Isotope List Editing

If you use a custom isotopes.data file, you must recreate the file when upgrading your Marvin application.

MarvinSketch from the Marvin Beans package refers to the same relative path to access the isotopes list.

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. Download and open isotopes.txt or elements.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. Refresh isotopes.txt or elements.txt:

    • Marvin Beans:

      1. Copy the file to the user_home/chemaxon/ folder

      2. Overwrite chemaxon/isotopes.txt or chemaxon/elements.txt inside the ChemAxon-core.jar. ChemAxon-core.jar is a compressed archive file that you can extract/pack with any zip (un)compressor tool.

Old element and isotopic data:

  1. elements2005.txt

  2. isotopes2009.txt

  3. elements2013.txt

  4. isotopes2013.txt

Obsolete information for versions before 14.7.28:

All isotopes are listed in the binary file: chemaxon/isotopes.data , a compressed file which stores isotopes.txt in a heavily optimized versioned format.

To add or edit isotopes you can alter isotopes.txt source file found in the build subdirectory of the Marvin package.

To encode source file (isotopes.txt), use the IsotopeCompiler tool that creates a new copy of isotopes.data from the given source file.

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 the 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 or elements.zip:

  • Marvin Beans:

1. Copy the file to the user_home/chemaxon/ folder
2. Overwrite chemaxon/isotopes.data or chemaxon/elements.zip inside the chemaxon-core.jar. Chemaxon-core.jar is a compressed archive file that you can extract/pack with any zip (un)compressor tool.