Instantiate the plugin object

Calculator Plugin classes are placed in the chemaxon.marvin.calculations package. First import the necessary classes:

Instantiate a new ElementalAnalyserPlugin object with its default constructor:

Set the parameters of the calculation

After creating the ElementalAnalyserPlugin object the parameters of the calculation can be set with plugin specific setter methods. The precision of the results can be set with the setDoublePrecision(int) method:

Set the input molecule

All calculator plugins take a molecule (a Molecule object) as input, and perform the calculation on one molecule at a time. The input molecule can be set with the setMolecule(Molecule) method:

Run the calculation

To run the calculation, the run() method of the plugin should be invoked:

Get the results

It is plugin specific how results of the calculation can be retrieved. ElementalAnalyserPlugin can return several kinds of results, some of these are:

• mass and exact mass

  double mass = plugin.getMass();

  double exactMass = plugin.getExactMass();

• count of atoms and count of all atoms

  // the number of all atoms in the molecule

  int atomCount = plugin.getAllAtomCount();

  // carbon atom count

  int countOfC = plugin.getAtomCount(6);

  // carbon-14 isotope count

  int countOfC14 = plugin.getAtomCount(6, 14);

• formula

  String formula = plugin.getFormula();

• composition

  String composition = plugin.getComposition();

In the file ElementalAnalyserPluginExample.java a complete code example can be found which uses the code parts above. It reads input molecules from a file given as command line parameter and displays the results. The input file example_mols.sdf contains the chemical structures shown below:

To compile the example, MarvinBeans.jar has to be referenced in the CLASSPATH. After compiling the example can be run from command line like this:

  java ElementalAnalyserPluginExample [molFile]

For example:

The output is:

CC(=O)OC(CC(O)=O)C[N+](C)(C)C
  formula: C9H18NO4, mass: 204.2435, exact mass: 204.123583069
  number of atoms (32): C (9), C-14 (0)
  composition: C (52.93%), H (8.88%), N (6.86%), O (31.33%)

OC1[14CH]=CC=C(C1O)C(O)=O
  formula: C7H8O4, mass: 158.1286, exact mass: 158.045500732
  number of atoms (19): C (7), C-14 (1)
  composition: C (54.43%), H (5.1%), O (40.47%)

NCC(=O)COP(O)(O)=O
  formula: C3H8NO5P, mass: 169.0731, exact mass: 169.014008883
  number of atoms (18): C (3), C-14 (0)
  composition: C (21.31%), H (4.77%), N (8.28%), O (47.32%), P (18.32%)

CCN1[14CH]=[NH+]C2=C(N)[NH+]=[14CH]N=[14C]12
  formula: C7H11N5, mass: 171.1734, exact mass: 171.111171341
  number of atoms (23): C (7), C-14 (3)
  composition: C (52.61%), H (6.48%), N (40.91%)
 

Setting parameters and getting the results for MajorMicrospeciesPlugin

For setting the parameters method setpH(double) is used. Major microspecies at the specified pH will be generated.

 mmsPlugin.setpH(7.4); // major microspecies generation at pH = 7.4

For getting the results method getMajorMicrospecies() is used. It returns a Molecule object.

 Molecule majorms = mmsPlugin.getMajorMicrospecies();

Setting parameters and getting the results for TPSAPlugin

For setting the parameters method setpH(double) is used.

For getting the results method getSurfaceArea() is used.

Setting parameters and getting the results for logDPlugin

There are quite a few parameters that can be set for logD calculation. These are: Cl- ion concentration, Na+/K+ ion concentration, pH (for calculating logD at a single pH value), pH lower limit, pH upper limit, and pH step size.

The results of the logD calculation are returned by the method getlogDs(), the pH values are returned by the method getpHs(). Both methods return a double array (double[]), the logD array contains the logD values for corresponding pH-s in the pH array.

Getting the results for IUPACNamingPlugin

For getting the results method getPreferredIUPACName() is used, it returns the preferred IUPAC name. IUPACNamingPlugin has also the method getTraditionalName() to return the traditional name of the molecule.

The complete code example can be found in the file PluginExample.java. After compiling the example can be run from command line:

java PluginExample [molFile]
 

Example:

The result is written to the results.sdf file.

The above examples can also be run by run.sh shell script (Linux/UNIX) or RUN.BAT batch file (Windows).