ChemDoodle 3.1 has been released! We provide this upgrade, free of charge, to our existing customers. Just open up ChemDoodle and follow the directions to automatically update ChemDoodle.

Executive Summary

ChemDoodle 3.1 provides three new file formats: ACD/ChemSketch Document, MDL RXNFile (both V2000 and V3000) and MDL RDFile. ChemDoodle now reads and writes the formats of all chemical sketchers. Also implemented is a complete interface to the ChemExper database providing structures and properties from the MolGrabber widget and access to chemical suppliers for structures that you draw. The NMR simulation algorithms have been greatly improved. Many bugs have been fixed.


  1. Incorporated the input and output of the ACD/ChemSketch Document format.
  2. Incorporated the input and output of the MDL RXNFile format for storing single reactions. Both V2000 and V3000 connection tables are supported
  3. Incorporated the input and output of the MDL RDFile format for storing reaction schemes.
  4. Integration of the ChemExper database.

    -Access to structures and properties provided in the MolGrabber widget.

    -Access to to chemical suppliers for the chemicals drawn by clicking the Chemical Suppliers menu item in the Structure menu.
  5. Search widget now displays a drop box for placing the search structure in, replacing the spinner that was previously there and making the use of the widget much more intuitive.
  6. More restriction options have been added for the Search widget, and those options are now accessible right from the widget.

    -Restricting result set size.

    -Excluding PDB files.
  7. NMR simulation algorithms greatly improved.

    1H: anisotropic effects, ring strain, hydrogen bonding effects, rapid exchange, diastereocenters, heteroaromatics

    13C: alkane improvements, alkene improvements, alkyne improvements, decreased quaternary peak intensities, heteroaromatics
  8. When atoms are hovered, the enter key will now set the hovered atom’s label to the last typed atom label. Opening a previously typed atom label will set the enter key text to that label.
  9. When bonds are hovered, the arrow keys will orient the bond in the pressed direction from start atom to end atom, rotating the entire molecule it is contained in.
  10. When objects are hovered, pressing the comma key will open that object’s visual specifications formatting window.
  11. Added a visual specification for reactions to set the padding for reaction condition text if that text is centered. When cleaned, reaction arrows will now fit their text based on this padding. Reaction arrows with no text will have a length equal to twice this value; 30px by default.
  12. Added a visual specification for attributes to determine the amount of reduction for font text size in attributes that contain text.
  13. Included a new file specification for MDL connection tables to include/exclude Hydrogen counts.
  14. Added a style sheet to quickly produce 2D graphics for 3D data and scenes.


  1. Fixed issue that caused a flashing of the mouse cursor when using the lasso tool and hovering over shape anchors.
  2. Fixed issue where the close icons weren’t being rendered on tabs on Windows/Linux.
  3. Fixed issue where clicking on a terminal atom didn’t select it.
  4. Atom Label Tool icon has been changed to stick out more.
  5. Fixed bug where nothing happened when deducing the stereochemistry of an ambiguous stereocenter.
  6. Structure cleaning algorithm runtime has been greatly improved when complex embedded rings are present. Previously, this runtime lasted about 30 seconds, it is now instantaneous.
  7. Added more preset templates to the structure cleaning algorithm.
  8. The cleaning of very wide reactions has been greatly improved.
  9. The default reaction constituent buffer has been halved to 20px.
  10. Fixed problem where the File menu would temporarily disappear if reading a file in ChemDoodle that wasn’t recognized.
  11. Fixed issue where rarely a file will be duplicated on the recent files list on Windows.
  12. Delete key properly removes all attribute objects selected, regardless of type.
  13. Radical attributes can now be properly deleted.
  14. Attribute fonts can now be changed properly.
  15. Nudging content with the arrow keys now properly moves attributes.
  16. The quote character is no longer stacked in atom labels.
  17. Pasted molecular properties from the Descriptors submenu in the Structure menu all now paste a title description as well.
  18. Fixed bug where choosing empty colors in the color choosers on Windows/Linux caused errors.
  19. Removed duplicated ChemDoodle Document checkbox in the Windows Filetype Association window.
  20. Fixed NMR SignalSeek widget bug in the peak breakdown that displayed duplicated peak labels.
  21. Heteroatoms that split nuclei are now properly highlighted in breakdowns from the NMR SignalSeek widget.
  22. Shift contributions are now right-aligned to align the decimal points in the shift explanations from the NMR SignalSeek widget.
  23. Fixed 13C NMR shift explanations in the NMR SignalSeek widget.
  24. The NMR SignalSeek widget temperature is now properly described in Kelvins.
  25. Fixed bug in the NMR simulation algorithms where some functional groups were being defined past their bounds.
  26. Bond breakers are now rendered properly.
  27. Bond z-order is now preserved when copying and pasting structures.
  28. Fixed issue where changing the bond stroke styles could not be undone.
  29. Fixed issue where valency warnings were incorrectly displayed on cations.
  30. Fixed issue where files that were opened and changed the size of the page didn’t do so according to the selected viewing scale.
  31. Fixed issue where opening multiple files didn’t immediately perform checks.
  32. Fixed certain checks after using keyboard shortcuts.
  33. Fixed issue where changing tabs may not have reset the out-of-bounds warnings.
  34. ChemDoodle Documents can now be recognized by ChemDoodle even if the extension is changed.
  35. Fixed minor issues related to reading files that do not have the correct extensions.
  36. The Format Atom window is now restricted to 500px in height.
  37. Improved the look of file choosers on Mac OS X.
  38. Improved warning message that is displayed on Windows when open files are locked by another application and cannot be saved.
  39. Greatly improved the rendering of tabs on Windows/Linux.
  40. Fixed bug where tab titles in the Preference window were cutoff on Windows.
  41. Minor graphical and text improvements.