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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.
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.


For a more detailed and thorough description of '''NEEMP''''s methods and implementation we refer the user to the links at the bottom of this page ([[NEEMP:References | References]]).
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===[[NEEMP:Compilation & Running | Compilation & Running]]===
===[[NEEMP:Getting started | Getting started]]===
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===[[NEEMP:Modes | Modes]]===
===[[NEEMP:Modes | Modes]]===
#[[NEEMP:Modes#Info | Info]]
#[[NEEMP:Modes#Calculation mode | Calculation mode]]
#[[NEEMP:Modes#Cover | Cover]]
#[[NEEMP:Modes#Parametrization mode | Parametrization mode]]
#[[NEEMP:Modes#Charges | Charges]]
##[[NEEMP:Modes#Linear Regression (LR) | Linear Regression (LR)]]
#[[NEEMP:Modes#Cross-validation | Cross-validation]]
##[[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:parametrization | EEM parameters computation]]===
 
#[[NEEMP:parametrization#k settings | k settings]]
===[[NEEMP:Reports | Reports Generation ]]===
#[[NEEMP:Discarding | Discarding]]
##[[NEEMP:Discarding#Simple | Simple discarding]]
##[[NEEMP:Discarding#Iterative | Iterative discarding]]
#[[NEEMP:parametrization#Other options | Other options]]
#[[NEEMP:parametrization#Miscellaneous | Miscellaneous]]
#[[NEEMP:parametrization#Parallelism | Parallelism]]
#[[NEEMP:parametrization#Statistics | Statistics computation]]
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#[[NEEMP:files#PAR file | PAR file]]
#[[NEEMP:files#PAR file | PAR file]]
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===[[NEEMP:Examples | Examples]]===
===[[NEEMP:Examples | Examples]]===
#[[NEEMP:Examples#Example 1 | Example 1]]
#[[NEEMP:Examples#Example 1 - Training set information | Example 1 - Training set information]]
#[[NEEMP:Examples#Example 2 | Example 2]]
#[[NEEMP:Examples#Example 2 - Calculation mode | Example 2 - Calculation mode]]
#[[NEEMP:Examples#Example 3 | Example 3]]
#[[NEEMP:Examples#Example 3 - Parametrization mode | Example 3 - Parametrization mode]]
#[[NEEMP:Examples#Example 4 | Example 4]]
#[[NEEMP:Examples#Example 4 - Parametrization mode k search | Example 4 - Parametrization mode k search]]
#[[NEEMP:Examples#Example 5 | Example 5]]
#[[NEEMP:Examples#Example 5 - Parametrization mode simple discard | Example 5 - Parametrization mode simple discard]]
#[[NEEMP:Examples#Example 6 | Example 6]]
#[[NEEMP:Examples#Example 6 - Parametrization mode DE-MIN | Example 6 - Parametrization mode DE-MIN]]
#[[NEEMP:Examples#Example 7 | Example 7]]
#[[NEEMP:Examples#Example 7 - Coverage validation | Example 7 - Coverage validation]]
#[[NEEMP:Examples#Example 8 | Example 8]]
#[[NEEMP:Examples#Example 8 - Quality validation | Example 8 - Quality validation]]
#[[NEEMP:Examples#Example 9 | Example 9]]
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===[[NEEMP:Options | Options list]]===
===[[NEEMP:Options | Options list]]===
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===[[NEEMP:References | References]]===
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Latest revision as of 06:19, 28 June 2016


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.

Getting started

[edit]

Modes

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  1. Calculation mode
  2. Parametrization mode
    1. Linear Regression (LR)
    2. Differential Evolution + Minimization (DE-MIN)
  3. Validation mode
    1. Coverage validation
    2. Quality validation

Reports Generation

[edit]

Used file formats

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  1. SDF file
  2. CHG file
  3. PAR file

Examples

[edit]
  1. Example 1 - Training set information
  2. Example 2 - Calculation mode
  3. Example 3 - Parametrization mode
  4. Example 4 - Parametrization mode k search
  5. Example 5 - Parametrization mode simple discard
  6. Example 6 - Parametrization mode DE-MIN
  7. Example 7 - Coverage validation
  8. Example 8 - Quality validation

Options list

[edit]
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