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

-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, cross, cover (required).

-p, --params-method METHOD

set optimization method used for calculation of parameters. Valid choices are: lr-full, lr-full-brent, de, gm (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 or User.

--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 cross mode).

--chg-stats-out-file FILE

output charges statistics to FILE (used also by cross mode).

--random-seed

set random seed (used by DE, GM and iterative discarding LR)(optional).

--par-out-file FILE

output the parameters to FILE.

-s, --sort-by STAT

sort solutions by STAT. Valid choices are: R, R2, R_w, spearman, RMSD, RMSD_avg, D_max, D_avg. We strongly advise using R_w for method DE.

--check-charges

warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).

Options specific to mode params using linear regression

--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.

-d, --discard METHOD

perform discarding with METHOD. Valid choices are: iterative, 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 optimization methods (GM, DE)

--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 cross mode)

--chg-out-file FILE

output charges to FILE (required)