In all chemical drawing applications, identifiers are logically associated with an object, but not always spatially. Sometimes, identifiers may be misplaced, especially when structures are moved. Therefore problems occur when the initial logical association is ambiguous or forgotten, such as when opening an old file or opening one given to you by someone else. I guess in this way a single atom can be labelled as “cis” by itself, and also maybe “trans” as well. Also equally annoying is when these identifiers cannot be moved, being stuck on a structure in a position that is not aesthetically pleasing or obstructing some other object. The figure below shows how these problems can appear in other applications. In ChemDoodle v1.4, soon to be released, we introduce a new identifier object that can be associated with chemical objects. These new objects are not immobile and they are not spatially free, they are just right. In addition to this spatial restriction, when either an identifier or a chemical object is focused (bringing the mouse pointer over it in an appropriate drawing mode), any associations will be displayed. Two examples of these identifiers are atom charges and radicals in ChemDoodle; the way these objects worked in previous versions of ChemDoodle is very similar to how identifiers work as a whole.

UPDATE: ChemDoodle v1.4.0 was released on 12/19/08.

All chemical algorithms in ChemDoodle from now on will place results in identifiers associated with structures. Some examples are the new stereochemistry functions introduced in this version. After selecting an appropriate convention, either R/S identifiers will be associated with chiral atoms or E/Z (also cis/trans) will be associated with double bonds. The identifier objects that are associated with the atoms and bonds are placed in positions where object overlap is minimal, but they can be moved afterwards only within a specific radius. When moving atoms or bonds, any associated identifiers will follow. Also upon focus, any object will display its associations as demonstrated in the following screenshot where both charge and number identifiers are associated with atoms. When focused, the Sodium atom is shown to be associated with both a + charge and the number id 2.

The radius used to bind the identifiers is variable. In the Preferences window, under Visuals and under Identifiers there is an attribute for Allowed Distance. By altering this setting, you may increase the distance and move identifiers further away, or more tightly bind them to their associated chemical object.

Lastly, apart from the bulk identifiers ChemDoodle can assign, you may also add your own identifiers to chemical objects. This is done simply by focusing the object in question, right-clicking, and selecting the Add Identifier menu item. Just enter the identifier value to be displayed and a unique name, and the identifier will be placed as shown below. Using the same name on multiple identifiers will allow you to do more advanced queries and functions later. Identifier properties such as color and font can be altered by double-clicking on them in an appropriate mode or right-clicking on them and selecting the Format Identifier menu item.

This new system of using Identifier objects to display information that is both logically and spatially associated with a given chemical object is both convenient and necessary. As with all of our development, we aim to produce a chemical drawing tool that is far more intuitive than what is available. Expect ChemDoodle v1.4 to be released very shortly. We have delayed its release date a few weeks to thoroughly test the program, as well as simultaneously release new tutorial videos demonstrating some of the new features. We strive to only release the most high-quality products. As always, if you have any ideas, comments or suggestions, please leave a post in the forums or email us.