NEEMP:Options

This section provides a complete list of NEEMP options.

-h, --help: display help page and exit.
--version: display version information and exit.
--max-threads N: use up to N threads to solve EEM system in parallel.
-m STRING, ;--mode STRING: set STRING mode for NEEMP. Valid choices are: info, params, charges, cross, cover (required).
--sdf-file FILE: define the structural SDF file (required).
--atom-types-by METHOD: classify atoms according to the METHOD. Valid choices are: Element, ElemBond.
--list-omitted-molecules: list names of molecules for which we don't have charges or parameters loaded (mode dependent).

--chg-file FILE: FILE with ab-initio charges (required)(used also by cross mode).
--chg-stats-out-file FILE: output charges statistics to FILE (used also by cross mode).
--kappa-max VALUE: set maximum value for kappa (required).
--kappa VALUE: use only one kappa VALUE for parametrization.
--fs-precision VALUE: resolution for the full scan (required).
--kappa-preset PRESET: set kappa-max and fs-precision to safe values. Valid choices are: small, protein.
-f, ;--fs-only: do not use additional accuracy improvement.
--par-out-file FILE: output the parameters to FILE.
-d METHOD, ;--discard METHOD: perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.
-s STAT, ;--sort-by STAT: sort solutions by STAT. Valid choices are: R, R2, spearman, RMSD, D_max, D_avg.
--limit-iters COUNT: set the maximum number of iterations for discarding.
--limit-time HH:MM:SS: set the maximum time for discarding in format hours:minutes:seconds.
--check-charges: warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).