEnabled(boolean), getMrvWithSettings(), setMrvWithSettings(String), getImage(scale), getImage(size), getBoundRectSize().
  • MoleculeGraph.getLocalParity(int) to calculate local parity of an atom
  • Incompatible API changes:
    • MarvinPane.setAtomSymbolsVisible(boolean) applies to 3D molecules only; atom symbols are always visible in 2D.
    • MolAtom.getAtomSymbol(opts, aflags, lcenter, transform) uses SYM_* constant flags in its first argument instead of magic numbers.

July 27, 2005: Marvin 3.5.9

• Improved aromatization
• Svg export gives UTF-8 encoded output.
• Bugfixes:
  • In CmlImport
  • In 3D cleaning
  • In dearomatization

June 29, 2005: Marvin 3.5.8

• Bugfixes:
  • In plugin calculations.
  • In parity.
  • In 3D cleaning.
  • In displaying of implicit hydrogens

May 28, 2005: Marvin 3.5.7

• Minor bugfixes in plugin calculations.

May 17, 2005: Marvin 3.5.6

• 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.

March 29, 2005: Marvin 3.5.5

• 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.

January 31, 2005: Marvin 3.5.4

• 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.

January 24, 2005: Marvin 3.5.3

• Bugfix: Import of SMILES containing atoms with "unspecified atomic number" (*) is fixed.

January 11, 2005: Marvin 3.5.2

• 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

November 29, 2004: Marvin 3.5.1

• Extended SMILES export: d option to write C/T info for ring double bonds.
• API:
  • New methods: JMView.isEmpty(), MView.isEmpty, JMSketch.isEmpty(), JMSketch.getAtomCount(), JMSketch.isAtomSelected, MSketch.isEmpty(), MSketch.getAtomCount, MSketch.isAtomSelected().

November 5, 2004: Marvin 3.5

• Plugins:
  • TopologyAnalyserPlugin is available: calculates molecule properties from topology like number of various ring types, rotatable bonds.
  • Calculation of molecular polarizability is available in PolarizabilityPlugin.
  • Improved pKa and logP predictions.Test Results
  • Added calculation of aromatic system and aromatic ring total charges in ChargePlugin.
• Import/export:
  • Link nodes are imported and exported in MDL molfiles and MRV/CML. See also the related API changes.
  • MDL Molfiles:
    • Usg import option to ungroup all S-groups.
    • Atom coordinates are not rescaled in 2D V2 molfiles if the b import/export option is used with 0 argument.
    • MdlCompressor can compress Rxnfiles.
  • SMARTS import: d option for Daylight-conform meaning of "H". Importing ambiguous SMARTS gets a warning message when not using this option.
  • MRV (Marvin Document) and CML:
    • reaction arrow type is stored (default, resonance, retrosynthetic or equilibrium), see also the API changes.
    • valence is imported and exported
  • Image export:
    • Options for displaying chiral structures.
    • Automatic generation of atom coordinates for 0D molecules.
• API:
  • New methods and functions:
    • MolAtom methods related to link nodes: getMaxRepetitions(), setMaxRepetitions(int), getMinRepetitions(), setMinRepetitions(int), isLinkNode().
    • RxnMolecule methods for accessing reaction arrow type: getReactionArrowType(), getReactionArrowTypeName(), setReactionArrowType(int), setReactionArrowType(String).
    • MSketch, JMSketch, MView and JMView applet methods
      • for accessing molecule properties: getMolProperty(String), setMolProperty(String, String), getMolPropertyCount(), getMolPropertyKey(int), getMProperty(int, String), setMProperty(int, String, String), getMPropertyCount(int), getMPropertyKey(int, int),
      • for accessing extra atom label and alias strings: setAtomAlias(int, String), getAtomAlias(int), setAtomExtraLabel(), getAtomExtraLabel(int), setAtomAlias(int, int, String), getAtomAlias(int, int), setAtomExtraLabel(int, int, String), getAtomExtraLabel(int, int).
    • Added JavaScript functions in marvin.js to get JVM and GUI ("awt" or "swing"): marvin_get_jvm() and marvin_get_gui().
  • Changes:
    • Valence is not a query property any more, use MolAtom.setValenceProp(v) and getValenceProp() instead of setQProp("v", v) and getQPropAsInt("v").
    • The simpView applet parameter and MSketchPane.setSimpView(int) are deprecated, the simpView = 2 setting is removed. Use bondDraggedAlong and MSketchPane.setBondDraggedAlong(boolean) instead.
    • Serialization: DPoint3 and CTransform3D became Externalizable.

August 16, 2004: Marvin 3.4.3

• New applet parameter: molChanged0 to evaluate a JavaScript code when the molecule is loaded.
• Bugfixes: NullPointerException in shapely color mode, deadlock in MarvinSketch applet.

August 5, 2004: Marvin 3.4.2

• Bugfixes: memory leak and deadlock in sketcher bean.

July 29, 2004: Marvin 3.4.1

• Reaction AutoMapper class API is available.
• Calculator Plugin API usage examples in class headers.
• Atom symbol/label font can be changed using the atomFont applet parameter.

July 1, 2004: Marvin 3.4

• 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.

March 9, 2004: Marvin 3.3.3

• 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 pK_a, 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.

February 4, 2004: Marvin 3.3.2

• Bugfixes: in SMILES import.

January 29, 2004: Marvin 3.3.1

• Mac OS X: MarvinSketch and MarvinView applications use the screen menu bar.
• Bugfix in the drawing of R-group attachment points.

January 14, 2004: Marvin 3.3

• 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.
  • pK_a calculation have been extended to carbon-bases. Now basic pK_a estimation of Indole derivatives available. Both acidic and basic pK_a values are displayed. Microspecies distribution is shown on chart.
  • Accuracy of pK_a calculations is improved for heterocyclic compounds.
  • Calculation of polar surface area (PSA) based on 2D topological (TPSA) information of molecules are available.
• Others:
  • Recognition of more than four hundred chemical abbreviations.
  • Help documents can be specified by applet parameters: sketchHelp, sketchQuickHelp, viewHelp, viewQuickHelp.
  • Molecule.draw paints the molecule to a graphics context.
  • Standard residue names returned by MolAtom.residueSymbolOf(int) are not all upper case, only the first letter ("Ala" instead of "ALA").
  • Marvin GUI: Set the visibility of the atom chirality (R/S) labels from View/Misc menu.
  • Double click in Windows operating systems opens chemical files with the MarvinView application.
  • Deprecation: SketchMolecule (replaced by MDocument), SuperAtom.updateSgroupCrossings() (replaced by Sgroup.findCrossingBonds())
  • Incompatible change: chemaxon.struc.sgroup.Contractable interface removed, Expandable changed. This change was required because MDL's incomplete multiple group expansion had to be simulated for proper molfile export.
• Bugfixes: in MViewPanel.setParams, in Dreiding forcefield, PDB import, atom lists in V3 molfiles, resize of MViewPanel and MSketchPanel, R-logic, etc.

July 28, 2003: Marvin 3.2

• Enhanced stereochemical representation support in extended molfiles.
• Improved Charge and pKa calculation.
• Bugfixes:
  • In SMILES q option.
  • In flip.

June 30, 2003: Marvin 3.1.4

• 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.

June 2, 2003: Marvin 3.1.3

• 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.

May 6, 2003: Marvin 3.1.2

• MDL import/export improvements:
  • Extended reaction file import/export ("rxn:V3").
  • Rgroups are supported in extended molfile import/export.
  • RDfiles: Molecule and reaction type properties ($MFMT and $RFMT) are also imported and exported. Use the Molecule.getPropertyObject function to get such properties.
• S-groups: automatic contraction after import in sketcher and viewer.
• API changes:
  • MoleculeGraph.calcCenter returns the geometrical center instead of the center of mass.
• Bugfixes: R-logic bug.

April 30, 2003: Marvin 3.1.1

• JRE bug workaround (inappropriate lines were drawn on the Marvin panel).

April 29, 2003: Marvin 3.1

• 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:
    • Data fields can be imported from multi-column files.
    • Better error checking at import: exception is thrown if a ring is formed from two neighboring atoms.
  • PDB: residues are imported as Sgroups, Sgroups are exported as residues.
  • Molfiles:
    • Sgroups are also imported as (PDB) residues. As a consequence, the PDB-specific coloring styles, "shapely" and "group", are also applicable to molfiles containing Sgroups.
    • Extended (V3) molfile export.
    • Changes in V2 format:
      • 3D molecule coordinates are stored in Angstrom units. The unit can be specified as an import option.
      • Illegal atom map values (from molfiles generated by the IDBS ChemXtra data cartridge) are not considered to be error at import.
• API changes
  • New RgMolecule method: RgMolecule.addRgroupsTo.
  • New flag RxnMolecule.RGROUPED for the getStructure(flags, f) method.
  • New methods related to explicit Hydrogen removal: MoleculeGraph.calcDehydrogenizedGrinv, implicitizeHydrogens, MolAtom.isImplicitizableH.
  • The protected removeNode(..., boolean changeNodes) and removeEdge(..., boolean changeNodes) methods in CGraph, MoleculeGraph, Molecule, etc. are replaced by removeNode(int i, int cleanupFlags), removeNode(CNode node, int cleanupFlags), removeEdge(int i, int cleanupFlags), removeEdge(CEdge edge, int cleanupFlags).
  • Removed the malfunctioning RxnMolecule(parent) and RgMolecule(parent) constructors.

March 21, 2003: Marvin 3.0.2

• Bugfixes: contracted S-groups are automatically expanded before exporting in molecule file formats (PDB, SMILES, XYZ, ...)

March 17, 2003: Marvin 3.0.1

• 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.

February 10, 2003: Marvin 3.0

• 3D cleaning.
• New applet paremeters and bean properties
  • detachable paremeter in the viewer.
  • atomSymbolsVisible parameter instead of labels which became deprecated.
• API improvements and simplifications:
  • chemaxon.struc:
    • CGraph and Molecule are not thread safe any more but their methods became 20-30% faster.
    • Created the SelectionMolecule class for molecule selections, removed the CGraph.selection field.
    • Created the MoleculeGraph class as the direct ancestor of SelectionMolecule and Molecule.
    • RgMolecule and RxnMolecule changes:
      • Nodes and edges are only stored in subgraphs (root structure, R-groups, product/reactant/agent structures).
      • The graph union is returned by the MoleculeGraph.getGraphUnion() method.
      • Methods like getNodeCount(), getEdgeCount(), getNode(i), getEdge(i) call the root structure's corresponding method in RgMolecule or the graph union's method in RxnMolecule.
    • CGraph.findFrags() and CGraph.findFrags(boolean) are replaced by CGraph.findFrags(Class) and Molecule.findFrags()
    • CGraph.cloneNodes() and cloneEdges() renamed to getNodeVector, getEdgeVector.
    • CGraph.reallyContains(CEdge) and countRealEdges() removed.
    • CGraph.getSSSR() returns an int[][] array instead of CEdge[][]
    • The MolAtom.flags, MolAtom.countFlags and MolBond.flags fields became private.
  • Molecule import/export:
    • MolExportModule.convert(Molecule) and close() throw MolExportException instead of IOException.
    • MolImporter.read() and importMol(byte[]) returns RgMolecule object only if R-groups are present.
  • Initialization file saving:
    • MarvinSketch and MarvinView has a common initialization file in the $HOME/.chemaxon subdirectory.
    • MarvinPane.saveIni(), loadIni(), getIniFile() and setIniFile() are removed and replaced by UserSettings.save(String), UserSettings.tryToLoad(), and DotfileUtil.setDotDirName(String).
  • Other bean related changes
    • Buttons and checkboxes in molecule cells can fire java.awt.event.ActionEvents and java.awt.event.ItemEvents as javax.swing.AbstractButton objects.
    • MViewPane.getCanvasComponent is deprecated. Use MViewPane.getVisibleCellComponent.
• Template button title is specified using the abbreviation SDF property instead of title.
• Bugfix: in Rxnfile import

September 13, 2002: Marvin 2.10.5

• 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.

August 12, 2002: Marvin 2.10.4

• 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).

August 2, 2002: Marvin 2.10.3

• grinv is a new applet/bean parameter and property.
• Bugfix: in SDfile import.

July 26, 2002: Marvin 2.10.2

• Bugfixes:
  • Improved printing layout of MView tables.
  • Improvements in Copy / Paste of reactions.
  • Fixed calculation of molecule bounds.

July 19, 2002: Marvin 2.10.1

• Molweight calculation.
• Handling agents of reactions.
• Bugfix: MolConvert.convert() cleans imported SMILES.

July 5, 2002: Marvin 2.10 (2.9.13)

• 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.

April 23, 2002: Marvin 2.9.12

• Import/Export
  • CML import and better export.
  • Atom map support for Rxnfiles and reaction SMILES.
  • Atom label font size and double bond width can be set for image export using the atsiz and bondw options.
  • If an error occurs while reading a multi-molecule file (an SDfile for example), the remaining parts of the current molecule can be skipped and the file pointer can be positioned to the next one.
    • MolImportIface interface changed, the skipToNext() method introduced
    • MolImporter.skipToNext()
• Stereochemistry
  • chiralitySupport applet/bean parameter
  • ezVisible applet/bean parameter
• Other new applet/bean parameters and properties
  • popupMenusEnabled bean property
  • atomNumbersVisible applet/bean parameter
• Other API changes
  • The MolAtom.SELECTED and VALENCE_ERROR constants are not public any more, they are replaced by the isSelected, setSelected, hasValenceError and setValenceError methods.
  • deprecated methods removed: MolAtom.getAbbrev() and abbrevOf() replaced by getSymbol() and symbolOf()
  • CNode.copy(CNode), MolAtom.copy(CNode) does not copy the edges, CNode.clone() became abstract, MolAtom.clone() does not clone the edges.
• Fixed: memory leak and printing problems with Java Plugin, atom lists in molfile, bugs during reaction drawing, MarvinView stdin reading, etc.

February 18, 2002: Marvin 2.9.11

• SMARTS improvements: "a" (aromatic) and "A" (aliphatic) atom primitives recognized even outside of brackets, ":" (aromatic bond) symbol recognized at file format recognition.
• New importConv option (c) to automatically clean up the molecule.
• Image export improvements
  • scale option
  • getImageSize method
• bondWidth applet parameter and setBondWidth bean method.
• API changes
  • Molecule.toFormat, toBinFormat, toObject, MolExportModule.open and MolExportModule.parseOption throw IllegalArgumentException instead of IOException if bad format string was specified
  • "mag" property renamed to "scale", setMag, getMag, maxMag methods became deprecated (MSketchPane, MSketch, JMSketch, MolPrinter) and replaced by setScale, getScale, maxScale
• Fixed: delayed printing, image export option parsing, cml:A, etc.

January 29, 2002: Marvin 2.9.10

• 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:
  • Scalable Vector Graphics (svg) format.
  • Implicit Hydrogen display options can be specified for the MolConverter utility and the toObject and toBinFormat methods.
• MViewPane.applyRotationMatrix, applyRotationMatrixes: methods to apply the viewing transformation on the atomic coordinates appearing in the molfile

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 cell
  • getBestTabScale(i) to query the best magnification value for a cell
  • getBestTabScale() to query the smallest best scale value
• MViewPane bean only:
  • autoTabScale property enables automatic uniform scaling of cells.

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

• Rxnfile, RDfile and Reaction SMILES import/export
• Molecule.getComment() and setComment() methods
• New MarvinSketch applet parameter and bean methods: reactionSupport, getReactionSupport(), setReactionSupport().
• MolExportModule API changed: the open method has a return value

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, msketch or mview.
• MSketchPane: setMol(File, String) method added, where string can contain the import options, in one of the following forms: "format:options", "format:", "options". The old setMol(File) method removed. MViewPane: setM(int, File, String) added.
• MolExportModule.sbuf field renamed to stringBuffer.
• MolAtom.getAbbrev() and abbrevOf are deprecated, use getSymbol() and symbolOf() instead.

June 12, 2001: Marvin 2.8

• New 3D rendering mode: sticks.
• Display quality can be controlled with an applet parameter.
• Molecule import/export:
  • New XYZ import options: bond length cut-off (f...) and maximum number of connections (C4,H1,Cl1)
  • Automatic dearomatization after molecule loading.
  • All export modules recognize the "a", "+a" (aromatize) and "-a" (dearomatize) options. Example: "smiles:a"
• Class library, beans
  • Molecule.aromatize()
  • Bugfix: MViewPane.getCellCount() returns the total number of cells, not just the number of visible cells.
  • PropertyChangeEvents generated when the molecule is changed in the sketcher or viewer component.
  • Event handling fix: PropertyChangeEvent source is the the bean component, not the internal SketchPanel or ViewPanel.

May 17, 2001: Marvin 2.7.11

• New rendering style: "ball & stick".
• Class library, beans:
  • New image export options: rendering style and color scheme.
  • Image export options must be separated by commas in format descriptor strings.
  • Molecule.toBinFormat method to convert molecules into binary formats such as JPEG/PNG/PPM.
  • The type of the rendering, colorScheme, implicitH, downWedge, navmode properties in PropertyChange events is String just like the argument type of their set methods. (Previously, the two types did not match.)

May 4, 2001: Marvin 2.7.9

• Binary export formats: GZIP, JPEG, PNG, PPM
• User defined export module creation by overriding chemaxon/marvin/util/MolExportModule.

April 1, 2001: Marvin 2.7.6

• Text field (T) component for MView tables.
• cacheMols applet parameter for caching loaded molecules.
• loadMols applet parameter for preloading molecules.
• Molecule.getProperty(key) is not case sensitive.

March 27, 2001: Marvin 2.7.5:

Optional spin vector.

March 14, 2001: Marvin 2.7

• File formats
  • New: XYZ import
  • New: Extended Molfile (V3.0) import.
  • CML export options changed, cml:1 -> cml, cml:0 -> cml:A, cml:A writes three coordinates for each atom even if the molecule is 2D (so Jmol can read the file)
• MView applet:
  • Animated XYZ files can be displayed
  • New parameters: animFPS, animDelay, animSync.
• MarvinSketch Applet/Bean:
  • New: File/New menu item in the bean. If your application using the bean has a File/New Window menu item, then File/New should be moved to File/New/Clear current, and File/New Window should be moved to File/New/New Window. See the MarvinSketch application source (marvinbeans/examples/sketch/chemaxon/marvin/Sketch.java) for details.
  • "Visual fragment placement" can be disabled: use the simpView parameter or the View/Misc/Object in Hand option if you do not like to see what you are doing.
  • Bond length related changes.
• Class library:
  • Changes related to atomic coordinates and transformations
    • New: CTransform3D class for general 3D transformations (like in Java3D)
    • Molecule.rot(...), tra(...), magnify(...) removed, use transform(CTransform3D T) instead
    • Atom coordinates became absolute
    • Molecule.getO() and setO() replaced by getLocation() and setLocation()
    • Molecule.getCenter() renamed to calcCenter(), and it calculates center of mass instead of geometrical center
    • New:Molecule.moveTo(location)
  • CGraph.indexOf changes
    • Splitted into two methods, indexOf(CNode atom) and indexOf(CEdge bond)
    • Speed improvement. CNode and CEdge has an index field that contains the object's index in its parent graph. Calling the parent graph's indexOf method returns the value of this field. The index is only searched (in the old way) when the CGraph is not the direct parent.
  • Valence rules
    • New: MolAtom.ionChargeOf(Z)
    • MolAtom.negoxOf(Z, boolean) removed, negOxOf(Z), posOxOf(Z) created instead
  • SDF properties
    • "name" and "informat" are no longer stored in the properties hashtable, they became fields of Molecule
    • Molecule.getProperties() removed
    • Molecule.clearForImport() -> clearForImport(name)
    • New methods in Molecule: getName, setName, getInputFormat, setInputFormat, getPropertyCount(), getPropertyKey(n), getPropertyKeys()
  • Bond length related changes.
• API simplification: internal bond length of Marvin fixed to be MolBond.CCLENGTH
  • bondlen, rescaling applet/bean parameters, setBondlen, getBondlen, setRescaling, getRescaling methods removed, use MSketch.getMol("mol:b=XXX") instead of <param NAME="bondlen" VALUE="XXX">
  • The bondlen argument of Molecule.clean(dim, bondlen, opts) removed, use clean(dim, opts)
  • MolBond.DEFAULT_LENGTH renamed to MolBond.CCLENGTH
  • MolBond.getDesiredLengthRatio() removed, use the new dimension dependent Molecule.getDesiredLength(bond) method instead
  • MolAtom.covalentRadiusOf(Z) -> covalentRadiusOf(Z, bondOrder)

December 10, 2000: Marvin 2.6

• The "style" applet parameter renamed to " rendering because of a conflict with a Netscape keyword. The getStyle, setStyle methods of the beans are also renamed to getRendering, setRendering.
• New rendering style: "Wireframe with Knobs".
• Atoms can be highlighted in the MView/JMView applets by specifying a selection.
• All query atoms and extra bond types can be enabled by omitting the queryAtoms, atomStrings, and extraBonds parameters.
• "Cis or Unspecified" and "Trans or Unspecified" bond types; "ctu" in extraBonds.
• Cleaning options can be specified using the cleanOpts applet parameter.
• Optional down wedge bond orientation (MDL or Daylight) using the downWedge parameter.
• New MView/JMView applet methods:
  • getAtomCount(moleculeIndex) to query the number of atoms in a molecule cell
  • isSelected(moleculeIndex, atomIndex) to query whether the specified atom is selected or not
  • selectAtom(moleculeIndex, atomIndex, select) to (un)select an atom
  • selectAllAtoms(moleculeIndex, select) to (un)select all atoms
• Real scrolling in MView!
  • The applet is scrollable if visibleRows is less than rows or visibleCols is less than cols.
  • The names of the layouti and parami parameters changed to layout and param for the molecule cells, layoutH and paramH for the optional header.
  • The scroll parameter ceased to exist.
• Class library:
  • RgMolecule for R-groups
  • Thread safe API for molecules
  • New methods in CGraph: getCtab(), getBtab(), fragments(), findFrag(), getFragIds(), getLock(), getParent(), etc.
  • New methods in CNode: getLigand(i), getEdge(i), getEdgeCount()
  • CNode.findFrag() and CGraph.fuseFrag() removed
  • CGraph.getEdge(i), CGraph.getNode(i), Molecule.getAtomArray() created; CGraph.getEdges(), CGraph.getNodes(), Molecule.getAtoms(), Molecule.getBonds() removed
  • Molecule.reuseAtom(Z, i) and Molecule.endReuse(na) created, MolAtom.reuse(Z, mol, i) removed
  • The two-argument MolAtom.setCharge method removed. Instead of a.setCharge(charge, false), use a.setCharge(charge); a.setFlags(0, MolAtom.FIX_CHARGE);

July 31, 2000: Marvin 2.5

• SMILES import
• Class library:
  • CGraph.fuseFrag(CNode a) has only one argument.
  • CGraph.removeNode and removeEdge instead of remove and removeRef; removeEdge leaves edge.node1 and edge.node2 unchanged (they were set to null in removeRef).
  • MolBond.setFlags(int flags, int mask) method introduced.
  • Stereochemistry: double bonds can also be UP/DOWN (not just CIS/TRANS); CIS and TRANS information can also be stored (not just EITHER). The MolBond.getStereo and setStereo methods and the UP, DOWN, EITHER constants ceased to exists, the STEREO1_UP, STEREO1_DOWN, STEREO1_EITHER, STEREO2_CIS, STEREO2_TRANS, STEREO2_EITHER, STEREO_CARE flags introduced instead.
  • MolBond.getTopology/setTopology ceased to exist, the TOPOLOGY_RING, TOPOLOGY_CHAIN flags introduced instead.

June 21, 2000: Marvin 2.4.2

• Scrolling in the MView and JMView applets. See the visibleRows parameter.

May 22, 2000: Marvin 2.4

• Structures are colorful by default. Colorization can be disabled by setting colors=mono, both in the sketcher and the viewer.
• Spacefill rendering can be enabled instead of wireframe by using the style parameter.
• Atom labels can be hidden with the labels parameter.
• Up/down and cis/trans either bonds
• Classes in chemaxon/beans moved to chemaxon/marvin/beans. The MarvinSketch bean is chemaxon.marvin.beans.MSketchPane, the MarvinView bean is chemaxon.marvin.beans.MViewPane.

March 20, 2000: Marvin 2.3.1

The basic applet tag for MSketch and MView is simplified, and also generalized to work with or without Sun's Java Plugin.

March 4, 2000: Marvin 2.3

• New file format: PDB (for simple, non-macro molecules)
• Changes in template handling
  • The four template sets that come with Marvin became default. Templates only have to be specified as applet parameter if you need a different template set.
  • Templates moved to directory chemaxon/marvin/templates/ (from templates/).
  • File extension changed to .t (from .cssdf).
    This change was required because of a Netscape restriction related to the loading of JAR file resources.
  • The JAR files marvin.jar and jmarvin.jar contain chemaxon/marvin/templates/generic.t, so the firewall problem ceased for the generic template set.
    If needed, the additional templates may also be put into the JARs by the user with the JAR utility (part of Sun's JDK). However, doing this increases the JAR size with a noticable amount.
• The MolImport module moved into marvin.jar because of the firewall problem.

January 15, 2000: Marvin 2.2

1. New query bond types: "single or double", "single or aromatic", "double or aromatic", "chain" and "ring".
2. SMARTS export handles the heteroatom (Q in molfile) type intelligently.
3. The heteroatom and the any atom types are specified in the queryAtoms parameter. The anyatom parameter became deprecated but is still present for backward compatibility, with slightly changed behaviour. Specifying anyatom with any value (empty string also) is equivalent to specifying "any,hetero" in queryAtoms.
4. Cell selection in MarvinView can be controlled using the selectable parameter.
5. New methods in MarvinSketch: getBondlen. getMag, getPiece, getRescaling. New method in MarvinView: setSelectedIndex, The setDispopts method ceased to exist. Display options can be set using the dispopts applet parameter only.
6. In Marvin 2.2 and later, the Java classes come only in packaged forms: marvin.jar and marvin.zip. It means that support is ceased for those archaic Java-compatible browsers that cannot handle the ARCHIVE option in the applet tag (Netscape 2 and MS Explorer 3). Reasons:
   1. Under certain circumstances, some Netscape versions try to load the class files one by one instead of using marvin.jar. The simplest way to keep Netscape from doing so is to remove the class files.
   2. Most of our users don't understand what ARCHIVE is, and don't use it properly. The consequence is a significantly increased download time.
      From now, a missing ARCHIVE option cannot be left unnoticed, because Marvin will simply not run. Much better than turning your user's hair gray.
   3. Marvin is rarely tested in the oldest (and buggiest) browsers.

   If you are absolutely sure that you want your Marvin page work with Netscape 2 and MS Explorer 3 too, you must unpack marvin.zip manually. However, we do not recommend this, because you will probably do something wrong. For example, once you will upgrade Marvin and forget to unpack the new marvin.zip. Mixing two different versions will result in malfunction.

October 4, 1999: Marvin 2.1.5:

Molecules in MarvinView are only editable if the editable applet parameter is set.

September 14, 1999: Marvin 2.1.1

• getCellCount() method in MarvinView.
• The anchor parameter in the layout also sets label alignment.

September 2, 1999: Marvin 2.1

1. CML (XML) export.
2. The getSelectedIndex() method in MarvinView.
3. Default value of the rescaling parameter in MarvinSketch is changed to "mag" because generally this value is the most useful.
4. The MarvinView-only package ceased to exist, the new Edit/Structure function made it irrelevant.

July 20, 1999: Marvin 2.0

1. Templates in MarvinSketch: From now on templates are stored in SDfiles (.sdf) or compressed SDfiles (.cssdf). The template file can be optionally compressed with GZIP, but the applet will only work in Java 1.1 compatible browsers in that case. The tmplmol, tmplpar, and ntmpls parameters no longer exist and are replaced by the much more easy to use tmpls parameters. The unit rotation angle can be specified as a new Marvin-specific property M MRV PHI in the template molecule files (instead of the tmplpar parameters).
2. Applet tags changed: Rewrite your applet tags according to the last solution in MarvinSketch Example 1. This applet tag can load the AWT and the Swing applets as well.
   Note that the file &{marvinjar}; is not packaged now (its name caused too many problems), so you must rewrite your applet tags, otherwise the download time with MS Explorer will not be optimal.
3. New in MarvinSketch: The menubar parameter enables or disables the menu bar in the Swing sketcher.
4. New in MarvinView: Molecules start rotating in 3D automatically if you set the animate parameter in MarvinView.
5. New in MarvinView: Border between cells in molecule tables.
6. Change in MarvinView: From now the colors can be specified in the same way as in MarvinSketch. Molecule background is molbg, normal table background is bgcolor. (Previously, bgcolor was also the molecule background.)
7. JavaScripter applet ceased to exist.
   Its functionality is moved into a MarvinView module that is automatically loaded at the first js: action.
   

   In the past, JavaScripter was required because scripting applets are not cached by older browsers (namely Netscape 3). An applet that has the MAYSCRIPT attribute is loaded from the net for each page that contains it. In Netscape 4 and later, there is no such problem. On the other hand, a bug (or feature?) in Netscape 4.6 makes the use of JavaScripter impossible as a separate applet. That's why we merged the two applets now.

8. New: Three new molecule file formats: "sybyl" (the SybylImport and SybylExport modules), "xyz" (XyzExport), and "pov" (PovExport).
9. New and changed: The "implicitH" option in the dispopts applet parameter instead of the showH parameter which ceased to exist.
   • "off" -> "implicitH=off"
   • "term" -> "implicitH=heteroterm" (because "term" ceased to exist)
   • "hetero" -> "implicitH=hetero"
   • "heteroterm" -> "implicitH=heteroterm" (default)
   • "all" -> "implicitH=all"
   New features: if you want the explicit H atoms to be invisible, use "explicitH=off" (default: "all").
   If you have 3D molecules, use "dim=3" for MarvinView, to let him know that you want 3D rotation as the default mouse drag action.

January 4, 1999: Marvin 1.3

1. New: The atomStrings parameter enables the usage of atom aliases and SMARTS strings in the sketcher.
2. Incompatible change: The setAtoms, setNoatoms, setNobonds methods, and the atoms, noatoms, nobonds applet parameters ceased to exist and replaced by elements, anyatom, queryAtoms, and extraBonds.
3. New: The new detach parameter makes it possible to detach the sketcher from the web page immediately when the applet is loaded.
4. Recommended: In molfiles and compressed molfiles written directly in HTML, you should end all the molfile lines with backslash and also a real newline character like here:

   ...
   000Wun+V70\
   iuzV000W60\
   iuzVGS2W60\
   K72WGS2W60\
   ...
   	

   Omitting the real newlines like in "000Wun+V70\iuzV000W60\iuzVGS2W60\K72WGS2W60\", seemed to be safe so far, while the Marvin applets were tested only in Sun, 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.
5. Removed: Backward compatibility with the old style (1.0-1.1) usage of getMol() and getM() removed. It didn't work with MSIE anyway.

November 29, 1998: Marvin 1.2

1. Incompatible change: MSketch.getMol(x) and MView.getM(n,x).

   In Marvin 1.1.4 and before, x was a boolean variable specifying the format of the generated molfile: MDL mol (false) or compressed mol (true).

   From version 1.2, x is a format descriptor string to ease the introduction of new molecule file formats as Marvin evolves. MDL molfile format is denoted by the string "mol", compressed mol is "csmol", SMILES is "smiles".

2. New: The preload applet parameter.

   "Extra features" are planned to be available as external modules in future releases of Marvin. External modules are downloaded only when needed. In Marvin 1.2.3, MDL mol, compressed mol and SMILES export are external modules.

   The problem is that older browsers such as Netscape 3, cannot load the external modules when the module is needed by a public method which is called from JavaScript. So if you want your web page containing Marvin to work perfectly with earlier releases of Netscape than 4, then you should preload all the modules which may be needed by JavaScript calls.

   For example, if you are using MSketch.getMol("smiles") on your page, then you should also have the following applet parameter:
   <param NAME="preload" VALUE="SmilesExport">.