WebChemistry Wiki - User contributions [en]

NEEMP:Getting started

2016-07-05T13:56:08Z

Krab1k:

'''NEEMP''''s binary and source codes are available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.zip'' file containing all the inputs needed to run the [[NEEMP:Examples | examples]] and get acquainted with the tool. These files include:

* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

* '''set02.sdf''' -- 4443 molecules extracted from LigandExpo (ideal coordinates) with high atomic element complexity (H, C, N, O, S, F, Cl, P, Br) and encoded in MOL V3000

* '''set01.chg''' -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

* '''set02.chg''' -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA

* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only

* '''ElemBond.par''' -- parameters calculated using set01 for atomic types determined by element + maximal bond order

'''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:

<code>~/neemp/$ ./neemp --help</code>

Click on the link to see the complete [[NEEMP:Options | options list]].

NEEMP:Examples

2016-07-05T10:44:02Z

Krab1k:

__NOTOC__

This section shows several use case examples. All of them use only data from ''examples'' directory.

'''NB:''' '''NEEMP is case-sensitive'''. Please follow carefully this section for insight on the correct syntax. Additional information can be found [[NEEMP:Options | here]].

=Example 1 - Training set information=

;./neemp -m info --atom-types-by ElemBond --sdf-file examples/set01.sdf

:Prints information about training set ''set01.sdf'', provided as argument of the <code>--sdf-file</code> option, grouping atoms according to chemical element and bond order. To override this behaviour and group atoms only by element, call '''NEEMP''' with <code>--atom-types-by Element</code> option.
<br style="clear:both" />

[[File:info_mode.png | thumb | 400px | center | '''''Figure 9:''''' Information about structures set ''examples/set01.sdf''.]]

=Example 2 - Calculation mode=

;./neemp -m charges --sdf-file examples/set01.sdf --par-file examples/ElemBond.par --chg-out-file eem_charges --max-threads 8

:Compute EEM charges and store them into the file ''eem_charges''. Use up to 8 threads for computation.

For more information on this mode and its output, refer to [[NEEMP:Modes#Calculation mode | Calculation mode]] section.

For details on ''eem_charges'' output file, see [[NEEMP:files#CHG file | CHG file]] paragraph, as the format is the same. The only different regards the third column, since in this case the '''EEM charges''' are listed in place of the '''ab-initio charges'''.

=Example 3 - Parametrization mode=

;./neemp -m params -p lr-full --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-out-file new_parameters.par --chg-stats-out-file stats

:Perform EEM parametrization using '''LR''' approach, save parameters into the file ''new_parameters.par'', output charge statistics for each molecule into the file ''stats''. No discarding is used.

'''NB:''' the parameters set file ''new_parameters.par'' presents the same identical format and layout as described [[NEEMP:files#PAR file | here]].

For additional information click [[NEEMP:Modes#Linear Regression (LR) | here]].

=Example 4 - Parametrization mode k search=

;./neemp -m params -p lr-full --sdf-file examples/set01.sdf --chg-file examples/set01.chg --kappa-max 1.0 --fs-precision 0.02 --sort-by RMSD -vv

:Similar to previous example, use custom range for k. Select best parameters according to ''RMSD''. Print k search progress.

Reference to [[NEEMP:Modes#Linear Regression (LR) | parametrization paragraph]] and [[NEEMP:Options | options list]] if necessary.

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto;" width="650px"
|-
| [[File:ksearch1.png| 550px]]
| [[File:ksearch2.png| 700px]]
|-
| '''''Figure 10:''''' Detailed view of the parametrization settings from the execution of the above command. In particular note the usage of a different evaluating statistics (''RMSD'') and the custom range for the k search.
| '''''Figure 11:''''' Abridged output for the k search progress. For each k value a set of parameters is generated and evaluated. In this particular instance, the parameters set with the lowest ''RMSD'' value is chosen.
|}

=Example 5 - Parametrization mode simple discard=

;./neemp -m params -p lr-full --sdf-file examples/set01.sdf --chg-file examples/set01.chg --discard simple -v --limit-iters 600 --limit-time <nowiki>00:30:00</nowiki>

:Perform simple discarding with '''LR''' approach and print its progress. Issue warning about molecules with abnormal values of statistical descriptors. The duration of the discarding procedure can be at most 600 iterations or 30 minutes (time format HH:MM:SS), whichever is reached first.
<br style="clear:both" />

[[File:simple_discard.png | thumb | 800px | center | '''''Figure 12:''''' Abridged output for the simple discard progress. The simple discarding requires as many iterations as the number of molecules in the set, unless the iterations or time limits are reached first. In this case the training set contains only 500 structures so the iteration limit doesn't affect the discarding. The time limit still holds on the other hand. Refer to the [[NEEMP:Modes#Linear Regression (LR) | parametrization paragraph]] for details.]]

=Example 6 - Parametrization mode DE-MIN=

;./neemp -m params -p de --sdf-file examples/set01.sdf --chg-file examples/set01.chg --om-pop-size 50 --om-iters 500 --random-seed 1234 -vv

:Compute parameters for the given molecules (''set01.sdf'') and ab-initio charges (''charges.chg''). The chosen optimization method: differential evolution + minimization will act on a parameter vector population consisting of 50 units. The optimization procedure will be carried out for at most 500 iterations. A user-defined seed is used, as well as an high level of verbosity.

For additional information click [[NEEMP:Modes#Differential Evolution + Minimization (DE-MIN) | here]].

=Example 7 - Coverage validation=

;./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/ElemBond.par

:Calculate coverage of supplied molecules set given a specific parameter set. For more information on this mode refer to [[NEEMP:Modes#Coverage validation | Cover validation]] section.
<br style="clear:both" />

[[File:cover_mode2.png | thumb | 400px | center | '''''Figure 13:''''' Output from ''Cover mode''. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode | ''Calculation mode'']] output for a similar low coverage circumstance.]]

=Example 8 - Quality validation=

;./neemp -m quality --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-file examples/ElemBond.par --chg-stats-out-file stats 2> warns > log

:Perform quality validation of EEM parameters for atoms grouped by atomic type. Save standard output into the file ''log'' and warnings into the file ''warns''. Moreover output charge statistics for each molecule into the file ''stats''.

For more information on this mode click [[NEEMP:Modes#Quality validation | here]].
<br style="clear:both" />

[[File:chg_stats.png | thumb | 900px | center | '''''Figure 14:''''' Close-up from ''stats'' file. Along with statistics for each molecule, ''ab-initio'' charges (3rd column), ''EEM'' charges (4th column) and their difference (5th column) are also printed out.]]

NEEMP:Getting started

2016-06-28T20:58:36Z

Krab1k:

'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the inputs needed to run the [[NEEMP:Examples | examples]] and get acquainted with the tool. These files include:

* '''set01.sdf''' -- 500 molecules extracted from DTP NCI with a low atomic element complexity (H, C, N, O, S) and encoded in MOL V2000

* '''set02.sdf''' -- 4443 molecules extracted from LigandExpo (ideal coordinates) with high atomic element complexity (H, C, N, O, S, F, Cl, P, Br) and encoded in MOL V3000

* '''set01.chg''' -- Reference QM charges for all molecules in set01. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

* '''set02.chg''' -- Reference QM charges for all molecules in set02. Theory level, basis set and population analysis: B3LYP/6-311G/NPA

* '''Element.par''' -- parameters calculated using set01 for atomic types determined by element only

* '''ElemBond.par''' -- parameters calculated using set01 for atomic types determined by element + maximal bond order

'''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:

<code>~/neemp/$ ./neemp --help</code>

Click on the link to see the complete [[NEEMP:Options | options list]].

NEEMP:UserManual

2016-06-22T21:18:43Z

Krab1k:

__NOTOC__

'''NEEMP''' is the first freely available software for EEM parametrization, EEM charges validation and EEM charges calculation.
This Wiki page is intended to guide the user through '''NEEMP''' functionalities, providing complete but simple descriptions of the software features and helpful examples on its usage.

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===[[NEEMP:Getting started | Getting started]]===
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===[[NEEMP:Modes | Modes]]===
#[[NEEMP:Modes#Calculation mode | Calculation mode]]
#[[NEEMP:Modes#Parametrization mode | Parametrization mode]]
##[[NEEMP:Modes#Linear Regression (LR) | Linear Regression]]
##[[NEEMP:Modes#Differential Evolution + Minimization (DE-MIN) | Differential Evolution + Minimization (DE-MIN)]]
#[[NEEMP:Modes#Validation mode | Validation mode]]
##[[NEEMP:Modes#Coverage validation| Coverage validation]]
##[[NEEMP:Modes#Quality validation | Quality validation]]

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===[[NEEMP:Reports | Reports Generation ]]===
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===[[NEEMP:files | Used file formats]]===
#[[NEEMP:files#SDF file | SDF file]]
#[[NEEMP:files#CHG file | CHG file]]
#[[NEEMP:files#PAR file | PAR file]]
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===[[NEEMP:Examples | Examples]]===
#[[NEEMP:Examples#Example 1 - Training set information | Example 1 - Training set information]]
#[[NEEMP:Examples#Example 2 - Coverage validation | Example 2 - Coverage validation]]
#[[NEEMP:Examples#Example 3 - Calculation mode | Example 3 - Calculation mode]]
#[[NEEMP:Examples#Example 4 - Quality validation | Example 4 - Quality validation]]
#[[NEEMP:Examples#Example 5 - Parametrization mode | Example 5 - Parametrization mode]]
#[[NEEMP:Examples#Example 6 - Parametrization mode k search | Example 6 - Parametrization mode k search]]
#[[NEEMP:Examples#Example 7 - Parametrization mode simple discard | Example 7 - Parametrization mode simple discard]]
#[[NEEMP:Examples#Example 8 - Parametrization mode DE-MIN | Example 8 - Parametrization mode DE-MIN]]
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===[[NEEMP:Options | Options list]]===
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