Example #1

In this basic example we implement a method that returns the string "Hello <molecule name>!", where <molecule name> is the name of the molecule generated by ChemAxon's S2N (Structure to Name) converting tool. The following code will do this:

Having compiled this code, pack the created class file(s) into a Java Archive (JAR) file. All Java IDEs can export Java files in a JAR file. In Eclipse it can be done by the File > Export menu item.

Fig. 1 JAR export window in Eclipse

After creating the JAR file, open MarvinSketch. Please note that version 5.6 or later is required. Select Edit > Preferences > Services from the menu. Then press the + button to add a new service.

Fig. 2 Adding new services via the Preferences window in MarvinSketch

To add a new service then proceed to press the Accept button. It will appear in the list of services.

Fig. 3 Adding new services to the list of services

As a result of these steps the new service will be available from the Tools > Services menu.

Fig. 4 Looking up the new services in MarvinSketch

Finally, to use the new service, select the Tools > Services > Hello1 menu item with an input molecule on the canvas. The calculation result appears in a new dialog.

Fig. 5 Calculation result shown in a new dialog

Now let's extend this example by addig a new method to the Hello.java class and adding Alias and Description annotations to it. Thus the new code will be:

Create a JAR file as above and name it hello2.jar. Call the new method (as a local service) from this JAR file. The name of the service, the description and the parameter names will be automatically filled during the setup.

Fig. 6 Setting us the new service from the JAR source

A result example in this case is:

Fig. 7 Result window showing the new service in action

Note that the result molecule format can be modified on the result display panel. Try it !

Example #2

The next example will be a bit more complicated as we will implement some microspecies related calculations. We want to

• calculate the major microspecies at a given pH;

• calculate microspecies count at a given pH;

• generate HTML report about the calculations.

The following code will do that:

Pack the MicrospeciesCalculator class into a JAR file as already described (mscalc.jar). Add all methods as local services to the service list. Finally you should have a list like follows:

The result of running the MMS calculation is the major microspecies molecule at a given pH.

Fig. 8. Calculated major microspecies as a result of the MMS calculated

The MSReport calculation generates the source code of an HTML page and returns it as a string. The HTML page is then rendered on the fly by the result display component.

Fig. 8 The MS report calculation results

Changes made on the molecule in MarvinSketch will be automatically updated on the results display (both structure and results), if the Calculate Automatically option is enabled.