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 6: 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 7: 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 - Charges mode

./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.

For more information on this mode and its output, refer to Charges mode section.

For details on eem_charges output file, see CHG file paragraph, as the format is the same. The only different regards the third column, since in this case the EEM charges are listed in place of the ab-initio charges.

Example 4 - Cross mode

./neemp -m cross --sdf-file examples/set02.sdf --chg-file examples/charges.chg --par-file examples/Element.par --chg-stats-out stats --atom-types-by Element 2> warns > log

Perform cross-validation of EEM parameters for atoms grouped by element only. Save standard output into the file log and warnings into the file warns. Moreover outputs charge statistics for each molecule into the file stats.

For more information on this mode click here.

Figure 8: Close-up from stats file. Along with statistics for each molecule, ab-initio charges (3rd column), EEM charges (4th column) and their difference (5th column) are also printed out. NB: this type of output file can be obtained via params mode as well (click here)

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Example 5 - Params mode

./neemp -m params --sdf-file examples/set01.sdf --chg-file examples/charges.chg --par-out-file new_parameters.par --chg-stats-out-file stats --kappa-preset small

Performs EEM parametrization, saves parameters into the file new_parameters.par, outputs charge statistics for each molecule into the file stats. Use default settings for k search for small molecules. No discarding is used.

NB: the parameters set file new_parameters.par presents the same identical format and layout as described here.

Refer to the parametrization paragraph for a thorough description of the mode.

Example 6 - Params mode k search

./neemp -m params --sdf-file examples/set01.sdf --chg-file examples/charges.chg --kappa-max 1.0 --fs-precision 0.02 --fs-only --sort-by RMSD -vv

Similar to previous example, use custom range for k. Select best parameters according to the RMSD with no iterative refinement (since it can be used only if sorting by R is used). Print k search progress.

Reference to parametrization paragraph if necessary

Figure 9: Detailed view of the parametrization settings from the execution of the above command. In particular note the usage of a different evaluating statistics (RMSD) and the custom range for the k search.	Figure 10: Abridged output for the k search progress. For each k value a set of parameters is generated and evaluated. In this particular instance, the parameters set with the lowest RMSD value is chosen.

Example 7 - Params mode simple discard

./neemp -m params --sdf-file examples/set01.sdf --chg-file examples/charges.chg --kappa-preset small --discard simple -v --check-charges

Perform simple discarding, print its progress. Issue warning about molecules with abnormal values of statistical descriptors.

Figure 8: Close-up from stats file. Along with statistics for each molecule, ab-initio charges (3rd column), EEM charges (4th column) and their difference (5th column) are also printed out. NB: this type of output file can be obtained via params mode as well (click here)

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Example 8 - Params mode iterative discard

./neemp -m params --sdf-file examples/set01.sdf --chg-file examples/charges.chg --kappa-preset small --discard iterative -v --limit-iters 10000 --limit-time 2:30:00

Perform iterative discarding, limit its duration to either 10000 iterations or 2 hours and 30 minutes, whichever is reached first

Reference to parametrization paragraph if necessary

Example 9 - Params mode tabu list

./neemp -m params --sdf-file examples/set01.sdf --chg-file examples/charges.chg --kappa-preset small --discard iterative -v --limit-iters 10000 --tabu-list 0.25

During iterative discarding, try each molecule again after at least 0.25x number of molecules in set01 iterations at earliest.

reference to parametrization paragraph if necessary