NEEMP:Options

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

Generic 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, --mode MODE
set mode for NEEMP. Valid choices are: info, params, charges, quality, cover (required).
-p, --params-method METHOD
set optimization method used for calculation of parameters. Valid choices are: lr-full, de (optional).
--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).

Generic options for mode params

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

--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).
-d, --discard METHOD
perform discarding with METHOD. Valid choices are: simple and off. Default is off.
--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.

Options specific to mode params using DE-MIN

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

Options specific to mode charges

--par-file FILE
FILE with EEM parameters (required)(used also by quality mode)
--chg-out-file FILE
output charges to FILE (required)