Editing NEEMP:Options

This section provides a complete list of '''NEEMP''' options. '''NB: NEEMP is case-sensitive''', so pay attention to the keywords syntax.

'''Generic options'''

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

'''Generic options for mode params'''

:;<code>--chg-file FILE</code>
::FILE with ab-initio charges (required)(used also by quality mode).
:;<code>--chg-stats-out-file FILE</code>
::output charges statistics to FILE (used also by quality mode).
:;<code>--random-seed</code>
::set random seed.
:;<code>--par-out-file FILE</code>
::output the parameters to FILE.
:;<code>-s</code>, <code>--sort-by</code> <code>STAT</code> 
::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'''

:;<code>--kappa-max VALUE</code>
::set maximum value for kappa (required).
:;<code>--kappa VALUE</code>
::use only one kappa VALUE for parametrization.
:;<code>--fs-precision VALUE</code>
::resolution for the full scan (required).
:;<code>-d</code>, <code>--discard</code> <code>METHOD</code>
::perform discarding with METHOD. Valid choices are: simple and off. Default is off.
:;<code>--limit-iters COUNT</code>
::set the maximum number of iterations for discarding.
:;<code>--limit-time HH:MM:SS</code>
::set the maximum time for discarding in format hours:minutes:seconds.

'''Options specific to mode params using DE-MIN'''

:;<code>--om-pop-size VALUE</code>
::set population size for optimization method (optional).
:;<code>--om-iters COUNT</code>
::set the maximum number of iterations for optimization method (optional).
:;<code>--om-threads N</code>
::set number of threads for optimization method (optional).
:;<code>--om-polish VALUE</code>
::apply local minimization on parameters. Valid choices: 0 (off), 1 (result), 2 (during evolving), 3 (at the initial population).

'''Options specific to mode charges'''

:;<code>--par-file FILE</code>
::FILE with EEM parameters (required)(used also by quality mode)
:;<code>--chg-out-file FILE</code>
::output charges to FILE (required)