Many of our customers have been requesting that we read in ChemDraw files. I am happy to announce, that with the release of ChemDoodle v1.3.0 (mid-August), ChemDoodle will not only be able to read ChemDraw files, but write them as well.

UPDATE: ChemDoodle v1.3.0 was released on 8/17/08.

ChemDraw has two formats that need to be considered, the ChemDraw Exchange format (cdx) and it’s xml sister (cdxml). The cdx format is a pure binary format (you wont be able to make sense of the objects inside when you open it in a text editor) while the cdxml format is text based and can be coherently read. Both formats are structurally identical and completely describe any group of ChemDraw objects. CambridgeSoft has been urging users to switch to the cdxml format due to its ease of use, but there are some drawbacks to the xml version due to its inherently larger size.

In the past, ChemDoodle utilized OpenBabel to import ChemDraw files. While OpenBabel is a great tool, it did not allow for the conversion of anything other than chemical atoms and bonds. Non-elemental atom labels, special bond types, text, shapes, fonts, colors, document settings and much more were all lost. Now that cdx and cdxml are native ChemDoodle formats (meaning we wrote the readers and writers with ChemDoodle’s API), every last tiny detail in these files is preserved when opened. (It should be noted that mutually exclusive objects are not compatible with this feature, such as multiplets generated in ChemDoodle, but we will be looking into ways to make those objects compatible in the future.) Not only that, but if your journal of choice is having trouble accepting ChemDoodle figures and structures with your manuscript, you may now just save them as ChemDraw files and submit those as well! With the inclusion of this feature, ChemDoodle is perfect for every user, especially students and those working with ChemDraw users who don’t want to pay an outrageous price for a ChemDraw package. ChemDoodle is also perfect for Mac and Linux users where ChemDraw may not be an option.

Now to the proof! The following set of images is of a ChemDraw file submitted by a ChemDoodle user with a complex group of structures. The left image is a screen shot of the file opened in ChemDraw, while the right image is a screen shot of the file opened in ChemDoodle. You will see that differences are almost non-existent. Notice that every last property, from label text, to bond type, to colors, to fonts, to the width of wedge bonds are all exactly preserved. It should be noted that ChemDoodle includes margins on the Doodle Sheet (which are set at half inches on all sides from the cdx file), so the ChemDoodle page is slightly larger. Click on either image to see a larger version.

Additionally, all shapes inclusive to both ChemDraw and ChemDoodle are also read and written properly. The shape system in ChemDoodle has been completely revamped to not only account for more shape properties, but to allow an easy way to manipulate them (described below). These next two images show a large range of these shapes. Left is a screenshot from ChemDraw and right is a screenshot from ChemDoodle. Again, keep in mind ChemDoodle includes page margins on the sheet.

We have covered a very broad range of chemical and non-chemical objects that can now be read and written to in ChemDoodle from ChemDraw’s file formats. We may have missed a few properties, so if you ever try to load your ChemDraw file into ChemDoodle and some objects are not preserved correctly, you are more than welcome to send us the file and we will do our best to account for the differences, if possible.

Lastly, I wanted to mention in addition to this great feature, five new bond types and a multitude of shape properties have been added to ChemDoodle v1.3.0. The new bond types are the wavy bond, the two electron bond, the bold and thin double bond, the quintuple bond and the sextuple bond. The new shape properties are numerous, and you now have the power to select line widths, hash patterns, arrow specifications, fill effects, shadows and much, much more with a simple dialog that appears after selecting the Format Shape menu item in the right-click menu. More buttons for quickly selecting different sets of shape properties have been added to the shapes toolbar. To make things more organized, each group of shape types now shares a very intuitive button group, that when pressed and held, will display a greater selection.

As always, we hope you enjoy ChemDoodle and we look forward to hearing your feedback!