NEEMP:Options - Revision history

Francesco at 14:57, 7 July 2016

2016-07-07T14:57:29Z

Francesco at 06:27, 28 June 2016

2016-06-28T06:27:43Z

← Older revision		Revision as of 06:27, 28 June 2016
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	::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).		::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>		:;<code>--kappa-max VALUE</code>
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	::set the maximum time for discarding in format hours:minutes:seconds.		::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>		:;<code>--om-pop-size VALUE</code>

Francesco at 12:17, 27 June 2016

2016-06-27T12:17:02Z

← Older revision		Revision as of 12:17, 27 June 2016
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	::set the maximum time for discarding in format hours:minutes:seconds.		::set the maximum time for discarding in format hours:minutes:seconds.

	'''Options specific to mode params using optimization ~~methods (GM,~~ DE)'''		'''Options specific to mode params using optimization method DE-MIN'''

	:;<code>--om-pop-size VALUE</code>		:;<code>--om-pop-size VALUE</code>

Francesco at 12:16, 27 June 2016

2016-06-27T12:16:17Z

@@ Line 64: / Line 64: @@
 :;<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'''

Francesco at 15:56, 20 June 2016

2016-06-20T15:56:34Z

@@ Line 35: / Line 35: @@
 ::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).
 :;<code>--kappa-max VALUE</code>
@@ Line 44: / Line 45: @@
 :;<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>
+:;<code>-f</code>, <code>--fs-only</code>
 ::do not use additional accuracy improvement.
-:;<code>-d METHOD</code>, ;<code>--discard METHOD</code>
+:;<code>-d</code>, <code>--discard</code> <code>METHOD</code>
 ::perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.
 :;<code>--limit-iters COUNT</code>
@@ Line 52: / Line 53: @@
 :;<code>--limit-time HH:MM:SS</code>
 ::set the maximum time for discarding in format hours:minutes:seconds.
 '''Options specific to mode charges'''

Francesco at 15:19, 20 June 2016

2016-06-20T15:19:30Z

← Older revision		Revision as of 15:19, 20 June 2016
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	:;<code>--max-threads N</code>		:;<code>--max-threads N</code>
	::use up to N threads to solve EEM system in parallel.		::use up to N threads to solve EEM system in parallel.
	:;<code>-m ~~STRING~~</code>, ;<code>--mode ~~STRING~~</code>		:;<code>-m</code>, <code>--mode</code> <code>MODE</code>
	::set ~~STRING~~ mode for NEEMP. Valid choices are: info, params, charges, cross, cover (required).		::set mode for NEEMP. Valid choices are: info, params, charges, cross, 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).
	:;<code>--sdf-file FILE</code>		:;<code>--sdf-file FILE</code>
	::define the structural SDF file (required).		::define the structural SDF file (required).
	:;<code>--atom-types-by METHOD</code>		:;<code>--atom-types-by METHOD</code>
	::classify atoms according to the METHOD. Valid choices are: Element, ElemBond.		::classify atoms according to the METHOD. Valid choices are: Element, ElemBond or User.
	:;<code>--list-omitted-molecules</code>		:;<code>--list-omitted-molecules</code>
	::list names of molecules for which we don't have charges or parameters loaded (mode dependent).		::list names of molecules for which we don't have charges or parameters loaded (mode dependent).

	'''~~Options specific to~~ mode params'''		'''Generic options for mode params'''

	:;<code>--chg-file FILE</code>		:;<code>--chg-file FILE</code>
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	:;<code>--chg-stats-out-file FILE</code>		:;<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 cross mode).
			:;<code>--random-seed</code>
			::set random seed (used by DE, GM and iterative discarding LR)(optional).
			:;<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.
			:;<code>--check-charges</code>
			::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).


	:;<code>--kappa-max VALUE</code>		:;<code>--kappa-max VALUE</code>
	::set maximum value for kappa (required).		::set maximum value for kappa (required).
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	:;<code>-f</code>, ;<code>--fs-only</code>		:;<code>-f</code>, ;<code>--fs-only</code>
	::do not use additional accuracy improvement.		::do not use additional accuracy improvement.
	~~:;<code>--par-out-file FILE</code>~~
	~~::output the parameters to FILE.~~
	:;<code>-d METHOD</code>, ;<code>--discard METHOD</code>		:;<code>-d METHOD</code>, ;<code>--discard METHOD</code>
	::perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.		::perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.
	~~:;<code>-s STAT</code>, ;<code>--sort-by STAT</code>~~
	~~::sort solutions by STAT. Valid choices are: R, R2, spearman, RMSD, D_max, D_avg.~~
	:;<code>--limit-iters COUNT</code>		:;<code>--limit-iters COUNT</code>
	::set the maximum number of iterations for discarding.		::set the maximum number of iterations for discarding.
	:;<code>--limit-time HH:MM:SS</code>		:;<code>--limit-time HH:MM:SS</code>
	::set the maximum time for discarding in format hours:minutes:seconds.		::set the maximum time for discarding in format hours:minutes:seconds.
	~~:;<code>--check-charges</code>~~
	~~::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).~~

	'''Options specific to mode charges'''		'''Options specific to mode charges'''

Francesco at 10:31, 30 May 2016

2016-05-30T10:31:14Z

← Older revision		Revision as of 10:31, 30 May 2016
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	This section provides a complete list of '''NEEMP''' options. '''NB: NEEMP is case-sensitive.'''		This section provides a complete list of '''NEEMP''' options. '''NB: NEEMP is case-sensitive''', so pay attention to the keywords syntax.

	'''Generic options'''		'''Generic options'''

Francesco at 10:30, 30 May 2016

2016-05-30T10:30:29Z

← Older revision		Revision as of 10:30, 30 May 2016
Line 1:		Line 1:
	This section provides a complete list of '''NEEMP''' options.		This section provides a complete list of '''NEEMP''' options. '''NB: NEEMP is case-sensitive.'''

	'''Generic options'''		'''Generic options'''

Francesco at 11:54, 28 May 2016

2016-05-28T11:54:12Z

← Older revision		Revision as of 11:54, 28 May 2016
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	::list names of molecules for which we don't have charges or parameters loaded (mode dependent).		::list names of molecules for which we don't have charges or parameters loaded (mode dependent).

	* '''Options specific to mode params'''		'''Options specific to mode params'''

	:;<code>--chg-file FILE</code>		:;<code>--chg-file FILE</code>
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	::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).		::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).

	* '''Options specific to mode charges'''		'''Options specific to mode charges'''

	:;<code>--par-file FILE</code>		:;<code>--par-file FILE</code>

Francesco at 11:53, 28 May 2016

2016-05-28T11:53:48Z

← Older revision		Revision as of 14:57, 7 July 2016
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	::use up to N threads to solve EEM system in parallel.		::use up to N threads to solve EEM system in parallel.
	:;<code>-m</code>, <code>--mode</code> <code>MODE</code>		:;<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>		:;<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>		:;<code>--sdf-file FILE</code>
	::define the structural SDF file (required).		::define the structural SDF file (required).
	:;<code>--atom-types-by METHOD</code>		:;<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>		:;<code>--list-omitted-molecules</code>
	::list names of molecules for which we don't have charges or parameters loaded (mode dependent).		::list names of molecules for which we don't have charges or parameters loaded (mode dependent).
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	:;<code>--chg-file FILE</code>		:;<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>		:;<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>		:;<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>		:;<code>--par-out-file FILE</code>
	::output the parameters to FILE.		::output the parameters to FILE.
	:;<code>-s</code>, <code>--sort-by</code> <code>STAT</code>		:;<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 LR'''		'''Options specific to mode params using LR'''
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	:;<code>--fs-precision VALUE</code>		:;<code>--fs-precision VALUE</code>
	::resolution for the full scan (required).		::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>		:;<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>		:;<code>--limit-iters COUNT</code>
	::set the maximum number of iterations for discarding.		::set the maximum number of iterations for discarding.
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	:;<code>--par-file FILE</code>		:;<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>		:;<code>--chg-out-file FILE</code>
	::output charges to FILE (required)		::output charges to FILE (required)

← Older revision		Revision as of 11:53, 28 May 2016
Line 19:		Line 19:

	* '''Options specific to mode params'''		* '''Options specific to mode params'''
	~~----~~
	;<code>--chg-file FILE</code>		:;<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 cross mode).
	;<code>--chg-stats-out-file FILE</code>		:;<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 cross mode).
	;<code>--kappa-max VALUE</code>		:;<code>--kappa-max VALUE</code>
	:set maximum value for kappa (required).		::set maximum value for kappa (required).
	;<code>--kappa VALUE</code>		:;<code>--kappa VALUE</code>
	:use only one kappa VALUE for parametrization.		::use only one kappa VALUE for parametrization.
	;<code>--fs-precision VALUE</code>		:;<code>--fs-precision VALUE</code>
	:resolution for the full scan (required).		::resolution for the full scan (required).
	;<code>--kappa-preset PRESET</code>		:;<code>--kappa-preset PRESET</code>
	:set kappa-max and fs-precision to safe values. Valid choices are: small, protein.		::set kappa-max and fs-precision to safe values. Valid choices are: small, protein.
	;<code>-f</code>, ;<code>--fs-only</code>		:;<code>-f</code>, ;<code>--fs-only</code>
	:do not use additional accuracy improvement.		::do not use additional accuracy improvement.
	;<code>--par-out-file FILE</code>		:;<code>--par-out-file FILE</code>
	:output the parameters to FILE.		::output the parameters to FILE.
	;<code>-d METHOD</code>, ;<code>--discard METHOD</code>		:;<code>-d METHOD</code>, ;<code>--discard METHOD</code>
	:perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.		::perform discarding with METHOD. Valid choices are: iterative, simple and off. Default is off.
	;<code>-s STAT</code>, ;<code>--sort-by STAT</code>		:;<code>-s STAT</code>, ;<code>--sort-by STAT</code>
	:sort solutions by STAT. Valid choices are: R, R2, spearman, RMSD, D_max, D_avg.		::sort solutions by STAT. Valid choices are: R, R2, spearman, RMSD, D_max, D_avg.
	;<code>--limit-iters COUNT</code>		:;<code>--limit-iters COUNT</code>
	:set the maximum number of iterations for discarding.		::set the maximum number of iterations for discarding.
	;<code>--limit-time HH:MM:SS</code>		:;<code>--limit-time HH:MM:SS</code>
	:set the maximum time for discarding in format hours:minutes:seconds.		::set the maximum time for discarding in format hours:minutes:seconds.
	;<code>--check-charges</code>		:;<code>--check-charges</code>
	:warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).		::warn about molecules with abnormal differences between QM and EEM charges (used also by cross mode).

	* '''Options specific to mode charges'''		* '''Options specific to mode charges'''

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