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ChemDoodle 3.2 has been released

ChemDoodle 3.2 has been released! This upgrade is free of charge to our existing customers. Just open up ChemDoodle and follow the directions to automatically update ChemDoodle.

ChemDoodle 3.2 is a significant update containing major new features and improvements. Notable features include orbital objects, the expansion of condensed formulas in atom labels (allowing for the automatic proper handling of condensed formulas by the Properties widget and other algorithms), a more robust abbreviations system (that can be used in atom labels for all atom models). Integration with the ChemSpider database now allows users to access structures via the MolGrabber.

Notable improvements include an evolution of the ChemDoodle rendering engine for improved rendering and performance as well as full control over the low level graphics settings, a new table layout for the Properties widget that conveniently updates when drawing a single molecule, and full compatibility to directly paste scalable vector graphics into the entire Microsoft Office suite on Windows and Mac OS X.


Orbitals can now be added to structures. These are 2D graphics that can be attached to atoms or bonds or can be standalone. A gradient is used to give them a 3D appeal. Supported are atomic orbitals (s, p, d, f), hybrid orbitals (sp lobe, sp3), and bonding orbitals. Orbitals can also be read from and written to ChemDraw files. There are two visual specifications for orbitals in the Preferences window under the Visuals tab under the Shapes subtab: Length Multiplier ‚Sets the default size of orbitals relative to the current bond length; Stroke Shaded Lobes, Sets whether or not outlines are drawn around shaded orbital lobes.
The graphics engine in ChemDoodle has seen a significant upgrade and graphics rendering has significantly improved. Performance has also been significantly improved. Graphics controls for low level rendering are now exposed in the Preferences window under the Advanced tab. Change these only if necessary to favor speed or to affect how graphics are rendered. These rendering options will only affect devices with resolutions, such as bitmap images and monitors; scalable vector graphics remain perfect and unchanged.
Added a new option to simulate soft clipping for bitmap images in the Advanced tab of the Preferences window. This makes Recessed bonds look much nicer.
A new system for expanding condensed formulas and abbreviations in atom labels to their all atom models. There are several features that benefit from this:
All calculations based on structures (properties, NMR spectra, etc.) will first expand the molecule, so proper results will now be obtained when using condensed formulas.
Atom label errors are improved. ChemDoodle will alert you of unknown tokens and will properly evaluate atom valencies. For instance, a terminal label of CH3 will be approved while a terminal label of CH4 will not.
Abbreviations can now be expanded. So Ph, Et, COOH, etc. will be properly expanded to the corresponding all atom models and can be used in condensed formulas. You can add your own custom abbreviations.
Atom label token stacking is more intelligent and will now stack based on token groups. For instance, the label CH2CH2COOCH2CN will stack as (CH2)(CH2)(COO)(CH2)(CN).
Complex shorthand notations are also supported, so C(CH3)3 will be expanded as a t-butyl fragment and CPh3 will be expanded as a triphenylmethyl fragment.
The ChemSpider database has been integrated into the MolGrabber widget.
The Properties widget now has a second mode that will be automatically activated when a single molecule, and only a single molecule, is being edited in the current document. The display will change to a table that will list the most important properties and will automatically update if allowed. There is a new checkbox at the top of the widget to disable automatic updating of the data, which will be useful for less powerful computers.
Scalable vector graphics can now be directly pasted into the entire Microsoft Office suite, including Powerpoint and Excel.
Added a Save Selection as Image‚ menu item to the File menu to quickly save just the selected content to an image.
Added a Copy As submenu to the Edit menu to quickly copy selected structures as various datatypes at maximum compatibility on the system clipboard.
Added a new drag erase gesture when using the Eraser tool. Press and drag over any objects to be removed and they will be highlighted. Release the mouse to delete all highlighted objects. If you drag over a previously highlighted object, it will be unhighlighted.
ChemDoodle Web Components v3.1 is now included. The ChemDoodle Web Component generator has been updated accordingly. New default sizes are provided for standard iOS device resolutions.
Molar Refractivity can now be calculated for structures.
Some widget settings are now saved in the workspace, including the last selected widget and the database choice in the MolGrabber widget.
The MolGrabber widget now provides a direct link to the chosen database’s website for the selected molecule. Press the Show Associated Data button and the top item will show the database’s compound id. Click on the compound id to visit the webpage for that molecule.
Menu items for unrepresented keyboard shortcuts have been added: Flip Bond, Align Bond and Add Attribute.
A new keyboard shortcut for adding attributes to hovered objects, Shift-A.
Added a new visual specification to set whether the second bond line in double lined bonds are shrunken when next to an atom label.
Radial gradient rendering is greatly improved for shapes to better portray 3D appeal.
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