The following code example shows how to use the assign partial charges. The program reads all of the molecules in the input file, assigns partial charges to each based on the selected method (the default is -method mmff94) and writes each charged molecule to the output file.
A description of the command line interface can be obtained by executing the program with the –help argument.
prompt> java AssignCharges --help
will generate the following output:
Simple parameter list Charging options -method : which set of charges to apply input/output options -in : Input molecule -out : Output molecule (usually an oeb)