MarvinBeans package contains cxcalx command line program that performs chemical calculations using calculator plugins. The calculations can be performed in single or batch mode.
You can read its documentation here: http://www.chemaxon.com/marvin/help/applications/calc.html
The available calculations are listed in the following page: http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html
and a simple example is given for every calculation: e.g.: http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html#conformers
For example, if you have an sdf file which contains thousands of molecules and want to calculate the conformers of them, you can run the following command on a command prompt.
C:\>cxcalc -o conformertest.sdf conformers inputmols.sdf
It will result in an output file , conformertest.sdf , which contains the conformers of your input molecules - stored in inputmols.sdf.
If you have any further question, please do not hesitate to contact us.