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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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===[[PatternQuery:Principles | Principles of the PQ language]]===
 
#[[PatternQuery:Principles#Example, Part One | Example - introduction]]
===[[NEEMP:Reports | Reports Generation ]]===
#[[PatternQuery:Principles#Basic Principles of the Language | Basic Principle]]
#[[PatternQuery:Principles#Example, Part One | Example - revised]]
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===[[PatternQuery:How to build a query | How to build a query]]===
 
#[[PatternQuery:How to build a query#How to think about queries | How to think about query]]
===[[NEEMP:files | Used file formats]]===
#[[PatternQuery:How to build a query#Ready-to-use examples | Ready-to-use examples]]
#[[NEEMP:files#SDF file | SDF file]]
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#[[NEEMP:files#CHG file | CHG file]]
===[[PatternQuery:Use Cases | Biological use cases]]===
#[[NEEMP:files#PAR file | PAR file]]
#[[PatternQuery:Use Cases#Find all post-translational modified amino acids | Post-translational modified aminoacids]]
#[[PatternQuery:Use Cases#Identify Zinc fingers | Zinc fingers]]
#[[PatternQuery:Use Cases#Identify all the residues, which contain a sugar ring | Residue containing carbohydrate moiety]]
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===[[PatternQuery:Explorer | PatternQuery Explorer]]===
# [[PatternQuery:Explorer#Launch PatternQuery Explorer app | Launch application]]
# [[PatternQuery:Explorer#Get started with PatternQuery Explorer | How to work with it]]
# [[PatternQuery:Explorer#Executing Query & interpreting results | Execute query]]
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===[[PatternQuery:Service Organization | Using PatternQuery Service]]===
===[[NEEMP:Examples | Examples]]===
# [[PatternQuery:Service Organization#Synopsis Page | Synopsis Page]]
#[[NEEMP:Examples#Example 1 - Training set information | Example 1 - Training set information]]
# [[PatternQuery:Service Organization#Job Submission | Job submission]]
#[[NEEMP:Examples#Example 2 - Calculation mode | Example 2 - Calculation mode]]
# [[PatternQuery:Specifics Page| Specifics Page (result analysis)]]
#[[NEEMP:Examples#Example 3 - Parametrization mode | Example 3 - Parametrization mode]]
## [[PatternQuery:Specifics Page#Calculation Summary| Calculation Summary]]
#[[NEEMP:Examples#Example 4 - Parametrization mode k search | Example 4 - Parametrization mode k search]]
## [[PatternQuery:Specifics Page#Pattern Details | Pattern Details]]
#[[NEEMP:Examples#Example 5 - Parametrization mode simple discard | Example 5 - Parametrization mode simple discard]]
## [[PatternQuery:Specifics Page#Structure Details | Structure Details ]]
#[[NEEMP:Examples#Example 6 - Parametrization mode DE-MIN | Example 6 - Parametrization mode DE-MIN]]
#[[NEEMP:Examples#Example 7 - Coverage validation | Example 7 - Coverage validation]]
#[[NEEMP:Examples#Example 8 - Quality validation | Example 8 - Quality validation]]
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===[[PatternQuery:Language_Reference | Language reference]]===
===[[NEEMP:Options | Options list]]===
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===[[PatternQuery:Command Line | Command line version & Technical details]]===
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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

[edit]
  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

[edit]
  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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