Bugfixes

Import/Export

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

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

Bugfixes

• Clipboard handling

  • Compounds in a reaction could not be copied.

• Import/Export

  • Structure to Name (s2n)

    • Name generation failed on some compounds with a radical, such as oxidanyls with a cyclic substituent. The error manifested itself as a StackOverflowError wrapped in an IOException.

New features and improvements

• Clipboard handling

  • When the clipboard content is not recognized as a chemical object, the format chooser dialog is not displayed. Forum

• MarvinView GUI

  • In MarvinView, the "Select" textbox was eliminated from the "Preview" tab of the "Open file" dialog.

• Import/Export

  • PDB

    • PDB import reads the following residue information of sequences: residue type, sequence number, atom ID in residue.

• Applet

  • Export of binary formats has become available from the applet API. Forum1, Forum2

Bugfixes

• Editing

  • The toolbar buttons could not be used to add charge to single hydrogen atoms if there were other atoms on the canvas.

  • When drawing cycles and bridges in peptides, the blue feedback remained around the first bond.

  • When a repeating unit was created from one atom only and then the structure was selected, the content of the repeating unit changed.

  • Connecting a bond to an S-group which did not have any free attachment points changed the S-group to a carbon atom.

  • In some special cases, it was possible to overwirte an atom by just hovering the mouse over it with an active atom editing tool.

  • Rotating selected molecules in 3D changed the type of all bonds to single.

  • When a bond was connected to a multicenter, the whole molecule disappeared from the canvas.

• Molecule Representation

  • Valence Check

    • Tin atom with charge +2 had incorrect valence. Forum

    • False valence error appeared on a sulfur atom having one negative charge and 5 or 6 bonds.

  • Clean 2D

    • Nucleic acid clean was not sensitive to arranging 5' to the left and 3' to the right end of the chain.

    • Two Dimensional Clean of Crown Ethers was ugly.

• Import/Export

  • MOL, SDF, RXN, RDF

    • Aromatic query property appeared after MDL MOL export and import on an aromatic atom having atom property.

  • SKC

    • Two single bonds of a cyclopropyl ring were read as coordinate bond. Forum

  • CDX/CDXML

    • Some CDX files that contain atom or bond label formatting were not read.

• Calculations

  • Stereo Analysis

    • CIP convention issue has been fixed.

    • Imine type structures were not recognized.

  • pKa

    • Calculation for boron compounds has been fixed.

Known issue

• MarvinSketch Applet

  • External checker classes do not load if browser uses Java SE 6. Please, use Java SE 7 for successful checker class loading.

New features and improvements

• MarvinSketch GUI

  • R* is displayed on the canvas if R-logic is unspecified for an R-group and the "View > Advanced > R-logic" visibility option is switched on.

  • R-logic is always displayed even if it is set to the default value when the relevant visibility option is switched on.

  • When R-group attachments are added to fragments not belonging to an R-group, the attachment order begins with "1" on each fragment.

  • "R/S" stereo label is displayed on atoms which are stereocenters and have a "Single Up or Down" bond if the relevant visibility option (in "View > Stereo > R/S Labels") is switched on.

  • Crosslinking peptide bridges are colored automatically if the "View > Colors > Peptide Bridges" visibility option is switched on. Documentation

• MarvinSketch Dialog

  • Character encoding information has been added to the "About" dialog. Documentation

  • In dialog "R-logic", "unspecified" is displayed in the "Occurrence range" field if it is not specified for an R-group.

• Editing

  • Molecules are no longer checked by MarvinSketch whether the "Absolute Stereo (CHIRAL)" flag can be added to them.

  • Drawing wedge bonds on a 3D canvas has been disabled. These bond types are active only when the canvas is in 2D mode.

• MarvinView GUI

  • "Save image" option has been added to the contextual menu of MarvinView

• MarvinSpace GUI

  • Hydrogen visualization toolbar button added.

  • Display/drawing settings saved on exit.

• Import/Export

  • SMILES/SMARTS

    • SMILES import handles CACTVS-type representation of coordinate bonds ('|' character). Please note that the export does not handle it.

  • Sequences, FASTA

    • Terminal H and OH are added to nucleic acids by nucleic acid import.

  • Name to Structure (n2s)

    • CAS Registry Numbers can be converted to structures even when they contain coordinate bonds, such as 56-24-6.

    • Conversion of nitrogen-substituted acetohydrazides is now supported.

    • Elements with isotopes, such as (14)C, are converted in name to structure by default, and, optionally, they can be converted with document to structure using the "d2s:elements" format option.

    • Some OCR errors have been fixed in carbon ranges for homology groups, for example, "Ci_10 alkyl".

    • Generic structure names (such as "alkyl" in English) are supported in Chinese as well, for instance, N-???-4-??? and C1-C4-??.

    • Polyspiro names with a polycyclic component, such as dispiro[cyclohexane-1,2'-indene-1',2"-imidazole], are supported.

  • Document to Structure (d2s)

    • For enzymes with a substrate in their name, such as "serine protease", the substrate (serine) is not converted by default. A new format option, "d2s:substrates", enables the recognition of the substrate in such cases.

    • New format option "d2s:specific" has been added to convert only specific structures. This option excludes structures with R-groups from the conversion.

    • More OCR error correction is performed.

    • In the case of processing XML fragments not starting with "<?xml version="..."?>", it has become possible to specify that the input text is in XML format by using the "d2s:content-type=application/xml" format option.

    • Metadata is also extracted from older (since 2001) USPTO patents in XML format: the section where a name is found is recorded as metadata (title, abstract, description, or claim number). Furthermore, document metadata is extracted as well: patent title and ID, inventors, IPC categories.

    • OCR error correction has been added for Chinese names.

  • Structure to Name (s2n)

    • In fused ring systems with an atom being in a non-standard valence state, the generated name conforms to the IUPAC rules by using the lambda notation only in front of the fused names and not inside the component name.
      See for instance: 1H,3H-2λ⁴-naphtho[2,3-c]thiophen-2-one.

    • Name generation has become faster by about 10%.

• Molecule Representation

  • R-logic

    • Default value of R-logic range has been changed: instead of ">0", now it is an empty string which means "as drawn". ">0" value is handled as non-default and is exported in file formats where ChemAxon supports R-logic information (MRV, SKC, MOL). From now on, if a file does not contain R-logic range information, then it is interpreted with the new default value: "as drawn". Documentation

  • Stereochemistry

    • Cahn-Ingold-Prelog (CIP) stereo recognition has been extended and it has been added to the public API.

  • Elemental Analyzer

    • Molecular mass calculation is more accurate.

• Image I/O

  • Structures can be exported in image formats "TIFF" and "EPS". Documentation1 (TIFF), Documentation2 (EPS)

  • S-group attachment point labels are not exported to image files (PNG, JPG, PPM, SVG, EPS, TIF, BMP). Exporting these labels to PDF files can be switched on/off using the "Edit > Preferences > Save/Load > Save/Load GUI Settings" checkbox.

  • During PDF export, text is also saved as image.

• Calculations

  • Stereo Analysis

    • New stereo analysis API. API Documentation

  • 3D alignment

    • Hydrogens are taken into consideration during alignment process.

  • Conformers

    • New Generate3D documentation has been added. Documentation

• Structure Checker

  • "Overlapping Atoms Checker", "Overlapping Bonds Checker", and "Bond Length Checker" report correctly for molecules containing S-groups.

• API

  • IsotopesCompiler in isotopescomp.jar creates a UI in order to show error messages and information when it was not started from the console. Forum

  • atomNumbersVisible parameter has been deprecated and has been replaced by the atomNumberingType parameter. API Documentation

• Third-party applications

  • The Java COM Bridge (Jacob) version was updated from v1.15-M3 to v1-17. Forum

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

  • Starting points of electron flow arrows drawn from radicals and/or lone pairs were changed when lone pair visibility was switched off and then on again.

  • R-logic label was not taken into account by zoom action even if visibility option "R-logic" was switched on.

• Painting

  • Electron flow arrows starting from an atom, a negative charge, or an automatically calculated lone pair disappeared when lone pair visibility was turned off and then turned on again.

• Editing

  • Menu option "Link Node" was not disabled when an atom had less than two bonds. Forum

  • A contracted tripeptide disappeared from view when it was expanded, but 2D Clean brought it back.

  • It was not possible to draw an electron flow arrow from an atom to an incipient bond between this atom and an abbreviated group. Forum

  • Erasing a structure without an R-group attachment left "1" on the canvas, which behaved as an atom.

  • When an atom was selected and the "R-group attachment" button of the Markush toolbar was used, the selected atom was changed to an R-group attachment point; however, a new R-group attachment should have been added to the selected atom in this case.

  • Dragging with the R-group attachment tool, a bond was created connecting two R-group attachments.

  • Using the R-group attachment tool, R-group attachments could be added to an existing R-group attachment.

• Load/Save handling in UI

  • Lone pairs were lost at "Copy As... > PDF" at Mac OS X. Forum

  • PDF export did not use the color scheme setting. Forum

• Clipboard handling

  • During PDF export, atom labels were turned upside down with some font types. Forum

• MarvinView GUI

  • Pasting a SMILES string into MarvinView did not work.

• Import/Export

  • MRV/CML

    • After MRV export and reimport of a structure, its text box font color turned into the frame color of the text box and the font color turned to a not defined color (black). Forum

  • Format recognition

    • '(S)-(-) Propanolol' was recognized as SMILES.

    • CAS numbers were recognized as MDL MOL format.

  • Name to Structure (n2s)

    • Automatic format recognition failed for names using unicode hyphens.

    • Names of some spiro compounds containing aromatic components were not converted. See, for instance, 6-(2, 5-dimethylphenyl)-5'-methylspiro[chroman-4,2'-imidazol]-4'-amine.

  • Document to Structure (d2s)

    • Some names containing a space character (for instance, "malonic acid") were not detected.

    • When using document to structure using the MRecordReader API, the MRecord.getMolString() method returned null.

    • The character position property of recognized names was sometimes wrong.

    • Spiro and fused ring system names were not recognized in HTML documents when the brackets were represented by HTML entities.

    • Processing an HTML document failed when the document was declared to be in XHTML format, but was not actually a valid XML (for instance, contained unclosed tags).

    • Processing a USPTO XML patent file in the current directory failed when it referred to CDX structures files.

    • Some structures embedded in Office documents were not extracted.

  • Structure to Name (s2n)

    • Names could not be generated for structures with lone pairs (MolAtom.LP).

    • The name generated for OH^- was "oxidanide" instead of the preferred form "hydroxide".

    • An extra locant was included in the name of cyclic structures with multiple hetero atoms with one of them having non-standard valence, for instance, 1λ⁶,4-thiomorpholine-1,1-dione instead of 1λ⁶-thiomorpholine-1,1-dione.

    • In cases where a cyclic substituent was connected indirectly to the parent through an ether, sometimes wrong names were generated.

    • Name generation failed for structures with a methanethione parent.

• Molecule Representation

  • S-groups

    • Flip property could be set on any polymer-type S-group resulting in structures with incorrect information. From now on, only ladder type polymer S-groups can have flip property, and it will disappear from invalid structures.

    • java.lang.ArrayIndexOutOfBoundsException was thrown when a multicenter atom being the only member of an S-group was removed.

  • Valence Check

    • Valence check did not accept chlorine and heavier halogens with 1 negative charge and with 2, 4 or 6 pieces of fluoride ligands.

  • Stereochemistry

    • Incorrect stereogenic center was found in some spiro compound. Forum

  • Aromatization

    • General aromatization handled selenium differently than sulfur.

• Clean 2D

  • Cleaning of position variation bonds could make bonds overlap.

• Datatransfer

  • OLE

    • The buttons in the Periodic Table and on the Atoms toolbar were not rendered properly in Marvin OLE.

• Applet

  • Missing resources prevented successful name import of bridged structures in applets. For instance, template based cleaning and pasting names did not work in these cases.

• Image I/O

  • Lone pairs were painted only at the second call of painting. Forum

  • R-logic label was not exported into images, although visibility option "R-logic" was switched on.

  • Circled charge font was not considered during image export.

  • During PDF export, stoichiometric numbers in subscript were placed wrongly. Forum

Deprecated and removed methods

Deprecated and removed methods