MDEDescriptor (cdk 2.2 API)

java.lang.Object
- org.openscience.cdk.qsar.AbstractMolecularDescriptor
- - org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor

All Implemented Interfaces:: IDescriptor, IMolecularDescriptor

public class MDEDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Calculates the Molecular Distance Edge descriptor described in (Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38). This class evaluates the 10 MDE descriptors described by Liu et al. and in addition it calculates variants where O and N are considered (as found in the DEDGE routine from ADAPT).

Table 1 - Description of the different MDE descriptors generated
MDEC-11	molecular distance edge between all primary carbons
MDEC-12	molecular distance edge between all primary and secondary carbons
MDEC-13	molecular distance edge between all primary and tertiary carbons
MDEC-14	molecular distance edge between all primary and quaternary carbons
MDEC-22	molecular distance edge between all secondary carbons
MDEC-23	molecular distance edge between all secondary and tertiary carbons
MDEC-24	molecular distance edge between all secondary and quaternary carbons
MDEC-33	molecular distance edge between all tertiary carbons
MDEC-34	molecular distance edge between all tertiary and quaternary carbons
MDEC-44	molecular distance edge between all quaternary carbons
MDEO-11	molecular distance edge between all primary oxygens
MDEO-12	molecular distance edge between all primary and secondary oxygens
MDEO-22	molecular distance edge between all secondary oxygens
MDEN-11	molecular distance edge between all primary nitrogens
MDEN-12	molecular distance edge between all primary and secondary nitrogens
MDEN-13	molecular distance edge between all primary and tertiary niroqens
MDEN-22	molecular distance edge between all secondary nitroqens
MDEN-23	molecular distance edge between all secondary and tertiary nitrogens
MDEN-33	molecular distance edge between all tertiary nitrogens

Author:: Rajarshi Guha
Dictionary pointer(s):: mde in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:mde]
Source code:: master
Belongs to CDK module:: qsarmolecular
Created on:: 2006-09-18

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`MDEC11`
`static int`	`MDEC12`
`static int`	`MDEC13`
`static int`	`MDEC14`
`static int`	`MDEC22`
`static int`	`MDEC23`
`static int`	`MDEC24`
`static int`	`MDEC33`
`static int`	`MDEC34`
`static int`	`MDEC44`
`static int`	`MDEN11`
`static int`	`MDEN12`
`static int`	`MDEN13`
`static int`	`MDEN22`
`static int`	`MDEN23`
`static int`	`MDEN33`
`static int`	`MDEO11`
`static int`	`MDEO12`
`static int`	`MDEO22`

Constructor Summary

Constructors
Constructor and Description

MDEDescriptor()

Constructors
Constructor and Description
`MDEDescriptor()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`DescriptorValue`	`calculate(IAtomContainer container)` Calculate the weight of specified element type in the supplied `IAtomContainer`.
`String[]`	`getDescriptorNames()` Returns an array of names for each descriptor value calculated.
`IDescriptorResult`	`getDescriptorResultType()` Returns the specific type of the DescriptorResult object.
`String[]`	`getParameterNames()` Gets the parameterNames attribute of the WeightDescriptor object.
`Object[]`	`getParameters()` Gets the parameters attribute of the WeightDescriptor object.
`Object`	`getParameterType(String name)` Gets the parameterType attribute of the WeightDescriptor object.
`DescriptorSpecification`	`getSpecification()` Returns a `Map` which specifies which descriptor is implemented by this class.
`void`	`initialise(IChemObjectBuilder builder)` Default implementation of initialise allows optional override.
`void`	`setParameters(Object[] params)` Sets the parameters attribute of the WeightDescriptor object.

Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor
clone

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.qsar.IDescriptor
initialise

- Field Detail
  - MDEC11
```
public static final int MDEC11
```
    See Also:
    
    Constant Field Values
  - MDEC12
```
public static final int MDEC12
```
    See Also:
    
    Constant Field Values
  - MDEC13
```
public static final int MDEC13
```
    See Also:
    
    Constant Field Values
  - MDEC14
```
public static final int MDEC14
```
    See Also:
    
    Constant Field Values
  - MDEC22
```
public static final int MDEC22
```
    See Also:
    
    Constant Field Values
  - MDEC23
```
public static final int MDEC23
```
    See Also:
    
    Constant Field Values
  - MDEC24
```
public static final int MDEC24
```
    See Also:
    
    Constant Field Values
  - MDEC33
```
public static final int MDEC33
```
    See Also:
    
    Constant Field Values
  - MDEC34
```
public static final int MDEC34
```
    See Also:
    
    Constant Field Values
  - MDEC44
```
public static final int MDEC44
```
    See Also:
    
    Constant Field Values
  - MDEO11
```
public static final int MDEO11
```
    See Also:
    
    Constant Field Values
  - MDEO12
```
public static final int MDEO12
```
    See Also:
    
    Constant Field Values
  - MDEO22
```
public static final int MDEO22
```
    See Also:
    
    Constant Field Values
  - MDEN11
```
public static final int MDEN11
```
    See Also:
    
    Constant Field Values
  - MDEN12
```
public static final int MDEN12
```
    See Also:
    
    Constant Field Values
  - MDEN13
```
public static final int MDEN13
```
    See Also:
    
    Constant Field Values
  - MDEN22
```
public static final int MDEN22
```
    See Also:
    
    Constant Field Values
  - MDEN23
```
public static final int MDEN23
```
    See Also:
    
    Constant Field Values
  - MDEN33
```
public static final int MDEN33
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MDEDescriptor
```
public MDEDescriptor()
```
- Method Detail
  - getSpecification
```
public DescriptorSpecification getSpecification()
```
    Returns a Map which specifies which descriptor is implemented by this class. These fields are used in the map:
    - Specification-Reference: refers to an entry in a unique dictionary
    - Implementation-Title: anything
    - Implementation-Identifier: a unique identifier for this version of this class
    - Implementation-Vendor: CDK, JOELib, or anything else
    Specified by:
    
    getSpecification in interface IDescriptor
    
    Returns:
    
    An object containing the descriptor specification
  - setParameters
```
public void setParameters(Object[] params)
                   throws CDKException
```
    Sets the parameters attribute of the WeightDescriptor object.
    
    Specified by:
    
    setParameters in interface IDescriptor
    
    Parameters:
    
    params - The new parameters value
    
    Throws:
    
    CDKException - if more than 1 parameter is specified or if the parameter is not of type String
    
    See Also:
    
    getParameters()
  - getParameters
```
public Object[] getParameters()
```
    Gets the parameters attribute of the WeightDescriptor object.
    
    Specified by:
    
    getParameters in interface IDescriptor
    
    Returns:
    
    The parameters value
    
    See Also:
    
    setParameters(java.lang.Object[])
  - getDescriptorNames
```
public String[] getDescriptorNames()
```
    Description copied from interface: IDescriptor
    
    Returns an array of names for each descriptor value calculated. Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value. In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the descriptor (e.g., the CPSA descriptor). Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element
    
    Specified by:
    
    getDescriptorNames in interface IDescriptor
    
    Returns:
    
    An array of descriptor names, equal in length to the number of descriptor calculated..
  - calculate
```
public DescriptorValue calculate(IAtomContainer container)
```
    Calculate the weight of specified element type in the supplied IAtomContainer.
    
    Specified by:
    
    calculate in interface IMolecularDescriptor
    
    Parameters:
    
    container - The AtomContainer for which this descriptor is to be calculated. If 'H' is specified as the element symbol make sure that the AtomContainer has hydrogens.
    
    Returns:
    
    The total weight of atoms of the specified element type
  - getDescriptorResultType
```
public IDescriptorResult getDescriptorResultType()
```
    Returns the specific type of the DescriptorResult object. The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.
    
    Specified by:
    
    getDescriptorResultType in interface IMolecularDescriptor
    
    Returns:
    
    an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object
  - getParameterNames
```
public String[] getParameterNames()
```
    Gets the parameterNames attribute of the WeightDescriptor object.
    
    Specified by:
    
    getParameterNames in interface IDescriptor
    
    Returns:
    
    The parameterNames value
  - getParameterType
```
public Object getParameterType(String name)
```
    Gets the parameterType attribute of the WeightDescriptor object.
    
    Specified by:
    
    getParameterType in interface IDescriptor
    
    Parameters:
    
    name - Description of the Parameter
    
    Returns:
    
    An Object whose class is that of the parameter requested
  - initialise
```
public void initialise(IChemObjectBuilder builder)
```
    Default implementation of initialise allows optional override.
    
    Specified by:
    
    initialise in interface IDescriptor
    
    Parameters:
    
    builder - chem object build

Class MDEDescriptor

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor

Methods inherited from class java.lang.Object

Methods inherited from interface org.openscience.cdk.qsar.IDescriptor

Field Detail

MDEC11

MDEC12

MDEC13

MDEC14

MDEC22

MDEC23

MDEC24

MDEC33

MDEC34

MDEC44

MDEO11

MDEO12

MDEO22

MDEN11

MDEN12

MDEN13

MDEN22

MDEN23

MDEN33

Constructor Detail

MDEDescriptor

Method Detail

getSpecification

setParameters

getParameters

getDescriptorNames

calculate

getDescriptorResultType

getParameterNames

getParameterType

initialise