In ChemDoodle 2, lines, arcs and reactions were all distinct objects. This was a simplistic and straightforward system meant to be easy to learn. In essence, these objects were merely different graphical classes and there were no semantics for reaction data. ChemDoodle 3 contains an entire system for building and managing reactions. We intend to grow this system into a very powerful reaction informatics system. Developing this system required more advanced control over the graphical components of reaction objects, so we have rebuilt our arrow system as well as merged the previously discrete line, arc and reaction objects into a single unified object. Conveniently, we believe this change has made creating the objects more intuitive as well as more powerful. ChemDoodle 3 is a free upgrade for all customers of ChemDoodle 1 or 2. We hope to begin beta testing late next week.
Arrow Toolbar
The New Reaction Object
Lines, arcs and reactions have been merged into a single, powerful reaction object. At any time, a line can be converted into an arc, have arrows added to it, or built into a reaction. These conversions are done through intuitive graphical user interface controls. To begin, if you place a line or an arc, a third anchor now appears at its midpoint. The arc angle can then be changed by clicking and dragging this midpoint, as is shown in the following animation.
Drag to edit arc angle
Going further, arrows can be added to either end of this object and they can be fully edited. To make things even easier, there is a new Arrow toolbar for quickly building arrows. You can specify the start arrow, end arrow and connector style, and then choose any of the object buttons to begin placement. Notice the new arrow decorations, such as the “no go” cross and slashes. These styles will persist with the object regardless of the arc angle.
 Start Arrow Options |
 Connectors |
 End Arrow Options |
Everything about this new object is customizable as can be seen in the Preferences menu.
Reaction Preferences
The Reaction Building System
In other applications, reactions are implicitly built by placing molecules around an arrow. Molecules to the left are reactants and molecules to the right are products. While simplistic, this system fails when building complex reaction schemes and trying to precisely create a reaction data file can be a nightmare (e.g. how do you accurately create a complex MDL RDfile?). The reaction building system in ChemDoodle 3 will allow you to explicitly create reactions and reaction schemes, and several reaction data formats will be provided for input/output.
In the Reaction menu, selecting the Edit Reaction… menu item will open the reaction builder interface for a selected reaction. It is a drag and drop interface. All molecules on the page are displayed in the bottom tray, while the left and right trays correspond to the constituent reactants and products respectively. Just drag and drop molecules from the bottom tray into the other two to set up the reaction. Once a molecule has been placed, it will be grayed out in the bottom tray and no longer selectable. You can transfer a placed molecule between the products and reactants by dragging between the side trays or remove it from the reaction completely by placing it back in the bottom tray.
Reaction Builder Interface
The same text editors for adding text above and below the reaction arrow from ChemDoodle 2 are also present here. Just click Done to set everything up. You will notice that ChemDoodle 3 has automatically added plusses between the reactants and products. However the reaction may not look perfect if it is sprawled all over the Doodle Sheet. To fix this, just select the new Clean function in the Reaction menu to clean it. Initially, the Clean function is only for single reactions, but we will be expanding it to layout entire, complex reaction schemes.
ChemDoodle 3 is an incredible chemical graphics application and contains advanced tools for managing structures, reactions and spectra. Beta testing will begin soon and we can’t wait to hear your reactions!