Bugfixes

• Import/Export

  • MOL, SDF, RXN, RDF

    • Valid MOL file header was not recognized and therefore the file was not imported. Forum topic

Bugfixes

• Import/Export

  • Name to Structure (n2s)

    • Names with ylium and uide suffixes are now supported.

• Calculations

  • NMR (HNMR, CNMR Prediction, ...)

    • Coupling of a nucleus with a group of magnetically equivalent nuclei was not handled properly.

    • NMR Predictor did not consider negative coupling constant values.

Bugfixes

• Molecule Representation

  • Conversion from explicit hydrogen to implicit one removed stereo centers not having explicit hydrogen ligand. Forum topic

• Import/Export

  • SMILES/SMARTS

    • Non ring bond information were imported as query strings from SMARTS.

    • After SMARTS import, those atoms that had no explicit aromatic property but had aromatic bond got query aromaticity property.

New features and improvements

• Import/Export

  • CDX/CDXML

    • S orbitals and oval shaped s or p orbitals are imported from CDX/CDXML. Forum topic

Bugfixes

• Painting

  • Charge symbol on carbon atoms was missing when the atom numbers were visible and the display of carbon atom labels was turned off.

  • When two atoms had more than one electron flow arrows between them, the electron flow arrows overlapped each other.

  • The second electron flow arrow started from a wrong position when a single electron and an electron pair flow arrow started from an atom which had a lone pair and a radical as well.

• Editing

  • Atom Lists and NOT Lists could not be created by typing atomic symbols separated with commas (e.g., "f,br,cl" or "!f,br,cl").

• Import/Export

  • MRV/CML

    • MRV and CML export wrote out characters incorrectly which are not supported by the character set.

  • MOL, SDF, RXN, RDF

    • SDF files having invalid header could not been imported.

    • Deuterium and tritium isotopes were converted to simple hydrogen atom if a molecule was exported to ChemAxon compressed MOL format (CSMOL).

  • SMILES/SMARTS

    • MolExporter.exportToObject() added an extra newline to SMILES.

    • Nitrogens connecting two aromatic rings had radical after import if nitrogen was bracketed in the SMILES representation. Forum topic

  • InChi/InChiKey

    • Absolute stereo flag was missing during InChi export/import and InChiKey export. Forum topic

• Molecule Representation

  • Valence check

    • Number of added implicit Hydrogen atoms were incorrect in some cases for positively charged sulfur atom.

• Calculations

  • Isomers (Tautomers, Stereoisomers)

    • After canonical tautomer generation, the information of "double cis or trans" bond type might have been lost in certain cases. Forum topic

New features and improvements

• MarvinSketch GUI

  • Typing abbreviated group names is now case sensitive. Documentation

• MarvinSketch Dialog

  • "Cancel" button has been added to the "Customize" dialog.

• Painting

  • The font size and type of circled charge symbols can be modified on the "Display" tab of the "Preferences" dialog. Documentation

  • Position variation bond has been recolored for better visibility in a projected presentation.

• Clipboard handling

  • When pasting unrecognized format onto the canvas, "Import as" dialog appears, and the user can choose the correct format.

  • Structures can be copied as "Daylight SMARTS" and "ChemAxon SMARTS (CXSMARTS)" formats. Documentation

• MarvinView GUI

  • Double-clicking on a molecule in MarvinView to open it in a separate window does not result in the disappearance of the original molecule from MarvinView while the separate window is open.

  • The original molecule does not disappear from MarvinView while it is edited in MarvinSketch.

• Applet

  • New applet parameter for specifying the URL of a name recognition and import service: namingWebServiceURL

• Import/Export

  • SKC

    • SKC import has been improved.

  • CDX/CDXML

    • Mapping of reaction agents can be imported.

  • Name to Structure (n2s)

    • Initial support for Chinese IUPAC and common names has been added, e.g., 2-??-4-????.

    • Names with extra closing brackets can be converted when OCR error correction mode is enabled.

    • Name to structure now also works when bridge and spiro numberings are represented by using unicode superscript numbers, such as: tetracyclo[12.4.0.0^2,6.0^7,12]octadecane.

    • Custom webservice to extend name to structure conversion - for instance using corporate IDs (e.g., ABC0001234) or common name dictionaries in addition to the default one - is supported. Documentation

    • Automatically fix and import spiro names where the superscript formatting has been lost, for instance, after copy-pasting. As an example, trispiro[2.2.2.29.26.23]pentadecane will be imported as if from the correct form, trispiro[2.2.2.2⁹.2⁶.2³]pentadecane.

    • Name to structure now works on names of bridged ring compounds where the superscript formatting of ring numbering is not present.

    • The custom dictionary can be encoded in UTF-8 - even if the system default encoding is not UTF-8 - providing a byte order mark (BOM) for the file. This can be used, for instance, to support dictionary in multiple languages on Windows OS.

  • Document to Structure (d2s)

    • Invalid hexadecimal character entities (e.g., "&#xblah") are now ignored instead of making the document processing fail.

    • Image to structure conversion using OSRA is working on Mac OS X.

    • Text OCR for scanned documents is now supported on Mac OS X.

    • Documents compressed in xml.bz2 and xml.xz formats can be processed directly.

    • The memory usage has been reduced when processing documents with several thousand hits. This improvement is in addition to the memory improvements already present in version 5.11.

    • Option "+/-groups" has been added to enable (+) or disable (-) the conversion of groups and fragments, such as "ethyl", "nitro", "phenoxy", etc.

    • OCR of scanned PDF documents has been improved on Windows OS thus reaching the same performance level as that of OCR on Mac OS X and Linux OSs.

  • Structure to Name(s2n)

    • The speed of batch conversion using a timeout (which is enabled by default) has been increased by about 15%; the earlier instability in case of timeout relying on the deprecated Thread.stop method has been avoided.

• Molecule Representation

  • The size of the Molecule object has been decreased.

• Data Transfer

  • OLE

    • New settings are available for both administrators and end-users (from the "Edit > Preferences > MarvinOLE" menu) to preset the displayed OLE document in a maximized child window.

    • MRV files are read and validated by DOM (document object model) in Marvin OLE.

• Clean 3D

  • MMFF94 forcefield has been added to Generate3D. Use option "[mmff94]" to switch it on; use "molconvert -H3D" for detailed help.

• Calculations

  • Isomers (Tautomers, Stereoisomers)

    • Performance improvement: Tautomerization will not apply "Clean2D" if the output result has no 2D coordinates. Forum topic

    • Resonance structure is taken into account in dominant tautomer generation.

  • Conformation (Conformers, Molecular Dynamics, ...)

    • New MMFF94 forcefield implementation has been introduced in Conformer Plugin and Molecular Dynamics Plugin.

  • Services

    • Result structure of Marvin Services result panel can be copied to clipboard.

• Structure Checker

  • New checkers have been introduced:

    • Absolute Stereo Configuration

    • Chiral Flag

    • E/Z Double Bond

    • Multiple Stereocenter

    • Relative Stereo

    • Wiggly Bond

  • Fixer of checker "Query Atom": "Convert to Carbon" has been added.

  • Fixer of checker "Query Bond": "Convert to Single Bond" has been added.

  • Excluded list of abbreviated groups can be specified in "Abbreviated group" checker, i.e., checker will not find (and fix) abbreviated groups that are indicated in this list. Documentation

  • Structure Checker configuration can be accessed via URL from MarvinSketch, Structure Checker application, and via Structure Checker API call. Documentation

  • Integration of external structure checkers and fixers into ChemAxon products has become easier via MarvinSketch GUI. Documentation

  • In case of more than one fixer, a logical order of priority has been preset. The priority list of fixers can be found on page List of available checkers.

• API

  • New property change event to indicate when an editable MarvinView component is opened in MarvinSketch: sketchInView.

  • New property change event to indicate when a new MarvinSketch or MarvinView window is opened from the viewer: windowOpened.

  • New property change event to indicate when a MarvinSketch or MarvinView window, opened from the viewer, is being closed: windowClosed.

• Java Web Start

  • Name to Structure and Document to Structure are now available in the Java WebStart distribution of Marvin.

Bugfixes

• MarvinSketch did not deal with java property initialization bug. Forum topic

• MarvinSketch GUI

  • When a group abbreviation differed from an atomic symbol only in upper and lower case letters (e.g., NO and No), the abbreviated group could not be reached by typing.

• MarvinSketch Dialog

  • Focus did not appear on the "Source" and "Import Name" dialogs with Java 7.

• Painting

  • The charge was not displayed in circle on the bracket of an S-group when the "Show charge in circle" was set on the "Preferences" panel.

  • Charge label masked the adjacent bond in several cases.

• Editing

  • Deleting "extra" explicit hydrogens from an atom with valence error resulted in the appearance of erroneous implicit hydrogens on this atom.

  • When there were several disconnected structures on the canvas, partial clean was very slow.

  • It was possible to create a molecule with R-group definition containing a single attachment point (and no other atoms or bonds).

  • Sprouting did not work for Alias atoms.

  • The two ways of deleting implicit hydrogens (with eraser directly or selecting them first then deleting) behaved differently.

• Load/Save handling in UI

  • "File > Open" dialog froze when an mrv file contained a dashed arrow and the preview pane was checked.

  • When opening a multi molecule file and selecting a range that is open ended, a false error message appeared, which stated that there were too many molecules selected to open.

  • IUPAC name with alpha or beta signs could not be imported.

  • MarvinView did not open when importing a file from command line failed.

  • It was not possible to append a name to an existing .name file in MarvinSketch.

• Clipboard handling

  • It was not possible to drag a structure from MarvinView in "Translate or Drag" mode.

  • Ctrl + V shortcut for pasting structures did not work in MarvinView in case of "Spreadsheet" view.

• Graphical object handling

  • MBracket object "BRACES" did not render correctly when the orientation was set as "SINGLE".

• Applet

  • After reloading an applet from the lifecycle cache, the propertyChange method was called in the javascript side regardless of the listenPropertyChange parameter.

• Image I/O

  • The source was not saved from MarvinView in png, jpg, and svg formats.

• Import/Export

  • Option -g of molconvert ignored only MolFormatException.

  • MRV, CML

    • MRV import could not handle contracted Superatom S-groups having less atoms than crossing bonds.

    • MRV export used operating system specific line ending, '\n'.

    • CML import failed on files that contained non-ASCII characters.

  • MOL, SDF, RXN, RDF

    • Superatom S-group brackets were imported from MDL files.

  • CXSMILES/CXSMARTS

    • CXSMARTS I/O lost the charge from generic metal atom.

  • CDX/CDXML

    • Reaction agent not having reactant and product (e.g., >CC1=CC=CC=C1>) was read as reactant from CDXML files.

  • Name to Structure (n2s)

    • RS - as the marker of racemates - was not converted properly, for instance in (2RS)-1-(Adamantan-1-ylamino)-3-phenoxypropan-2-ol.

    • Lower CamelCase chemical names (such as 2-cyclopropylPiperazine) were not converted to chemical structures.

    • Common names, which are also non-chemical names, were recognized as chemical names during automatic format recognition, e.g., "Royal Blue".

    • E/Z bonds were sometimes set to the opposite value (in cases of non-trivial CIP rules).

    • For some rare inputs, which are not valid names, n2s created invalid structures that could be exported to mol format but could not be opened.

    • Both "phenylene" and "phen-1,3-ylene" were wrongly converted to benzene. Now all forms convert to the correct structure with two attachment points, including "m-phenylene", "1,3-phenylene", and "phen-1,3-ylene" (similarly for the o-, p-, 1,2-, and 1,4- forms).

  • Document to Structure (d2s)

    • Processing of multiple XML documents in concurrent threads was slow and sometimes skipped some hits.

    • Names separated by the "non-breaking space" character were not recognized.

    • Some names split by extra spaces were not found.

    • English names were not recognized in Japanese documents when the ideographic comma character followed them.

    • SMILES with aromatic atom after non-aromatic ones ("Cc1...") and with triple(#) or explicit single(-) bonds were not recognized.

    • Text OCR failed when the images in PDF were encoded in a certain variant of the CMYK color space.

  • Structure to Name(s2n)

    • Some characteristic group names were missing when expressed as a prefix of a sulfonyl group, for instance, in "propanamidosulfonyl".

    • Names could not be generated for structures containing "-[N+]≡" substituent. They are now named using the "azaniumylidyne" IUPAC name component.

  • Peptide

    • During automatic format recognition, non-latin characters were recognized as peptide sequences.

• Molecule Representation

  • S-groups

    • Multiple S-group expanded incorrectly when it had an embedded S-group.

  • S-groups/R-groups

    • S-group creation was not possible for a structure within an R-group definition of a reaction; a warning message was given.

• Clean 2D

  • Wedge clean moved non-ring wedge bond between two rings into a ring. Forum topic

• Calculations

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • Microspecies calculation of furan returned incorrect molecular formula at low pH.

  • Charge (Charge, Polarizability, ...)

    • Resonant charge calculation generated exception when the major form of the molecule is invoked with explicit hydrogen atoms.

  • NMR (HNMR, CNMR Prediction, ...)

    • Outdated HOSE database caused NullPointerException when predicting 1H NMR spectrum for some rare diastereotpic molecules.

  • Isomers (Tautomers, Stereoisomers)

    • D, T count in region labels of multifragment generic tautomers was computed incorrectly.

    • TautomerizationPlugin API did not clean the explicit hydrogens in the result molecule after tautomer generation which might have resulted in wrong stereo (R,S) specifiaction on chiral centers. Forum topic

  • Geometry (Topology Analysis, Geometry, ...)

    • The result of topological polar surface area (TPSA) plugin depended on the call order of setMolecule() and setpH() methods.

• cxcalc

  • Calculation "ringcountofatom" returned only the ring count of atom number zero. Forum topic

  • cxcalc returned irrelevant error message for calculations containing "ANY" bonds. Forum topic

  • Thole polarizablility (tpol) calculation didn't interrupt when clean3D failed.

• Backend / Core

  • Removing explicit hydrogens on some large PubChem compounds caused infinite loop. Forum topic

• Structure Checker

  • "Remove Stereo Care Box" was offered as fixer for results returned by "Query Bond Checker".

  • Fixer "Expand group" not only expanded but also ungrouped the abbreviated groups when using it via structurechecker command-line.

• API

  • The default value of parameters chargeWithCircle and lonePairsAsLine has been changed. The current default value of these parameters is "false". On the "Preferences" dialog, the "Restore default" button sets both parameters to "false", too.

Deprecation

• Structure Checker

  • Deprecated checker action strings: aromaticity, chiralflag, circularrgroup, missingrgroup, rare, reactionmap, unusedrgroup, valence, wedge.

  • Deprecated fixer action strings: clearabsstereo, aliastocarbon, crossedtowiggly, converttosingle.

  • Deprecated fixer class names: AbsentChiralFlagFixer, AbsoluteStereoFixer, CrossedDoubleBondFixer, CovalentCounterionFixer, ExplicitHydrogenFixer, IsotopeFixer, RgroupReferenceFixer, WigglyDoubleBondFixer.

Bugfixes

• Datatransfer

  • Structures copied from ChemDraw, Accelrys Draw, or Symyx Draw could not be pasted onto MarvinSketch.

New features and improvements

• Datatransfer

  • The imageImportServiceURL setting also affects the behavior of clipboard operations (drag and drop, paste).

Bugfixes

• Painting

  • Rounding error occurred in case of nearly 180 degree bond angle and it caused overflow error when resizing the structure.

• Import/Export

  • New export option, BOM, is introduced for non-binary chemical file formats in order to write out Byte Order Mark (BOM) if UTF-8 encoding is used.

  • Structure to Name (s2n)

    • Since 5.11.0, names generated for bridged cyclic structures with explicit bridge head hydrogen contained a spurious "hydrogenio" prefix.

• Clean 2D

  • Clean 2D got stuck in an infinite loop when fullerene-like molecules were cleaned.

• Calculations

  • Atom index issue might have occurred when molecule contained explicit hydrogen.

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • "averagemicrospeciescharge" calculation in cxcalc and "Isoelectric Point" calculation in MarvinSketch threw "ArrayIndexOutOfBoundsException" in the reported cases. Forum topic

  • NMR (HNMR, CNMR Prediction, ...)

    • The calculated chemical shifts of equivalent atoms were not consistent in case of compounds with symmetric ring systems. Forum topic

Bugfixes

• MView applet

  • Atom and Bond set coloring was not working properly when Marvin View Applet was called from JavaScript.

• Image I/O

  • When imageImportServiceURL startup option was not set for MarvinSketch, the same setting on the Preferences panel was lost. By default shortcuts and startup scripts do not specify this command line startup option.

• Java WebStart

  • chemaxon-core.jar, fontbox-1.7.1.jar and pdfbox1.7.1.jar were missing.

• Calculator Plugins

  • Tautomerization Plugin threw exception during generic tautomer generation if the input structure contained metal ions with valence error.

New features and improvements

• Image I/O

  • Recently added rendering options are now available to be set from MolPrinter API (Absolute label visibility, Peptide display type, R-group visibility, Any bond style, Lone pair rendering style, Charge rendering style). Documentation

• MarvinSketch GUI

  • A new "imageImportServiceURL=[URL]" program argument was added to the MarvinSketch application.

• MarvinSketch applet

  • A new "imageImportServiceURL" was added as an applet parameter.

• Graphical object handling

  • When an MMidPoint object was set as an end point for an MPolyLine, getting the MMidPoint location caused a StackOverFlowError.

• Import/Export

  • Document to Structure (d2s)

    • Names broken over two lines with a hyphen (-) are now recognized.

    • Names followed by a superscript text, for instance, a reference or footnote number (e.g., "aspirin¹¹") are now recognized.

  • Name to Structure (n2s)

    • In some cases, such as "4-methylthiophenylmethyl", there is an ambiguity whether "thiophenyl" refers to a compound derived from thiophene or thiophenol. Name to Structure now gives priority to the thiophenol related compound interpretation; though, "thiophenyl" by itself will still be supported as thiophene derivatives.

Bugfixes

• Painting

  • If R-group visibility was turned off and any of the bonds had label(s) to paint, an ArrayIndexOutOfBounds exception was thrown.

• Image I/O

  • Display parameters of charge, lone pair, peptide could not be set for molexporter. The default values were charge "in a circle", lone pair "as line", peptide "three letter format". Image copy also used these values.

• Import/Export

  • MOL, SDF, RXN, RDF

    • Aliphatic query properties of atoms with query string were not read from MDL formats.

    • After importing Extended MOL files that contain superatom S-groups the orientation of S-groups could be changed.

    • Atom containing both aliphatic and unsaturated query properties were exported incorrectly to MDL formats.

    • SDF import returned structure with incorrect S-group embedding.

  • SMILES/SMARTS

    • SMILES T* option did not export all SDF fields, but only those which appeared in the first molecule.

• Molecule Representation

  • S-groups

    • Two superatom S-groups being each others' parents caused infinite loop. In these cases, now java.lang.IllegalStateException is thrown.

  • Valence Check

    • Phosphorous atom in hexafluorophosphate was not accepted by Valence Check. Forum topic, Forum topic

• Stereochemistry

  • Cloning of BicyclostereoDescriptor in RxnMolecules threw java.lang.ArrayIndexOutOfBoundException.

• Clean 2D

  • Terminal methyl-group in phosphate-ester was cleaned incorrectly.

  • Clean2D could not handle condensed adamantane derivatives. Forum topic

• Calculations

  • Other (HBDA, Huckel Analysis, ...)

    • The --pH command line option did not work in hydrogen bond acceptor-donor calculation.

• Structure Checker

  • If fixer action was not defined, default fixer was not applied in structurechecker command line tool.

New features and improvements

• Import/Export

  • Document to Structure (d2s)

    • Startup time of document to structure has been significantly reduced. This is especially important when processing very short text documents, such as a single sentence or paragraph. The speedup in such cases can be up to 10 times faster.

Bugfixes

• Calculations

  • NMR (HNMR, CNMR Prediction, ...)

    • NMR Prediction did not use the mixed prediction algorithm, so NMR shift predictions were less accurate.

• Chemical Terms

  • The -g (ignore error) option of evaluate did not work when -x (extract) option was used. Forum topic

• Structure Checker

  • WedgeCleanFixer threw ArrayIndexOutOfBoundsException when the erroneous wedge bonds were located inside an S-group. Forum topic

New features and improvements

• MarvinSketch GUI

  • Molecule properties like SDF fields can be added/edited/deleted in MarvinSketch GUI.

  • Bond properties can be added/edited/deleted in MarvinSketch GUI.

  • Lone pair can be displayed as a line. The option can be set from the "Preferences" panel.

  • Charge can be displayed in a circle. The option can be set from the "Preferences" panel.

  • An aromatic benzene template has been added to the Generic templates.

• Data transfer

  • Clipboard handling

    • Java wrapper for CXNSharedAddin library has been introduced to handle tabular data transfer from/to Microsoft Office applications.

• Import/Export

  • CDX/CDXML

    • Graphical arrows "retrosynthetic" and "equilibrium" are imported from CDX and CDXML files.

  • Name to Structure (n2s)

    • Names, such as "methyl ether", are used either to denote a group (CH3-O-*) or the dimethyl ether compound (CH3-O-CH3), as well. The default behavior still is to generate the complete compound, but a new name option "expectGroup" has been added to get the group instead.

    • A name converter can now prevent a name from being converted (even by other lower-priority converters). See the API of the chemaxon.naming.NameConverter class.

  • Document to Structure (d2s)

    • Peptide 3 letter abbreviations are now recognized in documents, for instance ValGlySerAla or Val-Gly-Ser-Ala.

    • A new option has been added to control the maximum time allowed for processing a document: format option "d2s:timeout=60" to allow a maximum of 60 seconds. Default is 0 meaning infinite timeout.

    • A new option has been added to disable the extraction of OLE embedded structures from Office documents (option name: "d2s:-ole").

    • Structures imported from the custom name dictionary now have the "Type" property set to "custom" instead of "common".

    • Memory usage has been significantly reduced when processing large PDF documents (for instance hundreds of scanned pages).

    • Structure image conversion by OSRA has become faster, resulting in more structures converted when previously a timeout was reached.

    • CAS names (which typically include commas) are not converted by default by d2s anymore (they are still converted by n2s). The old behavior can be activated by using the "d2s:CASnames" format option.

    • The unwanted interpretation of some common words as chemical names, that are frequent especially in patents, has been avoided. For example, the 'amino' group when used in the phrase 'amino acid', or 'Ser' when it is not the abbreviation of Serine but 'Ser. No.' for 'serial number'.

  • Structure to Name(s2n)

    • Multiple name generation tasks can now be run in parallel at full speed to make use of multiple CPUs and cores.

    • Multiple name import tasks now run faster, as partial locking is no longer required and has been removed.

    • Generated names now use unicode characters when needed, for instance, 6λ⁴-thiadispiro[5.2.5⁹.2⁶]hexadecane instead of 6$l^{4}-thiadispiro[5.2.5^{9}.2^{6}]hexadecane. The pure ASCII output can be generated using the "name:ascii" format option.

  • Image I/O

    • New parameter imageImportServiceURL has been added to the image importer module. The URL can be set on the "Preferences" dialog or as an import option.

  • VMN import

    • VMNs of type "display" are now read.

    • VMN abbreviated group list has been extended: carbon chains up to 50 members have been added.

    • AV (abnormal valence) property is now stored in atom property and not set as atom valence. The VMN valence representation will be revised in a later version.

    • Deuterium and tritium count property is handled properly in VMN (added as D and T ligands for non-homology atoms). D and T are transposed during the import in comparison to the VMN, as this represents the correct information in the majority of the MMS database.

    • Correcting incorrect atom types in VMNs: C0 is transformed to CHK; C1 is transformed to C; homology groups in ring are transformed to XX

    • Attachment bond type is set to parent R-atom bond type if different.

    • VMN import option is available for switching off corrections: Documentation

• Molecule Representation

  • New option, MolAtom.BRIDGEATOM_H, is added to Hydrogenize.removeHAtoms(MoleculeGraph, int) method to remove hydrogens connected to bridgehead atoms.

  • Valence Check

    • Local valence check has been introduced, which calculates the valence by considering only the neighboring atoms. Although the new valence check is the default, the old one is also available. Documentation

  • S-groups

    • ElementalAnalizerPlugin calculates Polymer Formula for molecules containing SRU or RepeatingUnit S-groups.

• Calculations

  • Charge (Charge, Polarizability, ...)

    • Dipole Moment Calculation plugin: calculates the net molecular polarity. Documentation

  • NMR (CNMR Prediction, HNMR Prediction)

    • New, mixed HOSE code/CXN model has been introduced, which results in more accurate NMR shift prediction.

    • C-F and H-F couplings are considered during NMR shift calculation.

    • Diastereotopic protons are supported in HNMR Prediction.

    • The tautomers of the predicted molecule are accessible via the Options > Select Tautomers... option of the NMR GUI. The spectra of the selected tautomers with defined percent composition are added to the predicted spectrum. Documentation

  • Chemical Terms

    • "molString" and "molFormat" Chemical Terms functions are accessible under the name "molConvert" as well.

• Structure Checker

  • New Structure Checker GUI has been introduced. Besides the redesigned GUI, new features are also available:

    • Profile management;

    • Filters in Report view.

    Documentation

  • Structure Checker is going to be moved to the MarvinBeans package. Until it is done, the new Structure Checker GUI is available in both JChem and MarvinBeans packages as Structure Checker JChem and Structure Checker, respectively.

  • Substructure Checker feature is accessible only in Structure Checker JChem until the complete relocation of Structure Checker.

  • Improved R-group Attachment Error Checker detects R-group definitions having incorrect R-group attachment orders. Fixer is not available for this feature yet.

  • New Explicit Hydrogen Checker options are ready for use. Documentation

  • Checkers that are not recognized as internal or external checker are called: "Invalid Checkers". Invalid Checkers cannot be used in valid Structure Checker configurations; they need to be removed to perform proper working behavior.

• Build/Installation

  • Marvin Beans and JChem installers - for Linux - bundled with Java 1.6.0_33 have been introduced.

Bugfixes

• MarvinSketch GUI

  • The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.

  • Several mnemonics were duplicated or missing in the menu of MarvinSketch.

• Painting

  • Bond topology representation was not visible in R-groups.

• Dialogs

  • Periodic table view 'Blocks' showed Helium color coded as a part of 'p block' instead of the correct 's block'.

• Import/Export

  • Load/Save handling in UI

    • MarvinSketch did not overwrite the former PDF file when changes were made and it was saved as a PDF again with the same file name.

  • MRV, CML

    • The string value of a query property was imported as element.

  • MOL, SDF, RXN, RDF

    • Registry number of a molecule that is a property of an other molecule was not imported from RD file.

  • SMILES/SMARTS

    • Cis/Trans information was not exported for bonds being in two rings.

  • CXSMILES/CXSMARTS

    • Query pseudo atoms represented by CXSMARTS lost their valence property during import.

    • R-group definition of an Rg-molecule described in CXSMARTS was imported as CXSMILES.

  • CDX/CDXML

    • Reaction agent was not possible to read from CDXML file.

    • From CDXML file containing only a product of a reaction, the product was imported as reactant.

  • Name to Structure (n2s)

    • Names ending with "group", such as: "cyclohexyl group" were not imported.

    • Chirality specified without locant was sometimes not included in the generated structure, for instance in (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate.

  • Document to Structure (d2s)

    • Several names separated by a comma were sometimes wrongly recognized as a single name.

    • Document to structure was leaking some memory in a way that was problematic for extremely large documents (tens of thousands of structures in a single document).

    • When using the d2s API, waiting threads could be left behind when large documents were converted but the structures were not read until the end. This is now fixed, provided the client calls MolImporter.close().

    • Document to structure was not processing text from PDFs with non-standard fonts, for instance English text encoded in Japanese fonts.

    • Certain images in PDFs were not processed correctly by OSRA during optional image-to-structure conversion.

    • Names found in documents may have included unwanted trailing characters when the next word started with an open bracket, for instance, "cholesterol [28]" instead of "cholesterol".

  • Structure to Name(s2n)

    • The group "[NH3+]-" was given traditional name "aminio", instead of the correct "ammonio".

    • Names were generated for structures with link nodes, as if the link nodes had been absent.

    • Incorrect names were generated for structures with one attachment point.

• Molecule Representation

  • Meitnerium appeared at a wrong position in the periodic table of MarvinSketch.

  • Explicit hydrogen that connects to an atom having more than one wedge bond was not converted to implicit one.

  • S-groups

    • When an expanded SuperAtom-Sgroup was inside an other S-group, its attachment points had invalid implicit hydrogen count.

  • Stereochemistry

    • Stereoinformation were not recognized on cyclohexane-1,3,5-triol.

• Clean 2D

  • Calling clean 2D on a 3D molecule resulted in short bond length between a Hydrogen and an other atom

  • Clean 2D inserted wiggly bond into a Kekule form of a 0 dimensional aromatic molecule.

• Aromatization/Dearomatization

  • Basic aromatization method aromatized rings containing sulfur atom that have four ligands.

  • Basic aromatization method aromatized rings with -S= substructure.

• Calculations

  • Isomers (Tautomer, Stereoisomers)

    • Cross bond was not handled correctly by canonical tautomer generator.

• Structure Checker

  • Abbreviated Group checker options did not work as expected: checker recognized both expanded and contracted groups regardless of the selected option.

• Build/Installation

  • Desktop icons were missing from the Marvin Beans for Linux installer.

New features and improvements

• Applet

  Class reorganization for more efficient applet loading.

New features and improvements

• Import/Export

  • MDocSource implements Iterable<Molecule>. Documentation

  • MOL, SDF, RXN, RDF

    • New option for MDL MOL format import, Fsg, has been introduced to ungroup superatom s-groups with more than two attachment points. Documentation

Bugfixes

• Import/Export

  • MRV

    • The string value of the query property was imported as element.

New features and improvements

• MarvinView Printing

  • Resolution of PDF printing has been increased.

• Datatransfer

  • Legacy MRV '\n\ header (5.7) format is supported in Marvin OLE.

New features and improvements

• Import/Export

  • MOL, SDF, RXN, RDF

    • Coordination bond is written and read from extended MOL file.

  • Name to Structure (n2S)

    • More extensive support for conversion of CAS numbers to structures.

• Clean 2D

  • New clean option, Toff, is introduced to ignore template based cleaning. Documentation, Forum topic.

  • Coordinate bond length has been increased for a better view of its arrow representation between atom labels.

Bugfixes

• MarvinView

  • MarvinView did not display the SD file property if no property values were attributed to the first entries.

• Painting

  • The bond related label backgrounds hid the bond partially if the bond was almost parallel with the horizontal axis.

• Editing

  • Transfer button did not appear on the "Sketch new substituent..." popup window when the 'Insert>New Substituent' menu item was selected.

• Import/Export

  • Byte Order Mark (BOM) was not written out during the export.

  • Default line separator was not unique in MolExporter.

  • CDX/CDXML

    • Empty CDX and CDXML files could not been imported.

• Molecule Representation

  • S-groups

    • Contracted Superatom S-groups drawn to MarvinSketch and having only one crossing bond had no attachment point information.

  • Stereochemistry

    • Absolute chiral flag calculation terminated with "java.lang.OutOfMemoryException" for large, symmetric molecules, e.g., fullerene derivatives. Forum topic

• Calculations

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • Major microspecies calculation threw "ArrayIndexOutOfBoundsException" in the reported case. Forum topic

New features and improvements

• Import/Export

  • MOL, SDF, RXN, RDF

    • The template based coding of amino acids in MOL V3000 files are read as pseudo atoms. However, the template based structure of peptides cannot be read.

    • Method MolFileHandler.collectFileInfo() returns molecule and reaction identifiers $MFMT $MIREG, $MFMT $MEREG, $RFMT $RIREG, $RFMT $REREG, $MIREG, $MEREG, $RIREG, $REREG as well.

• Clean 2D

  • An option is introduced to set explicit C-H bond length to 1.0 instead of 1.54 in case of two dimensional cleaning. Documentation, Forum topic.

• Calculations

  • "Keep explicit hydrogens" option has been added to pKa plugin, Major Microspecies plugin, and Isoelectric Point plugin.

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • The speed of major microspecies calculation has been improved when "Take major tautomeric form" option is used.

  • NMR

    • The accuracy of the NMR predictor has been improved.

Bugfixes

• Painting

  • "Absolute" label was not visible when only contracted Sgroups contained stereo information and the "Absolute" stereo flag was set on the Molecule.

  • Joining two product structures of a reaction erased both structures. Forum topic

  • Joining aromatic rings drawn in Kekule form sometimes caused their aromatization.

• Editing

  • Atom labels could disappear when the structure was cleaned in 3D, rotated then cleaned in 2D.

• Import/Export

  • Byte Order Mark (BOM) was not written out during the export.

  • MRV/CML

    • Molconverter could not convert files containing multiple molecules to separate MRV/CML files.

    • Encoding could not been set during MRV and CML export.

  • MOL, SDF, RXN, RDF

    • Bond length of a molecule imported from MOL V3000 file was short, therefore the atoms overlapped.

    • RD file records written after an empty structure were not read correctly.

  • CDX

    • CDX files containing labels without chemical structures were not read. Now, these labels are read in text boxes.

  • SKC

    • SKC import put an R-group attachment point to Superatom S-groups.

    • Stereo information was lost at importing a peptide from an SKC file.

    • Wedge bond information of a contracted S-group was lost during the SKC import.

• Molecule Representation

  • Valence check

    • Valence check allowed any number of bonds on carbon atoms having implicit hydrogens.

  • R-groups

    • Method RgMolecule.fuse() resulted inconsistent molecule when it was invoked on RgMolecules having SuperAtom S-group in its definition.

  • Stereochemistry

    • Nitrogen being one of the fusion points of ring systems was detected as chiral when the carbon atom at the other fusion point had four explicit ligands.

• Aromatization/dearomatization

  • Dearomatization failed for porphyrin-like ring systems.

• Calculations

  • Charge (Charge, Polarizability, Orbital Electronegativity)

    • Charge calculation was not consistent on fragmented molecules.

  • Isomers (Tautomers, Stereoisomers)

    • Different rational canonical tautomers were generated for some molecules when they came from different sources (e.g., InChi and SMILES).

    • Tautomer distribution was not calculated for various porphyrin-like structures.

  • Geometry (Topology Analysis, Geometry, PSA, MSA)

    • Negative or zero Van der Waals and Solvent Accessible molecular surface area values were generated for molecules with inconsistent chemical structures.

• Structure Checker

  • Abbreviated group checker did not identify expanded and contracted groups correctly.

  • "substructre" action string did not work in command line.

New features and improvements

• MarvinSketch GUI

  • New graphical arrows: equilibrium arrow, curved arrow, dashed arrow, and crossed arrow has been introduced. Documentation, Forum topic

  • The built-in abbreviated groups can be easily extended and overridden with custom abbreviated group definitions. Documentation

  • New display option has been introduced: peptide sequence can be visualized in 1-letter form besides the original 3-letter form.

  • Cleaning preset is added to template sets. It can be controlled on the Template library dialog.

  • When opening an item of the Recent File list fails, the entry is deleted.

  • All query atoms and query properties are available from menu and toolbar by customization.

  • Names of homology groups on "Advanced" tab of "Periodic System Dialog" and in "Template Library" have been updated.

  • The elements of the Advanced tab on the Periodic System dialog are now available from MarvinSketch by typing as shortcuts.

  • The picture of custom defined template appears at the mouse tooltip when the name of the structure is unknown.

  • The name of reaction arrow: "Resonance" and graphical arrow "Two-Headed Arrow" have been changed. Forum topic

• MarvinSketch Printing

  • The page format settings on the print dialog is now stored and do not need to be reset when starting a printing job from MarvinSketch or MarvinView. Forum topic

• Import/Export

  • Load/Save handling in UI

    • Disconnected molecules can be saved separately in MarvinSketch. Documentation.

    • When saving a document opened by d2s in MView, MRV is offered as default format.

  • Structure to Name (s2n)

    • Extended and updated structure to common name dictionary.

    • L-amino acid structures are all converted to L- traditional name.

  • Name to Structure (n2s)

    • Improved conversion of systematic names, notably names expressed as amides of acids, such as "pyridine-4-carboxylic acid (2-methoxy-ethyl)-methyl-amide".

    • Extended and updated common name to structure dictionary.

    • All peptide abbreviations are now consistently converted to the L- stereo form structure.

    • Possibility to set custom name converter plugins for n2s and d2s (e.g., converting internal company compound IDs) specific to a single conversion in a thread-safe way has been introduced (see API of the new method: chemaxon.naming.NameConverters.addThreadLocal).

    • Fragments names such as phenyl can be converted with attachment points *C1=CC=CC=C1 |$_AP1|, using the "name:+rgroups" format option.

  • Document to Structure (d2s)

    • Document to Structure can be instructed to process only a subset of pages in a document using the new startPage and endPage format options.

    • The custom dictionary format option (dict=...) is available in Document to Structure.

    • Possibility to set custom name converter plugins for n2s and d2s (e.g., converting internal company compound IDs) specific to a single conversion in a thread-safe way has been introduced (see API of the new method: chemaxon.naming.NameConverters.addThreadLocal).

    • Acronyms such as BBC are not converted anymore (as BromoBenzyl Cyanide) since they most often have a non-chemical meaning. Conversion of acronyms can be enabled if desired by using the "d2s:+acronyms" format option.

    • Fragments names such as phenyl are converted with attachment points, such as *C1=CC=CC=C1 |$_AP1|.

  • DNA/RNA

    • DNA nucleic acid sequence can be imported in four ways: ACGT, A-C-G-T, dAdCdGdT or dA-dC-dG-dT. RNA nucleic acid import accepts sequences like both ACGU and A-C-G-U.

• Molecule Representation

  • Molecule/atom/bond properties

    • Similarly to MolAtom, general properties are possible to be added to MolBond.

    • New, simple way is provided to replace isotopes.data and elements.zip used in PeriodicSystem.java. Documentation.

  • S-groups

    • New method is introduced to set a data S-group to behave as relative after specifying its absolute position

  • R-groups

    • A new, fast method is available to delete one or more molecules from an R-group definition.

• Calculations

  • Isomers (tautomer., reson.)

    • Rational tautomer generation option has been introduced. Generation of All tautomers and Canonical tautomer can take this new option into consideration. Documentation

    • Improved generic tautomer generation in case of aromatic molecules.

  • NMR Predictor

    • NMR Predictor is available in MarvinSketch. It accurately predicts ¹³C and ¹H NMR spectra of standard organic molecules. See Product page and Documentation for more information.

  • Services

    • LocalService allows to set URL based JAR path.

• Structure Checker

  • New checker: Absent Chiral Flag checker; when the molecule is chiral and all stereo centers are precisely marked, absolute chiral flag can be applied to the molecule. Documentation

  • R-group Reference Error Checker is deprecated and has been split into three separate checkers:

    • Circular R-group Reference Checker;

    • Missing R-group Checker;

    • Unused R-group Checker.

  • Partial clean fixer is available for certain structure checkers: it can fix the erroneous part of the molecule exclusively.

• Stereochemistry

  • A new method is available that finds atoms that can become (s) or (r) stereo centers after the stereo arrangement of the bonds around the atom is specified.

• API

  • New parameter to set accessibility of special nodes in Advanced tab of Periodic System dialog: Documentation (Forum topic).

Bugfixes

• MarvinSketch

  • When MarvinSketch was launched from command line with -h or --help option, the application was not terminated after printing of help message.

  • When using MarvinSketchPane from an application, and pop it up as a modal dialog, its children could disappear behind the main application (e.g., DialogLauncher example).

• MarvinSketch GUI

  • Scaling bug occured on the button of the template toolbar if there was a contracted group displayed on the button.

  • "Calculations" menu did not appear in ISIS/Draw-like configuration.

• MarvinView GUI

  • The title of the MView application window was not updated on file open and save.

• MarvinSpace

  • MarvinSpace: JOGL 1.1 was replaced by the most recent version 2.0. This resolves various MSpace launch and initialization issues (in particular Applet problems on MacOSX). Forum topic

• Applet

  • Although a valid URL was given in sketchHelp applet parameter, Marvin applet loaded the default help by selecting Help->Help Content instead of the given URL.

  • "My templates" became unavailable in applet after modifying it from template library. Forum topic.

• Painting

  • The rb* atomic query property was not displayed at the mouse tooltip when it was set through its keyboard shortcut: ".rb*".

• Chemical Structure Painting

  • Positioning of R-group labels was incorrect.

• Datatransfer

  • Clipboard handling

    • Copy as PDF used 100x100px as image metrics and not the appropriate size for the current scale in Mac OSX.

• Import/Export

  • MOL, SDF, RXN, RDF

    • The subscript information of the S-group generic bracket was not exported to MOL V3000 and V2000 formats.

    • Export of compressed MOL files allowed too large coordinate values, which caused distortion in the molecule after importing it.

    • After importing an RDfile that contains an empty S-group, its brackets didn't appear.

  • SDF

    • Data S-groups were lost after exporting it to SDF format.

  • SMILES, SMARTS

    • Export to abbreviated group format did not work since 5.8.

  • CXSMILES, CXSMARTS

    • CXSMILES import added radicals to atoms that have coordinate bond to a central, metal atom.

    • I/O of atom alias "," was not working in CXSMILES format.

  • CML, MRV

    • Format mrv had missing closing tags at the end of the generic S-group lines.

    • MolExporter exported to MRV format using operating system specific line ending, '\n'.

  • CDX

    • Standalone list atoms and labels were read as text boxes from CDX files.

    • Component grouping was not recognized during CDX import.

  • SKC

    • During the export to SKC format, chiral flags were lost and "AND enantiomer" flags were displayed.

  • CDX/SKC

    • When opening a ChemDraw .cdx file or an ISIS/Draw .skc file containing structures with abbreviated groups, the attachment point of these groups was rendered incorrectly.

  • Structure to Name (s2n)

    • There were extraneous numbers in generated names for structures containing atom values.

    • Generation of IUPAC names for large structures might have stopped before the timeout.

  • Name to Structure (n2s)

    • The n2s import option to specify the location of the custom dictionary was not thread-safe, and was not accessible in d2s.

    • Name to structure failed to return a result on some very long names (several hundreds of characters).

  • Document to Structure (d2s)

    • Non-chemical data in embedded structures, for instance text labels, were not extracted from embedded documents.

    • Some embedded structures were not extracted from office documents.

    • Reactions embedded in documents were not extracted.

    • Some uppercase strings were wrongly interpreted as smiles, for instance "BOUCHON".

    • When OSRA was called by Document to Structure, it could run even after Marvin is stopped (on Windows only).

    • OSRA was not working on PDFs containing monochrome images.

  • Molconvert

    • A NullPointerException appeared in the console instead of an error message when using molconvert to convert an image with skiperror parameter set without OSRA installed.

• Molecule Representation

  • Valence Check

    • Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.

    • False positive valence error was on aromatic rings which have sulfur ligand that is part of a ring.

    • Removing explicit hydrogen atoms from LiH, CaH₂, SH₄, PH₅, PbH₂, PbH₄ did not keep the original hydrogen count.

    • Aromatic carbon cations having three ligands were handled incorrectly by the Valence check.

  • S-groups

    • Bracket positioning did not take the implicit hydrogen atoms into account.

    • If data were added as "relative", the cleaning or arrange methods did not take them along with the fragment/component/molecule.

    • The chirality of expanded S-group's atom changed, when there wasn't enough space in the canvas for the expanded S-group.

    • After expanding S-groups, atoms of the molecule could overlap.

    • Removal of explicit hydrogen being the only atom of an S-group was unsuccessful. New flag, SGROUP_H, has been introduced, for remove such hydrogens.

    • Exception was occurred when an abbreviated group was copied then pasted.

    • Method MulticenterTransform.transformMulticenters(Molecule mol) and MulticenterTransform.restoreMulticenters(Molecule mol) changed the number of implicit hydrogens of atoms.

  • R-groups

    • Fragmantation of an Rg-molecule resulted inconsistent molecules.

• Clean 2D

  • In case of selection, stereoinformation of the molecule during two dimensional cleaning was lost.

• Aromatization/dearomatization

  • General aromatization worked incorrectly in case of molecules with a bond connecting 2 rings but not being part of any ring. Solving this problem, deprecated method int[] getSSSRBondSet(), was removed and, instead, BitSet getSSSRBondSet() was introduced.

• Calculations

  • Protonation (pKa, reson.)

    • The predicted pKa of certain CH acids were extremly low.

  • Isomers (tautomer., reson.)

    • Tautomer generation was very slow on proteins.

    • Some deuterium atoms were removed during tautomer generation. Forum topic

    • The structure of the generated tautomer was not cleaned if the input molecule contained abbreviated group(s).

  • Conformation

    • Exception was thrown during conformer generation if Visualize H bonds option was selected.

• Structure Checker

  • Clean Wedge fixer of Wedge Error checker had no effect in case of wedge bond between two chiral centers.

  • Atoms and bonds inside S-groups were not handled correctly by certain checkers.

• Elemental Analyzer

  • Elemental analyzer calculated wrong molecular formula for molecules, that contains bond to a centroid.

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.

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. Forum topic

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.

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.

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.

Bugfixes

• Stereochemistry

  • Bicyclostereo information was calculated on symmetric ligands.

• Structure Checker

  • External fixers could not be applied properly in MarvinSketch.

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.

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.

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.

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.

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.

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.

Bugfix

• Import/Export

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

Bugfixes

• Import/Export

  • Data Sgroup was converted incorrectly to cxmiles.

  • Opening PDF files, NullPointerException occured in some cases.

New features and improvements

• MarvinSketch GUI

  • New mouse cursors have been introduced.

  • New structure templates have been added (Alpha D sugars, Beta D sugars, Deoxynucleosides, Flavonoids, Nucleobases, Nucleosides, Protoalkaloids, True Alkaloids, Vitamins, Functional Groups).

• 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.

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.

Bugfixes

• Calculator Plugins

  • Improved pKa prediction of the "OH" acid in oxim group.

• Structure Checker

  • SubstructureChecker did not work (requires JChem).

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 MarvinSketch window that has been opened from the MView pane, the closing of the MarvinSketch window (or clicking on the transfer button) transfers the selection back to the MView pane.

• Chemical structure painting

  • Drawing 2D projected views of 3D aromatic rings (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.

Bugfix

• MarvinSketch

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

New features and improvements

• MarvinSketch

  • Public database search in chemicalize.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.

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.

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 MarvinSketch 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 behavior 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).

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.

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.

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.

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.

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.

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.

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.

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

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.

Bugfixes

• Marvin Sketch

  • Structure Checker Progress bar remained on the screen during structure fixing.

• Applets

  • Chemical terms calculation did not work from MarvinSketch applet.

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 behavior to check graph invariants at CIS TRANS export.

  • IUPAC Name

    • Concise names generated for acyl-CoA (coenzyme A) derivatives.

    • Dictionary of common and traditional names have vastly improved and augmented.

    • Structure to name generates many more common names with the "traditional" option.

• Clean 2D

  • Use the template wedges in PartialClean.

  • Clean of adamantane structures is nicer.

• 3D Alignment

  • Alignment by pharmacophore types.

  • Alignment by Maximum common substructure.

• Calculator Plugins

  • Tooltips with help messages are displayed on Calculator Plugins options panels.

  • Some Calculator Plugin options panels have been redesigned, to fit small resolution displays (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.

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.

New features and improvements

• MarvinSketch

  • New icon is added to the "Add Attachment Point" action (forum topic).

  • New keyboard shortcuts: 5 - Single Up, 6 - Single Down, 7 - Wiggly bond.

• Molecule representation

  • Add function that returns improved information of parity.

Bugfixes

• MarvinSketch

  • Custom menus were not loaded after restarting MarvinSketch.

• MarvinView

  • Print All did nothing if multiple pages were sent to the printer from MarvinView.

• Licenses

  • Fixed the displayed state of licenses to be installed. (Replaced "Invalid" with "To be installed".)

• Applet

  • Complete the missing isLeopardSafari() method in marvin.js (marvin/sketch/index.jsp did not load in Mac Safari) (forum topic).

• Import/Export

  • Partial charges numeric format in mol2 is fixed (forum topic).

• Molecule representation

  • Nitrogen with double bond and explicit H gets stereo value (forum topic).

  • Bug was in setDim method in RgMolecule.

• Chemical Structure Painting

  • Bracket overwrote lone pairs, image generation clipped off lone pairs/charge symol ( forum topic).

• Calculator Plugins

  • Canonical tautomer calculation threw ArrayIndexOutOfBoundsException in some cases (forum topic).

New features and improvements

• API

  • New functions are added that return improved information of parity: Parity.asymmetricAtoms(MoleculeGraph), Parity.chiralAtoms(MoleculeGraph).

Bugfixes

• MarvinSketch

  • Initialization problem in MarvinSketch if it was initialized through MarvinOLEServer.

• Calculator Plugins

  • The chiralCenterCount function in TopologyAnalyser plugin returned now zero for the number of chiral centers of 1,4-dimethylcyclohexane.

New features and improvements

• MarvinSketch

  • A splash screen image is shown during the initialization of the MarvinSketch standalone version.

• Import/Export

  • Partial charges are saved in mol2 file format based on the calculation result of the charge plugin (charge license required; if it is not found then the mol2 file is created without charges). (forum topic).

  • Relative stereo descriptors (using enhanced stereo OR groups) is supported in name export.

  • Amino acid recognition in Name import has been improved: substituents are recognized, D/L configuration is supported.

  • Importing non standard names is more flexible: more freedom at numbering, bracers and dashes.

  • Cis/trans releated information is supported in name import.

• Clean 2D

  • The arrangement of wedge bonds using the 'Clean wedge bonds' option has been improved. (forum topic).

• Applet

  • The loading of MSketch Applet is sped up: the total size of the files downloaded during the first initialization has been reduced by 14% compared to the previous version.

  • The value of the "legacy_lifecycle" parameter is true in default in Marvin applets if you use marvin.js (see applet parameters).

  • New methods have been introduced in marvin.js, which return with the generated applet source instead of writing it into the html source: msketch_end_to_string(), mview_end_to_string() and mspace_end_to_string().

  • A new applet parameter has been introduced ("appletid") to identify applet in the propertychange event notification sent to JavaScript.

  • The marvin.js uses ID attribute instead of NAME to refer to the applet.

• Chemical Terms

  • New Chemical Terms functions have been introduced:

    • importMol()

    • isMarkush() (forum topic)

    • whereIsValenceError()

    • hasAromatizationError()

• Calculator plugins

  • A new method has been implemented in the Structural Frameworks plugin of the Geometry plugin: checkMolecule().

  • The major tautomer generation has been sped up (forum topic).

  • Stereoisomer plugin can generate stereoisomers with given chirality as constraint (forum topic).

Bugfixes

• MarvinSketch

  • The 'Recent file list' contained two separate (and incorrect) items if the filename contained a comma character (divided at the comma).

  • OLE failed with some repaint events when the canvas was in the background of other java components.

• Applet

  • The JVM version in the EMBED and the OBJECT tag in the marvin.js generated code was not up-to-date. In addition to the update the NAME attribute was changed to ID (forum topic).

  • The "viewCarbonVisibility" applet parameter did not work (forum topic).

• Import/Export

  • Some R/S and E/Z stereo descriptors were missing in generated names.

  • Failing on name generation of very complex structures was not handled too gracefully.

  • cxsmarts:h failed (forum topic).

  • MOLFiles with incorrect spaces at the end of the new type of Atom list definition lines can now be imported without error.

  • CDX import failed at some reaction mapping.

• Molecule representation

  • There was a NullPointerException in aromatization (forum topic).

  • Copy/paste and import/export of a molecule in mrv format having an S-Group with only one atom did not work (forum topic).

  • The getAromaticAndAliphaticRings method threw NullPointerException (forum topic).

• Calculator plugins

  • The exceptions of the Structural Frameworks plugin were sometimes improper (now it throws PluginException on error).

  • Projected surface area prediction produced inconsistent values (forum topic).

• Template handling

  • Homology templates were missing in applets.

• Installation

  • Marvin/JChem batch files could not handle quotes in the parameter list (forum topic).

• Licenses

  • The use of the setLicense or setLicenseFile API resulted in unusable client licenses unless they had the "Server Mode Allowed" field (forum topic).

New features and improvements

• MarvinSketch:

  • The Clear Atom List button is added to the Periodic System dialog window (forum topic).

  • Icon for Reaxys Generics is added.

• MolConverter:

  • Option -m produces multiple output files from multi-molecule input (forum topic).

• Applet:

  • New applet parameters for setting license files (forum topics: #3715, #4796).

• Import/Export:

  • InChi 1.02 version has been integrated.

  • InChiKey can be exported. New export option: inchi:key

• Calculator Plugins:

  • Added average microspecies charge calculations to cxcalc (averagemicrospeciescharge) and Chemical Terms (averageMicrospeciesCharge()) (forum topic).

• Documentation:

  • chemaxon.marvin.MolPrinter and chemaxon.formats.MolConverter API are improved.

• API:

  • 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.

New features and improvements

• MarvinSketch

  • Copy actions run in background thread.

  • Speed up OLE copy: MarvinOLEServer running in the background permanently.

• Applet

  • Customizable applet splash screen which is displayed while the applet is loading (live example).

• Import/Export

  • Allows aromatic boron in cxsmiles.

  • cxsmarts format stores attachment point data.

  • Support for atom values in cxsmiles.

  • Keep wedge arrangement in cxsmiles (forum topic).

• Calculator Plugins

  • Structural frameworks plugin is moved to Other plugin group, 3D Alignment plugin is moved to Conformation plugin group.

  • Added stereoDoubleBondCount calculation to TopologyAnalyserPlugin.

• Licenses

  • The Alignment plugin can be used with Conformation Plugin license.

• API

  • CGraph.cloneCopy() copies all relevant cached calculated data.

Bugfixes

• MarvinSketch

  • The first alteration of the structure couldn't be undone in MarvinSketch opened through MarvinView.

  • The .H+/.H- buttons could not be used in some cases.

  • Do not show carbon atoms when charge is on bracket.

  • Bold font is used for superscripts in case of charge for better visibility.

  • Missing bond problem after OLE copy: reimplementing bond-crossing drawing.

  • Missing bond crossing visualization when crossing a bond with a bond vertically.

  • The Insert > Groups dialog contained some empty elements.

• MarvinView

  • MarvinView hid the right side of text boxes.

  • MarvinView did not display SD file property when first entries are missing the value.

  • MarvinView freezing when molecule subset start index set to invalid value.

• MarvinSpace

  • MSpace debug printout is removed.

• Import/Export

  • Rdf conversion lost the reaction number (forum topic).

  • Fixed fusion bridge wrong lettering in name export (forum topic).

• Molecule Representation

  • Ungrouping of multilevel S-groups with Molecule.DEFAULT_UNGROUP caused NPE.

  • Empty DataSgroup-s are removed if an S-group gets empty (API, GUI).

  • Merge Brackets popup menu item was not available in some cases.

  • Rings were not cleaned perfectly.

• Calculator Plugins

  • MarkushEnumerationPlugin.getRandomStructure() did not return random structures, always the first enumerated was returned.

• Licenses

  • Markush license exception was incorrectly thrown by JChemSearch.

• API

  • MolImporter.getRecordCount returned 2* the expected number.

  • First (record number) column displays the value returned by MDocSource.getDocLabel.

New features and improvements

• Compatibility

  • Minimum Java requirement of Marvin is 1.5.

• MarvinSketch

  • Truly transparent structure painting method: higher quality drawings at crossing bonds and atom labels.

  • Vector graphics (EMF) copy place transparent picture to the clipboard.

  • New color schema options on the Periodic System dialog.

  • Charge can be assigned to the S-group and displayed on the molecule bracket.

  • Drawing attachment points outside S-groups.

  • Homology group drawing.

• MarvinView

  • Copy/Paste transfers molecule properties.

  • "Go To" option in Table menu.

  • New values of edited data fields and molecules are stored permanently in memory even in case of large (cached) viewer tables.

• Import/Export

  • Extended support for the generation of fused names (from 75% to 80%) in IUPAC name export.

  • CAS naming and simple fused systems supported in name import.

  • Transparent background in image export (EMF, SVG, PNG).

• Molecule representation

  • New option for adding an explicit hydrogen atom to chiral centers having no terminal atoms when 2D cleaning is performed.

• Calculator Plugins

  • New plugin: Flexible 3D alignment of multiple molecule structures to each other.

  • New plugin: structural framework calculation including Bemis-Murcko.

  • Markush enumeration:

    • Enumeration of homology groups.

    • Enumeration of X pseudo atoms [F,Cl,Br,I].

  • pKa calculator is trainable.

  • Total charge calculation in cxcalc ("totalcharge") (forum topic).

  • "Take major tautomeric form" option in MajorMicrospeciesPlugin.

  • 23 new ring related functions in TopologyAnalyser.

  • Resonance Plugin was moved to "Other" plugin group, and it can be used without license key (free) (forum topic).

• Chemical Terms

  • Flexible plugin parameter setting in Evaluator: "name1:value1 name2:value2 ...". (Example: markushEnumerations('random:true id:true', '1,2', 5).)

  • hasRadical(), radicalCount(), and hasIsotope() functions in Chemical Terms.

  • fragments() function in Chemical Terms (forum topic).

  • CT Editor is available in Marvin API.

• API

  • Transfer button: optional button to send the molecule to the specified target after closing MarvinSketch window.

  • Specify own background color separately for each cell in MarvinView via (applet) parameter.

  • New metal types can be specified in Periodic system.

  • Structure checker core classes and functions are implemented.

  • MViewPane enhanced table support.

  • PluginFactory creates new plugin and display instances for each getPlugin() and getDisplay() call in case of multimol display; added MOLECULES result domain type and canRepeat() in CalculatorPlugin

Bugfixes

• MarvinSketch

  • Disabled tooltips in menus.

  • The copied and generated structure with Data S-group is much bigger than needed (forum topic).

• MarvinView

  • Print All displayed only the first row on each page.

  • Multi-line SDF properties seem to be truncated in the cells until somone clicks on them (then a scrollbar appears).

  • Page Up/Page Down not working in spreadsheet view.

  • NullPointerException in empty mview when the "Show Fields" option was selected.

• Import/export

  • Cis Trans info defined by aromatic bonds in SMART / SMILES import. (forum topic

  • SMILES export of SuperAtom S-group in SuperAtom S-group did not work (forum topic).

• Molecule representation

  • 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.

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.

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.

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.

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.

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)

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).

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.

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.

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.

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.

Bugfixes

• MarvinSketch GUI:

  • Customization dialog was not displayed.

  • Complete missing configuration names.

• Licenses:

  • License management did not work via JavaScript calls (e.g. get molecule in "name" format) due to Sun's security restriction.

New features and Improvements

• MarvinSketch GUI:

  • 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).

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()