Bugfixes

• Import/Export

  • OLE objects from Accelrys Draw 4.1 and further versions could not be redirected by MarvinOLE server.

  • OLE opened in 3D rotation mode (F7) mode.

Bugfixes

• Applet

  • Missing resources caused issues in applets with bridged structures. For instance, template based cleaning and pasting names did not work in these cases.

Bugfixes

• Java Webstart

  • Java Webstart did not run on Macintosh computers.

Bugfixes

• Applet

  • The mol property change event was not fired when an empty molecule was set initially for the MarvinSketch applet. This could cause misbehaviour in cases where the client JavaScript code relied on this marker to know when the applet was initialized.

Bugfixes

• MarvinSketch GUI

  • MSketchPane setPiece(Molecule) method did not work, it set the molecule on the canvas instead of putting it on the cursor. Forum

• Import/Export

  • CXSMILES/CXSMARTS

    • CXSMARTS containing valence property information was recognized and read as SMARTS.

  • SKC

    • Some reaction was read as R-definition from SKC format.

New features and improvements

• MarvinSketch Dialog

  • 'Zoom to scaffold' checkbox option has been added to the "Preferences > Save/Load" tab. Documentation

• Structure Checker

  • External structure checker configuration file URL can be set via Java System Property.

Bugfixes

• Editing

  • Electron-flow arrow could not be drawn from the A-B bond to the incipient A-C bond of an A-B-C structure. Forum

• Import/Export

  • MolInputStream and MolImporter could have different format options.

  • MolImporter did not close its inputstream when an exception was thrown in the constructor.

  • MOL, SDF, RXN, RDF

    • Molecule type property was allowed in SDF, CSSDF export.

    • The coordinates of the sequence residue imported from SCSR MOL files were wrong if the residue had three attachment point.

  • CDX/CDXML

    • Color and text format of atom label is exported to CDX and imported from CDX and CDXML. Forum

    • Graphical brackets were not imported from CDX files.

  • Gaussian Z-matrix input format

    • Command line, title line, and extra input properties were not exported to Gaussian Z-matrix input format. Forum

• Clean 2D

  • Cleaning of position variation bonds could create overlapping bonds.

  • Cleaning of bridged systems could result in overlapping atoms. Forum

• Calculations

  • Topology Analysis

    • Missing method has been added: TopologyAnalyserPlugin.getFsp3(). API Documentation

  • logD

    • New logD training documentation has been added. Documentation

• Structure Checker

  • Fixer options in MarvinSketch are updated with newly defined settings.

  • External checkers can be loaded from JAR file in case the JAR file contains a space.

New features and improvements

• MarvinSketch GUI

  • Peptide cycles and bridges can be drawn according to IUPAC recommendations. Documentation

  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Advanced > Atom Numbering > IUPAC Numbering" menu item.

  • Lone Pair (LP button) was removed from the "Special nodes" group of the "Periodic Table > Advanced" tab, so it cannot be reached from the GUI anymore.

• MarvinSketch Menu

  • The "Calculations > Predictor" menu option has been removed from the default Marvin menu.

• Painting

  • Drawing of electron flow arrows has been changed. Single electron flow arrows can now start either from a radical or from an electron of a lone pair. Electron pair flow arrows can only start from lone pairs. Documentation

  • Atom property values belonging to the same atom are now separated with semicolons instead of commas.

  • When lone pairs were displayed on a structure, the charge symbol was nearly invisible.

• Load/Save handling in UI

  • The same last-used folder is saved for the "File > Open" and the "File > Insert file" functions.

• Graphical object handling

  • Electron flow arrows can be started from or targeted to multicenter atoms. Forum

• MarvinView GUI

  • IUPAC numbering can be displayed on the atoms of each molecule using the "View > Misc > Atom Numbers > IUPAC Numbering" menu item.

• Import/Export

  • MRV/CML

    • Namespace has been introduced to mrv format.

  • MOL, SDF, RXN, RDF

    • New export option, cc, is introduced to V2000 export in order to write absolute chiral flag if there are only ABS enhanced stereo labels in the molecule. Documentation

    • New import option, z, is introduced to MDL import that converts carbon atoms with "Z" label to R-group attachment points. Documentation

  • SMILES/SMARTS

    • [Z] is imported as R-group attachment point from SMILES. Documentation

  • CXSMILES/CXSMARTS

    • New export option, b, has been introduced to CXSMILES/CXSMARTS in order to turn off the export of bicyclostereo-information. Documentation

  • Name to Structure (n2s)

    • Name and corporate ID resolution webservice now supports NTLM authentication.

    • Names with a missing dash before the suffix locants are now recognized.

    • Non-standard IUPAC specification of stereochemistry inside suffix locants is supported.

    • Names with superscript locants of a bridged ring system numbering are denoted by spaces are now supported.

    • As a result of numerous improvements to the systematic name conversion algorithm, more names are converted by n2s and detected by d2s. The accuracy of structure generation has also increased. (For instance, 5% more names were detected and converted in a large, diverse set of patents.)

    • An example custom dictionary has been added to the documentation. Documentation

  • Document to Structure (d2s)

    • Chinese names are now detected in text documents using an approach which recognizes names in Chinese sentences without the spaces that separate words in English.

    • In addition to OSRA, the CLiDE and Imago Optical Structure Recognition tools (Chemical OCR) can be used to convert images to structures. These tools need to be installed separately from Marvin. Documentation

    • When processing USPTO patents in XML format, the section in which a name is found is recorded as metadata (title, abstract, citation, description, or claim number). Additionally, document metadata is extracted (patent title and ID, inventors and assignees, IPCR categories).

    • When processing a USPTO patent XML document, referenced CDX files are imported automatically if they are in the same directory as the XML file.

    • Processing of USPTO XML patents has become faster: an average 20% speed-up, more than ten times faster process for some patents.

    • PDF document pages with images in the JBIG2 format are now supported.

    • PDF documents generated by Adobe Acrobat Paper Capture Plug-In and ExperVision are now handled specially, since they contain both an original scanned image of text and the text resulting from OCR of the image. This allows much faster processing of such documents, and avoids double hits for the same text.

    • PDF documents with many small high-resolution images are now processed much faster, even when Optical Structure Recognition is used.

    • The document creation date property is stored as a java.util.Date object instead of string.

    • Structures returned by image recognition tools (OSRA, CLiDE, Imago) are better filtered to avoid false positives.

    • OCR processing for scanned texts can be disabled using the -ocr format option. Documentation

    • Processing of PDF documents with scanned black and white images (e.g., most non-searchable patent documents) has become approximately two times faster.

  • Structure to Name (s2n)

    • When converting a structure to CAS registry number, the InChiKey of the structure is used to search for the structure. This allows more structures to get a CAS registry number in such cases where several different SMILES with chemically irrelevant differences are associated with the structure.

• Molecule Representation

  • New method, SelectionMolecule.addAtom(MolAtom, boolean), is introduced. Forum

  • New methods, MolAtom.getBondArray() and Sgroup.getBondArray() are introduced. Forum

• Calculations

  • NMR (CNMR, HNMR Prediction...)

    • Various phosphorus-proton spin-spin coupling parameters have been added to the predictor database.

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

    • "Fsp3" option has been introduced in the Topology Analysis plugin for calculation of sp³ carbon atom fraction. Documentation

• Elemental Analyzer

  • Charge is taken into account in atomic mass calculation.

• Chemical Terms

  • Chemical Terms's (CT) Structure Checker functions accept XML configuration as string parameter, thus Structure Checker XML configurations can be used in JChem Cartridge via CT.

  • New checkErrorCount Chemical Terms function returns the number of errors/issues found by the checker(s) in the configuration. Documentation

• Structure Checker

  • Checker "substructure checker" has become available in Marvin Beans, so installing Marvin Beans will install the fully functional Structure Checker application.

  • Set Structure Checker configuration can be copied to the clipboard as action string from Structure Checker GUI and Structure Checker Editor. Documentation

  • The "excluded" list of Structure Checker's Abbreviated Group Checker accepts quotation marks in command-line. Possible definitions can be the following: "abbrevgroup:excluded=Ph,Ala,Gly", "abbrevgroup:excluded='Ph,Ala,Gly'" or "abbrevgroup:excluded="Ph,Ala,Gly"".

  • The checkers and fixers can be localized or customized according to individual requirements. Documentation

• Build/Installation

  • Mac OS X installer images were not digitally signed, and GateKeeper in newer OS X versions (10.7.5+) reported our installers as damaged and refused to install them.

Bugfixes

• MarvinSketch GUI

  • Aliphatic/Aromatic atom query property had three options ("a", "A", and "A,a") instead of the necessary two ("a" and "A").

• MarvinSketch Dialog

  • In case of long names, only a part of the whole name appeared on the naming panel.

• Editing

  • Deleting an atom having an R-group attachment did not delete the attachment.

  • The end of an arrow did not stick to the midpoint of an existing arrow.

• Load/Save handling in UI

  • In MarvinView, "File > Save All... > Advanced > Into SEPARATE FILES" did not save the last structure.

• History functions

  • When the "Stereo" atom property had been changed, Undo/Redo did not work properly and the IUPAC name was not updated.

• Graphical object handling

  • Labels written in text box were shifted when they were pasted either as an OLE object or as a PNG image.

• MarvinView GUI

  • When a structure which contained an R-group definition was opened from MarvinView for editing in MarvinSketch, the structure appeared with 0% zoom factor.

  • Text elements (atom labels, atom indices, text box contents, IUPAC name) were not resized in MarvinView while zooming the structure using the "View > Transform > Zoom" function. Forum

• Printing in MarvinView

  • When choosing "Print > All Visible", the structures overlapped in the preview, and "Print > All Visible > Print to PDF" resulted in an empty file.

• MarvinSpace

  • A bug occuring at PDB import has been fixed.

  • The "Edit > Cut" menu option has been fixed in the MarvinSpace menubar.

• Import/Export

  • Aliphatic and aromatic query property, when they are used together, is not imported and exported any more. The "no property", no aromatic or aliphatic query property, has the same meaning.

  • Only lower case file extensions were recognized.

  • MRV/CML

    • MRV files that contained circular R-group references without attachment point information could not be imported.

  • MOL, SDF, RXN, RDF

    • Export of structures containing multicenter S-groups to format MOL V2000 resulted in a non-standard file.

    • Newline characters in molecule name were not escaped.

    • MDL MOL import did not use MDL valence model for non-charged metals.

    • Atom list embedded to atom list in MDL file formats resulted in invalid atom list elements after import.

  • CDX/CDXML

    • Reactions containing anonymous alternative groups were not imported from CDX format. Forum

    • XML files with complex header could have been recognized as CDXML.

  • SMILES/SMARTS

    • Query Hydrogen atom with parity definition confused SMARTS import.

    • SMILES export did not throw exception when the molecule contained not supported reaction stereo information.

    • Newline characters in molecule name were not escaped.

    • SMILES import read Meitnerium atom (Mt) as any atom (*).

    • Strings containing valence property were recognized and imported as SMILES instead of SMARTS.

  • CXSMILES/CXSMARTS

    • Import of CXSMILES/CXSMARTS strings that describes the coordinates of atoms with option c added 'CIS OR TRANS' stereo information to double bonds in small rings.

    • Single or aromatic bonds could be lost during CXSMARTS export and import.

  • InChi/InChiKey

    • InChI was not recognized in MolConverter as one line molecular format that can be given as the argument of -s option without specifying the format.

  • PDF

    • Reactions could not be exported to PDF.

  • Name to structure (n2s)

    • Names with a cis- or trans-imine bond were failing to be converted to structures

    • Ions, such as "bismuth(3+)", were imported with valence property set to 0.

    • Ortho substitution on acetophenone generated wrong structures.

    • Some E/Z and R/S stereochemistry was missing in structures imported from names when the locant of the atom or bond with stereochemistry was not specified explicitly.

    • The "H^-" ion was missing from names containing "hydride", e.g., sodium hydride, they only had e.g., "Na⁺ instead of the correct NaH.

    • Names containing atoms with both a non-standard valence (λ) and a positive charge were converted to structures with an extra implicit hydrogen on that atom.

    • Primary and secondary amine oxides were represented as N-OH instead of [N⁺]-[O^-].

    • The "Name" format was not automatically recognized for names with XML/HTML character references, such as "β" or "α".

    • In some cases, amino acids with α, β, and γ prefixes were not converted.

    • Using n2s in the applet required the downloading of an unnecessary component. This, in turn, made the first applet usage much slower.

  • Document to structure (d2s)

    • Some common words such as "DUST" or "crank", were recognized as names because, e.g., DUST is a rare acronym for a chemical structure. These words are now ignored.

    • The insideTag format option was not working for XML and XHTML documents.

    • Some uppercase words were mistakenly recognized as SMILES strings, such as "CISCO" or "ON-OFF".

    • Some embedded images were returned with 'PNG' type instead of 'OSR', and the usual OSRA options and properties (e.g., timeout, confidence filtering) were missing as well.

    • When d2s was interrupted (for instance, by a timeout), an OCR or OSR process could be left running in the background until it was completed. In similar cases such processes are now stopped immediately.

    • Extracted names sometimes contained some irrelevant characters at the end, such as "4-(trifluoromethyl)-2-((1H-1,2,4-triazol-1-yl)phenyl)-methanamine 2e" instead of "4-(trifluoromethyl)-2-((1H-1,2,4-triazol-1-yl)phenyl)-methanamine".

    • In some cases, single names separated by space were imported as if they were one compound, for instance, "2-hexanoyloxyethyl 1-formyloxypropyl".

    • Embedded structures in Office documents were always imported with the absolute chiral flag set.

  • Structure to name (s2n)

    • When generating names in parallel in multiple threads, some E/Z stereo bond modifiers were missing from the output.

    • Wrong names were generated for structures with multiple attachment points. These cases are now detected and no name is generated for them. Generating a name in this case will be implemented in the future.

• Molecule Representation

  • Valence Check

    • Valence check changed standalone Bi to BiH₃.

    • Valence error was not shown on a Carbon atom having a triple and an aromatic bond.

    • Valence Check accepted Stannane with any number of implicit hydrogens.

  • Implicit/Explicit Hydrogen Conversion

    • Stereoinformation was lost during explicit Hydrogen removal from stereocenter when all ligands of the stereocenter were also stereogenic.

    • Conversion of explicit Hydrogen to implicit one thrown exception when there is only a Hydrogen atom in an R-group definition or in a definition member.

• Image I/O

  • Text box contents, atom labels and atom attributes (e.g., atom indices, stereo labels), and IUPAC names were not exported to PDF as text. When the "Save/Load GUI settings" checkbox was checked in the Preferences dialog, text attributes (e.g., font type, size) were not exported either.

• Clean 2D

  • Clean removed stereo centers around the contracted superatom S-groups.

  • Clean2D got stuck and error message was thrown for some more complex molecules imported from SMILES.

• Stereochemistry

  • Cis-Trans stereoisomerizm was recognized on flexible Nitrogen atoms.

  • Stereo information could lost in symmetric bridged systems with explicit Hydrogen atoms.

• Calculations

  • Elemental Analysis

    • ElementalAnalyser.setMolecule(String) threw exception if the formula contained () brackets (e.g. C6H11N3.2(HCl)). API documentation, Forum topic

  • Protonation (pKa, Major Microspecies, Isoelectric Point)

    • Minor bug has been fixed on the distribution chart.

  • Isomers (Tautomers, Stereoisomers)

    • Stereoisomers plugin failed to generate all stereoisomers for tricyclic compounds. Forum topic

    • Generic tautomer generation threw exception on some molecules.

    • Some invalid 3D structures were not filtered out during stereoisomer generation although 3D-filter option was turned on. Forum topic

    • Some cycloolefine stereoisomers were mistakenly filtered out as duplicates, so they were missing from the generated list of stereoisomers. Forum topic

• Structure Checker

  • In Structure Checker GUI, the scroll bar was missing in the report tab if the report contained four to six structures.

  • When the Structure Checker configuration contained multiple substructure checkers, their order would change during structure checking process.

Deprecated and removed methods