NEEMP:Examples

This section shows several use case examples. All of them use only data from examples directory.

NB: NEEMP is case-sensitive. Please follow carefully this section for insight on the correct syntax. Additional information can be found here.

Example 1 - Info mode

./neemp -m info --atom-types-by ElemBond --sdf-file examples/set01.sdf

Prints information about training set, group atoms according to chemical element and bond order.

Figure 5: Output for the Info mode. For more information on this mode refer to Info mode section.

Example 2 - Cover mode

./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/Element.par --atom-types-by Element

Calculate coverage of supplied EEM parameters and molecules set.

Figure 6: Complete output for the Cover mode summarizing information about the input files, molecules set composition and coverage. For more information on this mode refer to Cover mode section.

Example 3

./neemp -m charges --sdf-file examples/set01.sdf --par-file examples/ElemBond.par --chg-out-file eem_charges --max-threads 8

Compute EEM charges and store them into the file eem_charges. Use up to 8 threads for computation.