ChemDoodle 3 is a very powerful chemical graphics and publishing environment. We have also invested a lot of effort over the last year in providing a credible and thorough database of elemental data as well as an advanced engine for performing cheminformatics algorithms to power ChemDoodle. While the function of ChemDoodle is still to create beautiful chemical graphics, we intend to grow the ChemDoodle environment to accommodate other tasks. ChemDoodle 3 is a free upgrade for all customers of ChemDoodle 1 or 2.
The dynamic periodic table in ChemDoodle
Elemental Data
ChemDoodle 3 has access to an extensive database of elemental data compiled from published resources. This database allows ChemDoodle to perform many tasks, from filling the dynamic periodic table to deducing covalent bonds to calculating a molecular mass. The data itself can be viewed by opening various data tables in ChemDoodle or by using the dynamic periodic table. This database will continue to grow as ChemDoodle evolves.
 ChemDoodle has access to a thorough elemental database |
 Ionization Energies |
 Isotope Data |
All data within this database is associated with a unit (if not unitless) and the reference source it originated from so you may asses its quality. The entire set of references can be viewed at any time by selecting the References menu item in the Help menu.
Compiled references for all published data and algorithms in ChemDoodle
Cheminformatics Engine
You will notice significant changes to the graphical user interface of ChemDoodle when version 3 is released, but you may not notice the significant amount of work on the underlying engine that manages the data structures. To make the Java application fast, precise and efficient, we completely reengineered how molecules were stored and manipulated. It is now faster than ever to handle a large number of molecules on screen all at once.
Along with this improved system, we have been steadily including many published algorithms in cheminformatics. Most of these algorithms have to do with creating graphics, such as ring perception and structure depiction. But also, there is growing number of descriptors that ChemDoodle can generate from structures. Most of this output can be calculated for lassoed content via the Properties widget. Noting that the goal of ChemDoodle is to produce beautiful chemical graphics, it is not very essential for it to perform advanced cheminformatics tasks. In my understanding, a user may draw a molecule and wish to see the monoisotopic mass, but he or she is less likely to want to use ChemDoodle to do QSAR studies, as the user interface is based on a virtual sheet of sketching paper rather than a spreadsheet one would need for more robust cheminformatics. However, we would not like to see these advancements go to waste, and we intend to take full advantage of them by extending the ChemDoodle environment.
The Properties widget calculates and displays information on lassoed molecules
Extending the ChemDoodle Environment
Currently under development are several extensions to ChemDoodle that perform functions separate from 2D graphics. Several are experimental ideas, but the two main ones are a 3D graphics environment and a cheminformatics system. As with all our products, we will support Windows, Mac OSX and Linux.
We are very interested in 3D graphics, as can be seen with our 3D ChemDoodle Web Components library. We are also working on a 3D chemical graphics package and modeler. The graphics will be hardware accelerated and OpenGL based. Therefore, the ChemDoodle environment will be the complete answer for anyone looking to generate any kind of chemical graphics.
The database and cheminformatics system have proven extremely valuable to our development team, allowing us to perform large bulk scripts and to generate other forms of data, such as the Javascript ElementalData content that is used by the ChemDoodle Web Components. Since ChemDoodle’s use of the database and cheminformatics engine is quite simple, we would like to allow access from a more in-depth informatics application. We have begun work on a new spreadsheet based product that will perform advanced cheminformatics functionality including bulk scripts, interfaces to databases like PubChem and the Protein Data Bank and powerful graphing and visualization capabilities. In the end, we intend for this product to aid in education, QSAR studies and drug discovery.