This section provides a complete list of NEEMP options. NB: NEEMP is case-sensitive, so pay attention to the keywords syntax.
- display help page and exit.
- display version information and exit.
- use up to N threads to solve EEM system in parallel.
- set mode for NEEMP. Valid choices are: info, params, charges, quality, cover (required).
- set optimization method used for calculation of parameters. Valid choices are: lr-full, de (optional).
- define the structural SDF file (required).
- classify atoms according to the METHOD. Valid choices are: Element, ElemBond.
- list names of molecules for which we don't have charges or parameters loaded (mode dependent).
Generic options for mode params
- FILE with ab-initio charges (required)(used also by quality mode).
- output charges statistics to FILE (used also by quality mode).
- set random seed.
- output the parameters to FILE.
- sort solutions by STAT. Valid choices are: R, R2 (default for lr-full), R_w, spearman, RMSD, RMSD_avg (default for de), D_max, D_avg.
Options specific to mode params using LR
- set maximum value for kappa (required).
- use only one kappa VALUE for parametrization.
- resolution for the full scan (required).
- perform discarding with METHOD. Valid choices are: simple and off. Default is off.
- set the maximum number of iterations for discarding.
- set the maximum time for discarding in format hours:minutes:seconds.
Options specific to mode params using DE-MIN
- set population size for optimization method (optional).
- set the maximum number of iterations for optimization method (optional).
- set number of threads for optimization method (optional).
- apply local minimization on parameters. Valid choices: 0 (off), 1 (result), 2 (during evolving), 3 (at the initial population).
Options specific to mode charges
- FILE with EEM parameters (required)(used also by quality mode)
- output charges to FILE (required)