NEEMP:Options: Difference between revisions

Latest revision as of 14:57, 7 July 2016

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)

@@ Line 10: / Line 10: @@
 ::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, cross, cover (required).
+::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, lr-full-brent, de, gm (optional).
+::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 or User.
+::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).
@@ Line 23: / Line 23: @@
 :;<code>--chg-file FILE</code>
-::FILE with ab-initio charges (required)(used also by cross mode).
+::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 cross mode).
+::output charges statistics to FILE (used also by quality mode).
 :;<code>--random-seed</code>
-::set random seed (used by DE, GM and iterative discarding LR)(optional).
+::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, R_w, spearman, RMSD, RMSD_avg, D_max, D_avg. We strongly advise using R_w for method DE.
+::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.
-:;<code>--check-charges</code>
-::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).
-'''Options specific to mode params using linear regression'''
+'''Options specific to mode params using LR'''
 :;<code>--kappa-max VALUE</code>
@@ Line 43: / Line 41: @@
 :;<code>--fs-precision VALUE</code>
 ::resolution for the full scan (required).
-:;<code>--kappa-preset PRESET</code>
-::set kappa-max and fs-precision to safe values. Valid choices are: small, protein.
-:;<code>-f</code>, <code>--fs-only</code>
-::do not use additional accuracy improvement.
 :;<code>-d</code>, <code>--discard</code> <code>METHOD</code>
-::perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.
+::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.
@@ Line 54: / Line 48: @@
 ::set the maximum time for discarding in format hours:minutes:seconds.
-'''Options specific to mode params using optimization method DE-MIN'''
+'''Options specific to mode params using DE-MIN'''
 :;<code>--om-pop-size VALUE</code>
@@ Line 68: / Line 62: @@
 :;<code>--par-file FILE</code>
-::FILE with EEM parameters (required)(used also by cross mode)
+::FILE with EEM parameters (required)(used also by quality mode)
 :;<code>--chg-out-file FILE</code>
 ::output charges to FILE (required)