org.openscience.cdk.qsar.descriptors.molecular
Class MDEDescriptor

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class MDEDescriptor
extends java.lang.Object
implements IMolecularDescriptor

Calculates the Molecular Distance Edge descriptor described in [Liu, S. and Cao, C. and Li, Z. , Approach to Estimation and Prediction for Normal Boiling Point (NBP) of Alkanes Based on a Novel Molecular Distance Edge (MDE) Vector, lambda, Journal of Chemical Information and Computer Sciences, 1998, 38:387-394]. 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).

* The variants are described below:

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

Belongs to the set:

qsar-descriptors

Created on:

2006-09-18

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

mde in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:mde]

Source code:

revision 11779

Field Summary

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

MDEDescriptor()

Method Summary

DescriptorValue	calculate(IAtomContainer container) Calculate the weight of specified element type in the supplied IAtomContainer.
java.lang.String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
java.lang.String[]	getParameterNames() Gets the parameterNames attribute of the WeightDescriptor object.
java.lang.Object[]	getParameters() Gets the parameters attribute of the WeightDescriptor object.
java.lang.Object	getParameterType(java.lang.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	setParameters(java.lang.Object[] params) Sets the parameters attribute of the WeightDescriptor object.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mdec11

public static final int mdec11

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mdec12

public static final int mdec12

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mdec13

public static final int mdec13

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mdec14

public static final int mdec14

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mdec22

public static final int mdec22

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mdec23

public static final int mdec23

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mdec24

public static final int mdec24

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mdec33

public static final int mdec33

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mdec34

public static final int mdec34

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mdec44

public static final int mdec44

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mdeo11

public static final int mdeo11

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mdeo12

public static final int mdeo12

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mdeo22

public static final int mdeo22

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mden11

public static final int mden11

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mden12

public static final int mden12

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mden13

public static final int mden13

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mden22

public static final int mden22

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mden23

public static final int mden23

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mden33

public static final int mden33

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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(java.lang.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 java.lang.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

@TestMethod(value="testNamesConsistency")
public java.lang.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 decsriptor (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 java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the WeightDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public java.lang.Object getParameterType(java.lang.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