Isotope list editing

All isotopes are listed in a binary file: chemaxon/isotopes.data. MarvinSketch reads it by startup. It is the encoded/compressed version of isotopes.txt. The file itself is a compressed file which stores the data in a heavily optimized versioned format. The source file (isotopes.txt) can be found in the build subdirectory of the Marvin package. You can add or edit the isotopes by altering isotopes.txt. To encode source file (isotopes.txt), use IsotopeCompiler tool that creates a new copy of isotopes.data from the given source file. This tool is bundled with both Marvin Beans and Marvin Applets packages. It is wrapped into isotopescomp.jar in the build subdirectory.

If you use a custom isotopes.data file, please note that, you have to recreate the file when upgrading your Marvin application!

Marvin applets reads the precompiled isotopes list from chemaxon/isotopes.data location from the marvin directory. MarvinSketch from the Marvin Beans package refers to the same relative path to access the isotopes list. But - in this case - the path indicates the location of the file inside MarvinBeans.jar (or jchem.jar by JChem package). You can find "MarvinBeans.jar" in the lib subdirectory of Marvin Beans package.

The following values are in the tab-separated columns:

• Atom number
• Number of neutrons
• Mass (exact mass of the isotope, preferably at least 5 decimal places)
• Abundance (values normalized to the most abundant natural isotope; main isotope - 100.00, artificial isotope - 0)

To add a custom isotope:

1. Open build/isotopes.txt.
2. Edit (or copy) a line next to the other isotopes of the given atom number. Fill in the other data. Save the file.
3. Regenerate isotopes.data: enter into the build directory and type the following command:

   java -jar isotopescomp.jar isotopes.txt

   The output will be isotopes.data in the same directory.
4. Refresh isotopes.data:
   • Marvin Applets: Overwrite old isotopes.data with the new one in the chemaxon subdirectory of the Marvin Beans package.
   • Marvin Beans: There are two ways to replace the isotopes.data file. You can copy the file to the user_home/chemaxon/ folder or you can overwrite chemaxon/isotopes.data inside the MarvinBeans.jar (or jchem.jar by JChem package). MarvinBeans.jar is actually a compressed archive file that you can extract/pack with any zip (un)compressor tool. Consult with the manual of your (un)compressor tool how to update certain file in an existing zip file.