NEEMP:Modes - Revision history

Francesco: /* Validation mode */

2016-06-29T14:02:07Z

Validation mode

← Older revision		Revision as of 14:02, 29 June 2016
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	To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required for the generation of the charge correlation graphs and the quality assessment reports (see [[NEEMP:Reports \| here]]).		To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out-file filename</code> option. As describe in the next section this file is required for the generation of the charge correlation graphs and the quality assessment reports (see [[NEEMP:Reports \| here]]).

	For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.		For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.

Francesco: /* Quality validation */

2016-06-29T08:07:05Z

Quality validation

← Older revision		Revision as of 08:07, 29 June 2016
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	To assess the quality of the EEM parameters on a different set than one they were based on, '''NEEMP''''s <code>quality</code> mode can be called.		To assess the quality of the EEM parameters on a different set than one they were based on, '''NEEMP''''s <code>quality</code> mode can be called.

	Required input files are: ''EEM parameters'' (passed as argument of option <code>--par-file</code>) and a ''new set of molecular structures'' ~~(argument of <code>--sdf-file</code>)~~ for which ''ab-initio charges'' have been computed (~~argument~~ of <code>--chg-file</code>).		Required input files are: ''EEM parameters'' (passed as argument of option <code>--par-file</code>) and a ''new set of molecular structures'' for which ''ab-initio charges'' have been computed (arguments of respectively <code>--sdf-file</code> and <code>--chg-file</code>).

Francesco: /* Quality validation */

2016-06-29T08:05:42Z

Quality validation

← Older revision		Revision as of 08:05, 29 June 2016
Line 90:		Line 90:


	To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required ~~to generate~~ the charge correlation graphs and the quality assessment reports (see [[NEEMP:Reports \| here]]).		To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required for the generation of the charge correlation graphs and the quality assessment reports (see [[NEEMP:Reports \| here]]).

	For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.		For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.

Francesco: /* Quality validation */

2016-06-29T08:04:21Z

Quality validation

← Older revision		Revision as of 08:04, 29 June 2016
Line 90:		Line 90:


	To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required to generate the charge correlation graphs and the quality assessment reports (see [[NEEMP:here]]).		To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required to generate the charge correlation graphs and the quality assessment reports (see [[NEEMP:Reports \| here]]).

	For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.		For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.

Francesco: /* Quality validation */

2016-06-29T08:03:48Z

Quality validation

← Older revision		Revision as of 08:03, 29 June 2016
Line 89:		Line 89:
	Required input files are: ''EEM parameters'' (passed as argument of option <code>--par-file</code>) and a ''new set of molecular structures'' (argument of <code>--sdf-file</code>) for which ''ab-initio charges'' have been computed (argument of <code>--chg-file</code>).		Required input files are: ''EEM parameters'' (passed as argument of option <code>--par-file</code>) and a ''new set of molecular structures'' (argument of <code>--sdf-file</code>) for which ''ab-initio charges'' have been computed (argument of <code>--chg-file</code>).

	~~For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.~~

	To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required to generate the charge correlation graphs and the quality assessment reports (see [[NEEMP:here]]).		To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required to generate the charge correlation graphs and the quality assessment reports (see [[NEEMP:here]]).

			For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.

Francesco: /* Quality validation */

2016-06-29T08:02:06Z

Quality validation

← Older revision		Revision as of 08:02, 29 June 2016
Line 90:		Line 90:

	For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.		For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.
	~~<br style="clear:both" />~~

	~~[[File:cross_mode.png \| thumb \| 700px \| center \| '''''Figure 5:''''' ''Quality mode'' output for structures~~ file ''~~examples/set02.sdf~~'', ~~charge file ''examples/charges.~~chg~~'' and parameters set ''examples~~/~~Element~~.~~par'' . Note~~ the ~~block at~~ the ~~bottom where~~ the ~~statistics descriptors for the whole set and for each chemical element are displayed.~~]]		To redirect to a file helpful information about the per-atom ''QM vs EEM'' charge comparison, utilize <code>--chg-stats-out filename</code> option. As describe in the next section this file is required to generate the charge correlation graphs and the quality assessment reports (see [[NEEMP:here]]).

Francesco: /* Quality validation */

2016-06-29T07:51:04Z

Quality validation

← Older revision		Revision as of 07:51, 29 June 2016
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	'''''<u>BASIC USAGE:</u>''''' ''./neemp -m quality --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-file examples/Element.par		'''''<u>BASIC USAGE:</u>''''' ''./neemp -m quality --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-file examples/Element.par

	To assess the quality of the EEM parameters on a different set than one they were based on, '''NEEMP''''s <code>quality</code> mode can be ~~used~~.		To assess the quality of the EEM parameters on a different set than one they were based on, '''NEEMP''''s <code>quality</code> mode can be called.

	Required input files are: ''EEM parameters'' (passed as argument of option <code>--par-file</code>) and a ''new set of molecular structures'' (argument of <code>--sdf-file</code>) for which ''ab-initio charges'' have been computed (argument of <code>--chg-file</code>).		Required input files are: ''EEM parameters'' (passed as argument of option <code>--par-file</code>) and a ''new set of molecular structures'' (argument of <code>--sdf-file</code>) for which ''ab-initio charges'' have been computed (argument of <code>--chg-file</code>).

	For details on the syntax and additional output, see the [[NEEMP:Examples#Example 4 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.		For details on the syntax and additional output, see the [[NEEMP:Examples#Example 8 - Quality validation \| examples]] or [[NEEMP:Options \| option list]] section.
	<br style="clear:both" />		<br style="clear:both" />

	[[File:cross_mode.png \| thumb \| 700px \| center \| '''''Figure 5:''''' ''Quality mode'' output for structures file ''examples/set02.sdf'', charge file ''examples/charges.chg'' and parameters set ''examples/Element.par'' . Note the block at the bottom where the statistics descriptors for the whole set and for each chemical element are displayed.]]		[[File:cross_mode.png \| thumb \| 700px \| center \| '''''Figure 5:''''' ''Quality mode'' output for structures file ''examples/set02.sdf'', charge file ''examples/charges.chg'' and parameters set ''examples/Element.par'' . Note the block at the bottom where the statistics descriptors for the whole set and for each chemical element are displayed.]]

Francesco: /* Coverage validation */

2016-06-29T07:44:25Z

Coverage validation

← Older revision		Revision as of 07:44, 29 June 2016
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	'''''<u>BASIC USAGE:</u>''''' ''./neemp -m cover -sdf-file examples/set01.sdf --par-file examples/Element.par''		'''''<u>BASIC USAGE:</u>''''' ''./neemp -m cover -sdf-file examples/set01.sdf --par-file examples/Element.par''

	[[File:cover_mode.png \| thumb \| 500px \| right \| '''''Figure 4:''''' Percentage of molecules in set ''examples/~~set02~~.sdf'' covered by the displayed parameters set ''examples/Element.par'']]		[[File:cover_mode.png \| thumb \| 500px \| right \| '''''Figure 4:''''' Percentage of molecules in set ''examples/set01.sdf'' covered by the displayed parameters set ''examples/Element.par'']]

	To see how many molecules from the set are covered by the provided parameters, simply pass '''NEEMP''' those two files (options <code>--sdf-file</code> and <code>--par-file</code>). '''''Figure 4''''' shows a close-up from the <code>cover</code> mode output for ''set01.sdf'' and the parameters set ''Element.par'', both present in the ''examples'' directory (for details on the syntax and the complete output, see the [[NEEMP:Examples#Example 7 - Coverage validation \| examples]] or [[NEEMP:Options \| option list]] paragraph)		To see how many molecules from the set are covered by the provided parameters, simply pass '''NEEMP''' those two files (options <code>--sdf-file</code> and <code>--par-file</code>). '''''Figure 4''''' shows a close-up from the <code>cover</code> mode output for ''set01.sdf'' and the parameters set ''Element.par'', both present in the ''examples'' directory (for details on the syntax and the complete output, see the [[NEEMP:Examples#Example 7 - Coverage validation \| examples]] or [[NEEMP:Options \| option list]] paragraph)

Francesco: /* Coverage validation */

2016-06-29T07:38:51Z

Coverage validation

← Older revision		Revision as of 07:38, 29 June 2016
Line 78:		Line 78:
	[[File:cover_mode.png \| thumb \| 500px \| right \| '''''Figure 4:''''' Percentage of molecules in set ''examples/set02.sdf'' covered by the displayed parameters set ''examples/Element.par'']]		[[File:cover_mode.png \| thumb \| 500px \| right \| '''''Figure 4:''''' Percentage of molecules in set ''examples/set02.sdf'' covered by the displayed parameters set ''examples/Element.par'']]

	To see how many molecules from the set are covered by the provided parameters, simply pass '''NEEMP''' those two files (options <code>--sdf-file</code> and <code>--par-file</code>). '''''Figure 4''''' shows a close-up from the <code>cover</code> mode output for ''set01.sdf'' and the parameters set ''Element.par'', both present in the ''examples'' directory (for details on the syntax and the complete output, see the [[NEEMP:Examples#Example 2 - Coverage validation \| examples]] or [[NEEMP:Options \| option list]] paragraph)		To see how many molecules from the set are covered by the provided parameters, simply pass '''NEEMP''' those two files (options <code>--sdf-file</code> and <code>--par-file</code>). '''''Figure 4''''' shows a close-up from the <code>cover</code> mode output for ''set01.sdf'' and the parameters set ''Element.par'', both present in the ''examples'' directory (for details on the syntax and the complete output, see the [[NEEMP:Examples#Example 7 - Coverage validation \| examples]] or [[NEEMP:Options \| option list]] paragraph)
	<br style="clear:both" />		<br style="clear:both" />

Francesco: /* Coverage validation */

2016-06-29T07:38:22Z

Coverage validation

← Older revision		Revision as of 07:38, 29 June 2016
Line 78:		Line 78:
	[[File:cover_mode.png \| thumb \| 500px \| right \| '''''Figure 4:''''' Percentage of molecules in set ''examples/set02.sdf'' covered by the displayed parameters set ''examples/Element.par'']]		[[File:cover_mode.png \| thumb \| 500px \| right \| '''''Figure 4:''''' Percentage of molecules in set ''examples/set02.sdf'' covered by the displayed parameters set ''examples/Element.par'']]

	To see how many molecules from the set are covered by the provided parameters, simply pass '''NEEMP''' those two files (options <code>--sdf-file</code> and <code>--par-file</code>). '''''Figure 4''''' shows a close-up from the <code>cover</code> mode output for ''~~set02~~.sdf'' and the parameters set ''Element.par'', both present in the ''examples'' directory (for details on the syntax and the complete output, see the [[NEEMP:Examples#Example 2 - Coverage validation \| examples]] or [[NEEMP:Options \| option list]] paragraph)		To see how many molecules from the set are covered by the provided parameters, simply pass '''NEEMP''' those two files (options <code>--sdf-file</code> and <code>--par-file</code>). '''''Figure 4''''' shows a close-up from the <code>cover</code> mode output for ''set01.sdf'' and the parameters set ''Element.par'', both present in the ''examples'' directory (for details on the syntax and the complete output, see the [[NEEMP:Examples#Example 2 - Coverage validation \| examples]] or [[NEEMP:Options \| option list]] paragraph)
	<br style="clear:both" />		<br style="clear:both" />